Fluorine in Peptide Design and Protein Engineering

4,4-Difluoroproline as a Unique 19F NMR Probe of Proline Conformation

Despite the importance of proline conformational equilibria (trans versus cis amide and exo versus endo ring pucker) on protein structure and function, there is a lack of convenient ways to probe proline conformation. 4,4-Difluoroproline (Dfp) was identified to be a sensitive 19F NMR-based probe of proline conformational biases and cis-trans isomerism. Within model compounds and disordered peptides, the diastereotopic fluorines of Dfp exhibit similar chemical shifts (ΔδFF = 0-3 ppm) when a trans X-Dfp amide bond is present. In contrast, the diastereotopic fluorines exhibit a large (ΔδFF = 5-12 ppm) difference in chemical shift in a cis X-Dfp prolyl amide bond. DFT calculations, X-ray crystallography, and solid-state NMR spectroscopy indicated that ΔδFF directly reports on the relative preference of one proline ring pucker over the other: a fluorine which is pseudo-axial (i.e., the pro-4R-F in an exo ring pucker, or the pro-4S-F in an endo ring pucker) is downfield, while a fluorine which is pseudo-equatorial (i.e., pro-4S-F when exo, or pro-4R-F when endo) is upfield. Thus, when a proline is disordered (a mixture of exo and endo ring puckers, as at trans-Pro in peptides in water), it exhibits a small Δδ. In contrast, when the Pro is ordered (i.e., when one ring pucker is strongly preferred, as in cis-Pro amide bonds, where the endo ring pucker is strongly favored), a large Δδ is observed. Dfp can be used to identify inherent induced order in peptides and to quantify proline cis-trans isomerism. Using Dfp, we discovered that the stable polyproline II helix (PPII) formed in the denatured state (8 M urea) exhibits essentially equal populations of the exo and endo proline ring puckers. In addition, the data with Dfp suggested the specific stabilization of PPII by water over other polar solvents. These data strongly support the importance of carbonyl solvation and n → π* interactions for the stabilization of PPII. Dfp was also employed to quantify proline cis-trans isomerism as a function of phosphorylation and the R406W mutation in peptides derived from the intrinsically disordered protein tau. Dfp is minimally sterically disruptive and can be incorporated in expressed proteins, suggesting its broad application in understanding proline cis-trans isomerization, protein folding, and local order in intrinsically disordered proteins.

"Fluorine Effects" in Conformational Orchestration of α/β Hybrid Peptide with a 9-membered Pseudo β-Turn Motif

Fluorine, the tiny robust atom, with its unique features has captured the attention of scientists in recent times, especially in drug discovery with its integration in small molecules, peptides, and proteins. However, studies to understand the 'fluorine effects' on the conformation of molecules that follow 'beyond the rule of 5' are in the infancy yet significant in molecular design and function. For the first time, using short hybrid peptide sequence as an appropriate model, we examined the substitution effect (size, stereoelectronic effect, and hydrogen bonding) using X-ray diffraction, 2D-NMR, and CD studies. The comparative study on their folding patterns with hydrogen-substituted analogs can provide valuable insights into fluorinated substrates' design.

Fluorinated 2-arylchroman-4-ones and their derivatives: synthesis, structure and antiviral activity

A number of new biologically interesting fluorinated 2-arylchroman-4-ones and their 3-arylidene derivatives were synthesized based on the p-toluenesulfonic acid-catalyzed one-pot reaction of 2-hydroxyacetophenones with benzaldehydes. It was found that obtained (E)-3-arylidene-2-aryl-chroman-4-ones reacted with malononitrile under base conditions to form 4,5-diaryl-4H,5H-pyrano[3,2-c]chromenes. The structures of the synthesized fluorinated compounds were confirmed by 1H, 19F, and 13C NMR spectral data, and for some representatives of heterocycles also using NOESY spectra and X-ray diffraction analysis. A large series of obtained flavanone derivatives as well as products of their modification (35 examples) containing from 1 to 12 fluorine atoms in the structure was tested in vitro for cytotoxicity in MDCK cell line and for antiviral activity against influenza A virus. Among the studied heterocycles 6,8-difluoro-2-(4-(trifluoromethyl)phenyl)chroman-4-one (IC50 = 6 μM, SI = 150) exhibited the greatest activity against influenza A/Puerto Rico/8/34 (H1N1) virus. Moreover, this compound appeared active against phylogenetically distinct influenza viruses, A(H5N2) and influenza B (SI's of 53 and 42, correspondingly). The data obtained suggest that the fluorinated derivatives of 2-arylchroman-4-ones are prospective scaffolds for further development of potent anti-influenza antivirals.

Impact of hydrophobicity on local solvation structures and its connection with the global solubilization thermodynamics of amphiphilic molecules

The relationship between the local solvation structures and global thermodynamics, specifically in the case of amphiphilic molecules, is a complex phenomenon and is not yet fully understood. With the prior knowledge that local solvation structures can impose a significant impact on the overall solvation process, we here combine THz spectroscopic analysis with MD simulations to investigate the impact of the altered hydrophobicity and polarity of amphiphilic solute molecules on the local solvation configurations. We use two water soluble alcohols: ethanol (EtOH) and its fluorinated counterpart, 2,2,2-trifluoroethanol (TFE), as model solutes. Our study is aimed to determine the relative abundance of different hydrogen bonded conformers and to establish a correlation between the spectral signatures (as obtained from THz spectroscopic measurements) and microscopic solute-solvent interactions associated with the local solvation structures (as obtained from MD simulations). Finally, we estimate the possible energetic parameters associated with the alcohol solubilization process. We found that while both the alcohols are completely water soluble, they receive a contrasting solvation energy share in terms of entropy and enthalpy. We understand that these findings are not limited to the specific system studied here but can be broadly extrapolated to other amphiphilic aqueous solutions.

Photoredox Microfluidic Synthesis of Trifluoromethylated Amino Acids

Fluorinated amino acids are a class of highly valuable building blocks that are widely employed in biological science and pharmaceutical industry for improved stability, activity, and folding property of proteins. However, the synthetic approach has conventionally been constrained by harsh conditions and limited substrate range. We demonstrate a general synthetic protocol for photoinduced α-CF₃ amino acids using continuous flow technology that benefits from enhanced fusion and precise control of reaction time, making it potentially useful in large-scale peptide synthesis.

Recent advances in the synthesis of fluorinated amino acids and peptides

The site-selective modification of amino acids, peptides, and proteins has always been an intensive topic in organic synthesis, medicinal chemistry, and chemical biology due to the vital role of amino acids in life. Among the developed methods, the site-selective introduction of fluorine functionalities into amino acids and peptides has emerged as a useful approach to change their physicochemical and biological properties. With the increasing demand for life science, the direct fluorination/fluoroalkylation of proteins has also received increasing attention because of the unique properties of fluorine atom(s) that can change the protein structure, increase their lipophilicity, and enable fluorine functionality as a biological tracer or probe for chemical biology studies. In this feature article, we summarized the recent advances in the synthesis of fluorinated amino acids and peptides, wherein two strategies have been discussed. One is based on the fluorinated building blocks to prepare fluorinated amino acids and peptides with diversified structures, including the transformations of fluorinated imines and nickel-catalyzed dicarbofunctionalization of alkenes with bromodifluoroacetate and its derivatives; the other is direct fluorination/fluoroakylation of amino acids, peptides, and proteins, in which the selective transformations of the functional groups on serine, threonine, tyrosine, tryptophan, and cysteine lead to a wide range of fluorinated α-amino acids, peptides, and proteins, featuring synthetic convenience and late-stage modification of biomacromolecules. These two strategies complement each other, wherein transition-metal catalysis and new fluoroalkylating reagents provide powerful tools to selectively access fluorinated amino acids, peptides, and proteins, showing the prospect of medicinal chemistry and chemical biology.

Synthesis of Functionalized Isoquinolone Derivatives via Rh(III)-Catalyzed [4+2]-Annulation of Benzamides with Internal Acetylene-Containing α-CF3-α-Amino Carboxylates

A convenient pathway to a new series of α-CF₃-substituted α-amino acid derivatives bearing pharmacophore isoquinolone core in their backbone has been developed. The method is based on [4+2]-annulation of N-(pivaloyloxy) aryl amides with orthogonally protected internal acetylene-containing α-amino carboxylates under Rh(III)-catalysis. The target annulation products can be easily transformed into valuable isoquinoline derivatives via a successive aromatization/cross-coupling operation.

Design and Synthesis of New α-hydroxy β-fluoro/β-trifluoromethyl and Unsaturated Phosphonates from Carbohydrate-Derived Building Blocks via Pudovik and Horner–Wadsworth–Emmons Reactions

Herein, we present the application of fluorinated carbohydrate-derived building blocks for α-hydroxy β-fluoro/β-trifluoromethyl and unsaturated phosphonates synthesis. Pudovik and Horner–Wadsworth–Emmons reactions were applied to achieve this goal. The proposed pathway of the key reactions is supported by the experimental results, as well as quantum chemical calculations. The structure of the products was established by spectroscopic (1D, 2D NMR) and spectrometric (MS) techniques. Based on our data received, we claim that the progress of the Pudovik and HWE reactions is significantly influenced by the acidic protons present in the molecules as assessed by pKa values of the reagent.

Synthesis of fluorinated leucines, valines and alanines for use in protein NMR

Efficient syntheses of fluorinated leucines, valines and alanines are described. The synthetic routes provide expedient access to various ¹³C/¹⁵N/D isotopologues requiring solely readily available and inexpensive isotope containing reagents such as NaBD₄, carbon-¹³C dioxide and sodium azide-1-¹⁵N. The lightly fluorinated leucines and valines were found to be good substrates for cell-free protein expression and even 3-fluoroalanine, which is highly toxic to bacteria in vivo, could be incorporated into proteins this way. ¹⁹F-NMR spectra of the protein GB1 produced with these amino acids showed large chemical shift dispersions. Particularly high incorporation yields and clean ¹⁹F-NMR spectra were obtained for GB1 produced with valine residues, which had been synthesized with a single fluorine substituting a hydrogen stereospecifically in one of the methyl groups.

Nickel-Catalyzed Cross-Coupling of Amino-Acid-Derived Alkylzinc Reagents with Alkyl Bromides/Chlorides: Access to Diverse Unnatural Amino Acids

Unnatural α-amino acids are important synthetic targets in the field of peptide science. Herein we report an efficient, versatile, and straightforward strategy for the synthesis of homophenylalanine derivatives via the nickel-catalyzed Csp³-Csp³ cross-coupling of (fluoro)benzyl bromides/chlorides with natural α-amino-acid-derived alkylzinc reagents. The current protocol features the advantages of a low-cost nickel catalyst system, synthetic convenience, and the tolerance of rich functionality and stereochemistry.

An infrared spectroscopic study of trifluoromethoxybenzene⋯methanol complexes formed in superfluid helium nanodroplets

We have studied the intermolecular complex formation between trifluoromethoxybenzene and methanol (CD₃OD) in superfluid helium droplets by infrared spectroscopy in the spectral range of 2630-2730 cm^-1, covering the O-D stretches of methanol-d₄ (CD₃OD). The cluster size associated with the observed bands is deduced from the variation of infrared intensity of a particular band with the partial pressures of trifluoromethoxybenzene and methanol. Quantum chemical calculations are performed at the MP2/6-311++G(d,p) level of theory to complement the experimental results. As a result, we have identified six different conformers of the trifluoromethoxybenzene⋯methanol intermolecular complex: three bound via O-H⋯O hydrogen bonds and the other three via O-H⋯π hydrogen bonds. Furthermore, to access the effect of fluorination on the methyl unit of anisole molecules, we compare the IR spectrum of trifluoromethoxybenzene (C₆H₅OCF₃)⋯methanol with our earlier reported spectrum of anisole (C₆H₅OCH₃)⋯methanol.

Synthesis of Quinolines via the Metal-free Visible-Light-Mediated Radical Azidation of Cyclopropenes

We report the synthesis of quinolines using cyclopropenes and an azidobenziodazolone (ABZ) hypervalent iodine reagent as an azide radical source under visible-light irradiation. Multisubstituted quinoline products were obtained in 34-81% yield. The reaction was most efficient for 3-trifluoromethylcyclopropenes, affording valuable 4-trifluoromethylquinolines. The transformation probably proceeds through the cyclization of an iminyl radical formed by the addition of the azide radical on the cyclopropene double bond, followed by ring-opening and fragmentation.

4-Fluoro-Threonine: From Diastereoselective Synthesis to pH-Dependent Conformational Equilibrium in Aqueous Solution

4-Fluoro-threonine, the only fluoro amino acid of natural origin discovered so far, is an interesting target for both synthetic and theoretical investigations. In this work, we lay the foundation for spectroscopic characterization of 4-fluoro-threonine. First, we report a diastereoselective synthetic route, which is suitable to produce synthetic material for experimental characterization. The addition of the commercially available ethyl isocyanoacetate to benzyloxyacetaldehyde led to the corresponding benzyloxy-oxazoline, which was hydrolyzed and transformed into ethyl (4S*,5S*)-5-hydroxymethyl-2-oxo-4-oxazolidinecarboxylate in a few steps. Fluorination with diethylamino sulfur trifluoride (DAST) afforded ethyl (4S*,5S*)-5-fluoromethyl-2-oxo-4-oxazolidinecarboxylate, which was deprotected to give the desired diastereomerically pure 4-fluoro-threonine, in 8-10% overall yield. With the synthetic material in our hands, acid-base titrations have been carried out to determine acid dissociation constants and the isoelectric point, which is the testing ground for the theoretical analysis. We have used machine learning coupled with quantum chemistry at the state-of-the-art to analyze the conformational space of 4-fluoro-threonine, with the aim of gaining insights from the comparison of computational and experimental results. Indeed, we have demonstrated that our approach, which couples a last-generation double-hybrid density functional including empirical dispersion contributions with a model combining explicit first-shell molecules and a polarizable continuum for describing solvent effects, provides results and trends in remarkable agreement with experiments. Finally, the conformational analysis applied to fluoro amino acids represents an interesting study for the effect of fluorine on the stability and population of conformers.

Facile Access to Hetero-poly-functional Arenes and meta-Substituted Arenes via Two-Step Dimetalation and Mg/Halogen-Exchange Protocol

The Grignard reagent, iPrMgCl and its lithium chloride-enhanced 'turbo' derivative iPrMgCl⋅LiCl have been employed to investigate the single iodo/magnesium exchange reactions of the trisubstituted arenes, 2,5-diiodo-N,N-diisopropylbenzamide 1, 1,4-diiodo-2-methoxybenzene 2, and 1,4-diiodo-2-(trifluoromethyl)benzene 3. These three arenes themselves were initially prepared by a double ortho-, meta'-deprotonation of N,N-diisopropylbenzamide, anisole and (trifluoromethyl)benzene, respectively, using the sodium magnesiate reagent [Na₄ Mg₂ (TMP)₆ (nBu)₂ ] (where TMP is 2,2,6,6-tetramethylpiperidide), and subsequent electrophilic quenching with iodine/THF solution. Thus, by following a combined deprotonation and magnesium/halogen exchange strategy, the simple monosubstituted arenes can be converted to trisubstituted diiodoarenes, which can ultimately be transformed into the corresponding mono-magnesiated arenes, in THF at -40 °C, within seconds in good yields. The other functional group (OMe, NiPr₂ or CF₃ respectively) present on the di-iodoarenes helps direct the exchange reaction to the ortho position, whereas subsequent addition of different electrophiles permits the preparation of hetero-poly-functional-arenes, with three different substituents in their structure. Intriguingly, if water is used as the electrophile, a new and facile route to prepare meta-substituted arenes, which cannot be easily obtained by conventional processes, is forthcoming. In contrast to directed ortho-metalation (DoM) chemistry, this reaction sequence can be thought of as InDirect meta-Metalation (IDmM). The scope of the chemistry has been tested further by exposing the initial unreacted iodo-functionality at the meta-position to a second Mg/I-exchange reaction and subsequent functionalization.

The Impact of Halogenated Phenylalanine Derivatives on NFGAIL Amyloid Formation

The hexapeptide hIAPP22-27 (NFGAIL) is known as a crucial amyloid core sequence of the human islet amyloid polypeptide (hIAPP) whose aggregates can be used to better understand the wild-type hIAPP's toxicity to β-cell death. In amyloid research, the role of hydrophobic and aromatic-aromatic interactions as potential driving forces during the aggregation process is controversially discussed not only in case of NFGAIL, but also for amyloidogenic peptides in general. We have used halogenation of the aromatic residue as a strategy to modulate hydrophobic and aromatic-aromatic interactions and prepared a library of NFGAIL variants containing fluorinated and iodinated phenylalanine analogues. We used thioflavin T staining, transmission electron microscopy (TEM) and small-angle X-ray scattering (SAXS) to study the impact of side-chain halogenation on NFGAIL amyloid formation kinetics. Our data revealed a synergy between aggregation behavior and hydrophobicity of the phenylalanine residue. This study introduces systematic fluorination as a toolbox to further investigate the nature of the amyloid self-assembly process.

Catalytic asymmetric synthesis of quaternary trifluoromethyl α- to ε-amino acid derivatives via umpolung allylation/2-aza-Cope rearrangement

In this study, we developed an efficient Ir-catalyzed cascade umpolung allylation/2-aza-Cope rearrangement of tertiary α-trifluoromethyl α-amino acid derivatives for the preparation of a variety of quaternary α-trifluoromethyl α-amino acids in high yields with excellent enantioselectivities. The umpolung reactivity empowered by the activation of the key isatin-ketoimine moiety obviates the intractable enantioselectivity control in Pd-catalyzed asymmetric linear α-allylation. In combination with quasi parallel kinetic resolution or kinetic resolution, the generality of this method is further demonstrated by the first preparation of enantioenriched quaternary trifluoromethyl β-, γ-, δ- and ε-amino acid derivatives.

Fluorinated phenylalanines: synthesis and pharmaceutical applications

Recent advances in the chemistry of peptides containing fluorinated phenylalanines (Phe) represents a hot topic in drug research over the last few decades. ᴅ- or ʟ-fluorinated phenylalanines have had considerable industrial and pharmaceutical applications and they have been expanded also to play an important role as potential enzyme inhibitors as well as therapeutic agents and topography imaging of tumor ecosystems using PET. Incorporation of fluorinated aromatic amino acids into proteins increases their catabolic stability especially in therapeutic proteins and peptide-based vaccines. This review seeks to summarize the different synthetic approaches in the literature to prepare ᴅ- or ʟ-fluorinated phenylalanines and their pharmaceutical applications with a focus on published synthetic methods that introduce fluorine into the phenyl, the β-carbon or the α-carbon of ᴅ-or ʟ-phenylalanines.

Close Amide NH···F Hydrogen Bonding Interactions in 1,8-Disubstituted Naphthalenes

In this note, we present a series of N-(8-fluoronaphthalen-1-yl)benzamide derivatives designed to maximize amide-NH···F hydrogen bond interactions therein. A combination of IR and NMR spectroscopy indicates a linear correlation between the high energy shift in NH stretching frequency and the electron withdrawing nature of the substituent, consistent with the trend predicted by DFT calculations. Additionally, a limiting case of hydrogen bonding is observed when the benzamide derivatives are replaced with trifluoroacetamide, causing an additional red shift of 44 cm^-1 in the NH stretching frequency. Most importantly, ¹H-¹⁹F coupling constants in this series are among the largest measured for amide-NH···F interactions. X-ray crystallography reveals face-to-face alignment of naphthalene rings in these derivatives resulting in part from the NH···F hydrogen bonds. This motif also dictates the formation of sheets composed of stacked naphthalene rings in the crystal structure as opposed to unfluorinated analogues wherein NH···OC hydrogen-bonding interactions force benzamide and naphthalene rings to engage in T-shaped π-π interactions instead. Additionally, the NH proton in the trifluoroacetamide derivative engages in extended H-bond interactions in its crystal structure.

Approaches to Obtaining Fluorinated α-Amino Acids

Fluorine does not belong to the pool of chemical elements that nature uses to build organic matter. However, chemists have exploited the unique properties of fluorine and produced countless fluoro-organic compounds without which our everyday lives would be unimaginable. The incorporation of fluorine into amino acids established a completely new class of amino acids and their properties, and those of the biopolymers constructed from them are extremely interesting. Increasing interest in this class of amino acids caused the demand for robust and stereoselective synthetic protocols that enable straightforward access to these building blocks. Herein, we present a comprehensive account of the literature in this field going back to 1995. We place special emphasis on a particular fluorination strategy. The four main sections describe fluorinated versions of alkyl, cyclic, aromatic amino acids, and also nickel-complexes to access them. We progress by one carbon unit increments. Special cases of amino acids for which there is no natural counterpart are described at the end of each section. Synthetic access to each of the amino acids is summarized in form of a table at the end of this article with the aim to make the information easily accessible to the reader.

Fluorine-Containing Drugs Approved by the FDA in 2018

Over the last two decades, fluorine substitution has become one of the essential structural traits in modern pharmaceuticals. Thus, about half of the most successful drugs (blockbuster drugs) contain fluorine atoms. In this review, we profile 17 fluorine-containing drugs approved by the food and drug administration (FDA) in 2018. The newly approved pharmaceuticals feature several types of aromatic F and CF₃ , as well as aliphatic (CF₂ ) substitution, offering advances in the treatment of various diseases, including cancer, HIV, malarial and smallpox infections.

Microbial Proteases Applications

The use of chemicals around the globe in different industries has increased tremendously, affecting the health of people. The modern world intends to replace these noxious chemicals with environmental friendly products for the betterment of life on the planet. Establishing enzymatic processes in spite of chemical processes has been a prime objective of scientists. Various enzymes, specifically microbial proteases, are the most essentially used in different corporate sectors, such as textile, detergent, leather, feed, waste, and others. Proteases with respect to physiological and commercial roles hold a pivotal position. As they are performing synthetic and degradative functions, proteases are found ubiquitously, such as in plants, animals, and microbes. Among different producers of proteases, Bacillus sp. are mostly commercially exploited microbes for proteases. Proteases are successfully considered as an alternative to chemicals and an eco-friendly indicator for nature or the surroundings. The evolutionary relationship among acidic, neutral, and alkaline proteases has been analyzed based on their protein sequences, but there remains a lack of information that regulates the diversity in their specificity. Researchers are looking for microbial proteases as they can tolerate harsh conditions, ways to prevent autoproteolytic activity, stability in optimum pH, and substrate specificity. The current review focuses on the comparison among different proteases and the current problems faced during production and application at the industrial level. Deciphering these issues would enable us to promote microbial proteases economically and commercially around the world.

Polar-π Interactions Promote Self-assembly of Dipeptides into Laminated Nanofibers

Precise incorporation of functional residues into sequences allows for tailoring the noncovalent interactions between peptides to guide their self-assembly into well-defined nanostructures, thus facilitating creation of artificial functional materials resembling natural systems. Here, we report on the self-assembly of dipeptides consisting of one fluorinated phenylalanine unit (Z residue) and one natural aromatic residue into laminated nanofibers predominately driven by polar-π interactions. On the basis of characterizations using transmission electron microscopy, scanning electron microscopy, atomic force microscopy, circular dichroism, Fourier transform infrared spectroscopy, and thioflavin T binding assay, we found that the face-centered stacking pattern of the dipeptides FZ, ZF, and ZY stabilized by the polar-π interactions and antiparallel β-sheet H-bonding interactions led to lamination of nanofibers and formation of ribbonlike nanostructures. Our findings demonstrate that incorporation of fluorinated aromatic units into short peptides not only promotes of polar-π interactions as alternative self-assembling driving forces but also governs the organizing pattern of peptides, thus benefiting creation of well-defined peptide nanostructures.

Synthesis of Quaternary α-Fluorinated α-Amino Acid Derivatives via Coordinating Cu(II) Catalytic α-C(sp3)-H Direct Fluorination

A coordinating, copper-catalyzed direct α-C(sp³)-H fluorination method has been developed to prepare vital quaternary α-fluorinated α-amino acid derivatives. A Cu(II) catalytic SET oxidative addition mechanism is proposed, involving a key fluoride-coupled Cu(II) charge transfer complex. The protocol can tolerate a rich variety of α-amino acids, for which the auxiliary group is removed in high yield and substituted for the direct preparation of dipeptide derivatives with detachable, single absolute configurations of the target compounds.

Rhodium(iii)-catalyzed CF3-carbenoid C–H functionalization of 6-arylpurines

An expedient route to access a new family of fluorine-containing purine derivatives via chelation-controlled rhodium(iii)-catalyzed carbenoid C–H functionalization has been developed.

Position-dependent impact of hexafluoroleucine and trifluoroisoleucine on protease digestion

Rapid digestion by proteases limits the application of peptides as therapeutics. One strategy to increase the proteolytic stability of peptides is the modification with fluorinated amino acids. This study presents a systematic investigation of the effects of fluorinated leucine and isoleucine derivatives on the proteolytic stability of a peptide that was designed to comprise substrate specificities of different proteases. Therefore, leucine, isoleucine, and their side-chain fluorinated variants were site-specifically incorporated at different positions of this peptide resulting in a library of 13 distinct peptides. The stability of these peptides towards proteolysis by α-chymotrypsin, pepsin, proteinase K, and elastase was studied, and this process was followed by an FL-RP-HPLC assay in combination with mass spectrometry. In a few cases, we observed an exceptional increase in proteolytic stability upon introduction of the fluorine substituents. The opposite phenomenon was observed in other cases, and this may be explained by specific interactions of fluorinated residues with the respective enzyme binding sites. Noteworthy is that 5,5,5-trifluoroisoleucine is able to significantly protect peptides from proteolysis by all enzymes included in this study when positioned N-terminal to the cleavage site. These results provide valuable information for the application of fluorinated amino acids in the design of proteolytically stable peptide-based pharmaceuticals.

Deciphering the Fluorine Code-The Many Hats Fluorine Wears in a Protein Environment

Deciphering the fluorine code is how we describe not only the focus of this Account, but also the systematic approach to studying the impact of fluorine's incorporation on the properties of peptides and proteins used by our groups and others. The introduction of fluorine has been shown to impart favorable, but seldom predictable, properties to peptides and proteins, but up until about two decades ago the outcomes of fluorine modification of peptides and proteins were largely left to chance. Driven by the motivation to extend the application of the unique properties of the element fluorine from medicinal and agro chemistry to peptide and protein engineering we have established extensive research programs that enable the systematic investigation of effects that accompany the introduction of fluorine into this class of biopolymers. The introduction of fluorine into amino acids offers a universe of options for modifications with regard to number and position of fluorine substituents in the amino acid side chain. Moreover, it is important to emphasize that the consequences of incorporating the C-F bond into a biopolymer can be attributed to two distinct yet related phenomena: (i) the fluorine substituent can directly engage in intermolecular interactions with its environment and/or (ii) the other functional groups present in the molecule can be influenced by the electron withdrawing nature of this element (intramolecular) and in turn interact differently with their immediate environment (intermolecular). Based on our studies, we have shown that a change in number and/or position of as subtle as one single fluorine substituent has the power to considerably modify key properties of amino acids such as hydrophobicity, polarity, and secondary structure propensity. These properties are crucial factors in peptide and protein engineering, and thus, fluorinated amino acids can be applied to fine-tune properties such as protein folding, proteolytic stability, and protein-protein interactions provided we understand and become able to predict the outcome of a fluorine substitution in this context. With this Account, we attempt to analyze information we gained from our recent projects on how the nature of the fluorine atom and C-F bond influence four key properties of peptides and proteins: peptide folding, protein-protein interactions, ribosomal translation, and protease stability. These results impressively show why the introduction of fluorine creates a new class of amino acids with a repertoire of functionalities that is unique to the world of proteins and in some cases orthogonal to the set of canonical and natural amino acids. Our concluding statements aim to offer a few conserved design principles that have emerged from systematic studies over the last two decades; in this way, we hope to advance the field of peptide and protein engineering based on the judicious introduction of fluorinated building blocks.

Perfluoro-tert-butyl Homoserine Is a Helix-Promoting, Highly Fluorinated, NMR-Sensitive Aliphatic Amino Acid: Detection of the Estrogen Receptor·Coactivator Protein-Protein Interaction by 19F NMR

Highly fluorinated amino acids can stabilize proteins and complexes with proteins, via enhanced hydrophobicity, and provide novel methods for identification of specific molecular events in complex solutions, via selective detection by 19F NMR and the absence of native 19F signals in biological contexts. However, the potential applications of 19F NMR in probing biological processes are limited both by the strong propensities of most highly fluorinated amino acids for the extended conformation and by the relatively modest sensitivity of NMR spectroscopy, which typically constrains measurements to mid-micromolar concentrations. Herein, we demonstrate that perfluoro-tert-butyl homoserine exhibits a propensity for compact conformations, including α-helix and polyproline helix (PPII), that is similar to that of methionine. Perfluoro-tert-butyl homoserine has nine equivalent fluorines that do not couple to any other nuclei, resulting in a sharp singlet that can be sensitively detected rapidly at low micromolar concentrations. Perfluoro-tert-butyl homoserine was incorporated at sites of leucine residues within the α-helical LXXLL short linear motif of estrogen receptor (ER) coactivator peptides. A peptide containing perfluoro-tert-butyl homoserine at position i + 3 of the ER coactivator LXXLL motif exhibited a Kd of 2.2 μM for the estradiol-bound estrogen receptor, similar to that of the native ligand. 19F NMR spectroscopy demonstrated the sensitive detection (5 μM concentration, 128 scans) of binding of the peptide to the ER and of inhibition of protein-protein interaction by the native ligand or by the ER antagonist tamoxifen. These results suggest diverse potential applications of perfluoro-tert-butyl homoserine in probing protein function and protein-protein interfaces in complex solutions.

Synthesis of Perfluoro-tert-butyl Tyrosine, for Application in 19F NMR, via a Diazonium-Coupling Reaction

A practical synthesis of the novel highly fluorinated amino acid Fmoc-perfluoro-tert-butyl tyrosine was developed. The sequence proceeds in two steps from commercially available Fmoc-4-NH₂-phenylalanine via diazotization followed by diazonium coupling reaction with perfluoro-tert-butanol. In peptides, perfluoro-tert-butyl tyrosine was detected in 30 s by NMR spectroscopy at 500 nM peptide concentration due to nine chemically equivalent fluorines that are a sharp singlet by ¹⁹F NMR. Perfluoro-tert-butyl ether has an estimated σ_p Hammett substituent constant of +0.30.

Symmetry-Adapted Perturbation Theory Energy Analysis of Alkyl Fluorine-Aromatic Interactions in Torsion Balance Systems

Symmetry-adapted perturbation theory (SAPT) calculations are carried out to elucidate the intermolecular interactions present between fluorinated and nonfluorinated alkyl chain groups and aromatic π systems in the folded and unfolded conformers of Wilcox torsion balance systems. The calculations predict the folded conformers to be 2.0-2.3 kcal/mol more stable than the unfolded conformers, with the preference for the folded conformer being greater in the fluorinated alkyl chain case. We also establish that a simple electrostatic analysis, based on atomic charges, is inadequate for understanding the conformational preferences of these systems. In the folded conformers, there are sizable charge penetration contributions that are not recovered by point charge models. Additionally, the SAPT analysis reveals that exchange-repulsion interactions make a significant contribution to the relative stability of the folded and unfolded conformer.

Designing Fluorinated Proteins

As methods to incorporate noncanonical amino acid residues into proteins have become more powerful, interest in their use to modify the physical and biological properties of proteins and enzymes has increased. This chapter discusses the use of highly fluorinated analogs of hydrophobic amino acids, for example, hexafluoroleucine, in protein design. In particular, fluorinated residues have proven to be generally effective in increasing the thermodynamic stability of proteins. The chapter provides an overview of the different fluorinated amino acids that have been used in protein design and the various methods available for producing fluorinated proteins. It discusses model proteins systems into which highly fluorinated amino acids have been introduced and the reasons why fluorinated residues are generally stabilizing, with particular reference to thermodynamic and structural studies from our laboratory. Lastly, details of the methodology we have developed to measure the thermodynamic stability of oligomeric fluorinated proteins are presented, as this may be generally applicable to many proteins.

Merging photoredox with copper catalysis: decarboxylative difluoroacetylation of α,β-unsaturated carboxylic acids with ICF2CO2Et

A novel decarboxylative difluoroacetylation of α,β-unsaturated carboxylic acids via a combination of visible light photocatalysis and cooper catalysis is reported.

Asymmetric Michael addition of α-fluoro-α-nitro esters to nitroolefins: towards synthesis of α-fluoro-α-substituted amino acids

α-Fluoro-α-nitro esters were used as reaction partners in Michael addition to nitroalkenes, and the products were obtained in excellent chemical yields and with high enantioselectivities. Moreover, α-fluoro-α-amino ester with a quaternary α-carbon was prepared for the first time.

Simple fluorinated moiety insertion on Aβ 16-23 peptide for stain-free TEM imaging

Peptide aggregation and fibre formation are one of the major underlying causes of several neurodegenerative disorders such as Alzheimer's disease. During the past decades the characterisation of these fibres has been widely studied in an attempt to further understand the nature of the related diseases and in an effort to develop treatments. Transmission electron microscopy (TEM) is one of the most commonly used techniques to identify these fibres, but requires the use of a radioactive staining agent. The procedure we report overcomes this drawback through simple addition of a fluorinated moiety to a short Amyloid β sequence via solid phase peptide synthesis (SPPS). This method is synthetically straightforward, widely applicable to different aggregation-prone sequences and, above all, allows for stain-free TEM imaging with improved quality compared to standard imaging procedures. The presence of the fluorinated moiety does not cause major changes in the fibre structure or aggregation, but rather serves to dissipate the microscope's electron beam, thus allowing for high contrast and straightforward imaging by TEM.