Highly Specific Heterodimerization Mediated by Quadrupole Interactions

Exploring Favorable Supramolecular Interactions of Multifluorinated Aromatics in Dendronized Push-Pull Chromophores for Electro-Optics

Multifluorinated aromatics serve as supramolecular synthons in the research of organic electro-optic (EO) materials by exploiting π-π stacking interaction between the aromatic hydrocarbon and multifluorinated aromatic groups for performance improvement. However, non-classical hydrogen bonding remains largely unexplored in fluorinated EO dendrimers. In this study, three Fréchet-type generation 1 benzyl ether co-dendrons were synthesized by replacing one benzyl group with 2,3,5,6-tetrafluorobenzyl (p-HF4Bz), pentafluorobenzyl (C6F5Bz), and 2,3,4,5-tetrafluorobenzyl (o-HF4Bz) groups, to afford the benzoic acid derivatives D1, D2, and D3, which were further bonded to the donor and π-bridge moieties to afford three co-dendronized push-pull phenyltetraene chromophores EOD1, EOD2, and EOD3, respectively. The weak C-H⋅⋅⋅X (X=O, F) interactions in the crystal structure of D1 cumulatively add to the benzoic acid dimers to form an extended hydrogen-bonded network, while D2 is crystallized into a centric one-dimensional chain with strong intermolecular interactions. The poled films of EOD1 with PMMA exhibited the largest and most stable EO activity with optical homogeneity among the series. The results identify the effectiveness of weak but favorable hydrogen bonds enabled by the enhanced carbon acidity of p-HF4Bz synthon in D1, over the interactions in D2 and D3, for the rational design of supramolecular EO dendrimers.

Expression and purification of fluorinated proteins from mammalian suspension culture

The site-specific encoding of noncanonical amino acids allows for the introduction of rationalized chemistry into a target protein. Of the methods that enable this technology, evolved tRNA and synthetase pairs offer the potential for expanded protein production and purification. Such an approach combines the versatility of solid-phase peptide synthesis with the scalable features of recombinant protein production. We describe the large scale production and purification of eukaryotic proteins bearing fluorinated phenylalanine in mammalian suspension cell preparations. Downstream applications of this approach include scalable recombinant protein preparation for ligand binding assays with small molecules and ligands, protein structure determination, and protein stability assays.

Tinker, Tailor, Soldier, Spy: The Diverse Roles That Fluorine Can Play within Amino Acid Side Chains

Side chain-fluorinated amino acids are useful tools in medicinal chemistry and protein science. In this review, we outline some general strategies for incorporating fluorine atom(s) into amino acid side chains and for elaborating such building blocks into more complex fluorinated peptides and proteins. We then describe the diverse benefits that fluorine can offer when located within amino acid side chains, including enabling 19F NMR and 18F PET imaging applications, enhancing pharmacokinetic properties, controlling molecular conformation, and optimizing target-binding.

Tailored Tolane-Perfluorotolane Assembly as Supramolecular Base Pair Replacement in DNA

Arene-fluoroarene interactions offer outstanding possibilities for engineering of supramolecular systems, including nucleic acids. Here, we implement the tolane-perfluorotolane interaction as base pair replacement in DNA. Tolane (THH) and perfluorotolane (TFF) moieties were connected to acyclic backbone units, comprising glycol nucleic acid (GNA) or butyl nucleic acid (BuNA) building blocks, that were incorporated via phosphoramidite chemistry at opposite positions in a DNA duplex. Thermodynamic analyses by UV thermal melting revealed a compelling stabilization by THH/TFF heteropairs only when connected to the BuNA backbone, but not with the shorter GNA linker. Detailed NMR studies confirmed the preference of the BuNA backbone for enhanced polar π-stacking. This work defines how orthogonal supramolecular interactions can be tailored by small constitutional changes in the DNA backbone, and it inspires future studies of arene-fluoroarene-programmed assembly of DNA.

On-Resin Recognition of Aromatic Oligopeptides and Proteins through Host-Enhanced Heterodimerization

Peptide dimerization is ubiquitous in natural protein conjugates and artificial self-assemblies. A major challenge in artificial systems remains achieving quantitative peptide heterodimerization, critical for next-generation biomolecular purification and formulation of therapeutics. Here, we employ a synthetic host to simultaneously encapsulate an aromatic and a noncanonical l-perfluorophenylalanine-containing peptide through embedded polar-π interactions, constructing an unprecedented series of heteropeptide dimers. To demonstrate the utility, this heteropeptide dimerization strategy was applied toward on-resin recognition of N-terminal aromatic residues in peptides as well as insulin, both exhibiting high recycling efficiency (>95%). This research unveils a generic approach to exploit quantitative heteropeptide dimers for the design of supramolecular (bio)systems.

Intramolecular Folding of Coil-Helix Block Copolymers Induced by Quadrupole Interactions

True tertiary architectures with defined local secondary structures are rare in synthetic systems. Adapting well-developed synthetic building blocks and controlling their folding through diverse interactions can be a general approach toward this goal. In this contribution, the synthesis of 3D hierarchical assemblies with distinct secondary domains formed through the intramolecular folding of a block copolymer containing a coil-like poly(styrene) (PS) block with a helical poly(isocyanide) block induced by phenyl-pentafluorophenyl quadrupole interactions is reported. The PS block is prepared via atom-transfer radical polymerization and end functionalized with a nickel complex that serves as a macroinitiator for the polymerization of chiral isocyanides bearing pentafluorophenyl pendants. The folding behavior of the coil-helix block copolymers is investigated by dynamic light scattering, NMR spectroscopy, wide-angle X-ray scattering, and differential scanning calorimetry.

Arene-Perfluoroarene Interactions in Solution

A systematic study of arene-perfluoroarene interactions in solution is presented. Using a combination of NMR titration experiments, X-ray crystallography, and computational analysis, we analyze the effects of fluorination, substituents, ring size, and solvation on the arene-perfluoroarene interaction. We find that fluorination, extension of the π systems, and enhancement of solvent polarity greatly stabilize the stacking energy up to 3 orders of magnitude (K_a = <1 to 6000 M^-1), with the highest K_a achieved for the interaction of water-soluble variants of perfluoronaphthalene and anthracene in buffered D₂O (pD = 12). Combining computational and experimental results, we conclude that this impressive binding energy is a result of enthalpically favorable electrostatic and dispersion interactions as well as the entropically driven hydrophobic effect. The enhanced understanding of arene-perfluoroarene interactions in aqueous solution sets the stage for the implementation of this abiotic intermolecular interaction in biology and medicine.

Host-Enhanced Phenyl-Perfluorophenyl Polar-π Interactions

Phenyl-perfluorophenyl polar-π interactions have been revisited for the design and fabrication of functional supramolecular systems. The relatively weak associative interactions (ΔG ≈ -1.0 kcal/mol) have limited their use in aqueous self-assembly to date. Herein, we propose a strategy to strengthen phenyl-perfluorophenyl polar-π interactions by encapsulation within a synthetic host, thus increasing the binding affinity to ΔG= -15.5 kcal/mol upon formation of heteroternary complexes through social self-sorting. These heteroternary complexes were used as dynamic, yet strong, cross-linkers in the fabrication of supramolecular gels, which exhibited excellent viscoelasticity, stretchability, self-recovery, self-healing, and energy dissipation. This work unveils a general approach to exploit host-enhanced polar-π interactions in the design of robust aqueous supramolecular systems.

A genetically encoded 19F NMR probe for lysine acetylation

Advances in acetylated protein-protein/DNA interactions depend on the development of a novel NMR (nuclear magnetic resonance) probe to study the conformational changes of acetylated proteins. However, the method for detecting the acetylated protein conformation is underdeveloped. Herein, an acetyllysine mimic has been exploited for detecting the conformational changes of acetylated p53-protein/DNA interactions by genetic code expansion and 19F NMR. This 19F NMR probe shows high structural similarity to acetyllysine and could not be deacetylated by sirtuin deacetylase in vitro/vivo. Moreover, acetylation of p53 K164 is reported to be deacetylated by SIRT2 for the first time.

Non-additive stabilization by halogenated amino acids reveals protein plasticity on a sub-angstrom scale

It has been a long-standing goal to understand the structure-stability relationship of proteins, as optimal stability is essential for protein function and highly desirable for protein therapeutics. Halogenation has emerged as a minimally invasive strategy to probe the physical characteristics of proteins in solution, as well as enhance the structural stabilities of proteins for therapeutic applications. Although advances in synthetic chemistry and genetic code expansion have allowed for the rapid synthesis of proteins with diverse chemical sequences, much remains to be learned regarding the impact of these mutations on their structural integrity. In this contribution, we present a systematic study of three well-folded model protein systems, in which their structural stabilities are assessed in response to various hydrogen-to-halogen atom mutations. Halogenation allows for the perturbation of proteins on a sub-angstrom scale, offering unprecedented precision of protein engineering. The thermodynamic results from these model systems reveal that in certain cases, proteins can display modest steric tolerance to halogenation, yielding non-additive consequences to protein stability. The observed sub-angstrom sensitivity of protein stability highlights the delicate arrangement of a folded protein core structure. The stability data of various halogenated proteins presented herein should also provide guidelines for using halogenation as a strategy to improve the stability of protein therapeutics.

Stabilization of peptides against proteolysis through disulfide-bridged conjugation with synthetic aromatics

We developed an efficient strategy for the stabilization of peptides against proteolysis, which involves noncovalent π–π interactions between aromatic amino acid residues in peptides and synthetic electron-deficient aromatics.

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.

Synthesis of protected enantiopure (R) and (S)-α-trifluoromethylalanine containing dipeptide building blocks ready to use for solid phase peptide synthesis

Considering the increasing importance of fluorinated peptides, the development of efficient and reliable synthetic methods for the incorporation of unnatural fluorinated amino acids into peptides is a current matter of interest. In this study, we report the convenient Boc/benzyl and Cbz/tert-butyl protection of both enantiomers of the quaternarized amino acid α-trifluoromethylalanine [(R)- and (S)-α-Tfm-Ala]. Because of the deactivation of the nitrogen atom of this synthetic amino acid by the strong electron withdrawing trifluoromethyl group, the peptide coupling on this position is a challenge. In order to provide a robust synthetic methodology for the incorporation of enantiopure (R)- and (S)-α-trifluoromethylalanines into peptides, we report herein the preparation of dipeptides ready to use for solid phase peptide synthesis. The difficult peptide coupling on the nitrogen atom of the α-trifluoromethylalanines was performed in solution phase by means of highly electrophilic amino acid chlorides or mixed anhydrides. The synthetic effectiveness of this fluorinated dipeptide building block strategy is illustrated by the solid phase peptide synthesis (SPPS) of the Ac-Ala-Phe-(R)-α-Tfm-Ala-Ala-NH2 tetrapeptide.

Substituent Effects on the Self-Assembly/Coassembly and Hydrogelation of Phenylalanine Derivatives

Supramolecular hydrogels derived from the self-assembly of organic molecules have been exploited for applications ranging from drug delivery to tissue engineering. The relationship between the structure of the assembly motif and the emergent properties of the resulting materials is often poorly understood, impeding rational approaches for the creation of next-generation materials. Aromatic π-π interactions play a significant role in the self-assembly of many supramolecular hydrogelators, but the exact nature of these interactions lacks definition. Conventional models that describe π-π interactions rely on quadrupolar electrostatic interactions between neighboring aryl groups in the π-system. However, recent experimental and computational studies reveal the potential importance of local dipolar interactions between elements of neighboring aromatic rings in stabilizing π-π interactions. Herein, we examine the nature of π-π interactions in the self- and coassembly of Fmoc-Phe-derived hydrogelators by systematically varying the electron-donating or electron-withdrawing nature of the side chain benzyl substituents and correlating these effects to the emergent assembly and gelation properties of the systems. These studies indicate a significant role for stabilizing dipolar interactions between neighboring benzyl groups in the assembled materials. Additional evidence for specific dipolar interactions is provided by high-resolution crystal structures obtained from dynamic transition of gel fibrils to crystals for several of the self-assembled/coassembled Fmoc-Phe derivatives. In addition to electronic effects, steric properties also have a significant effect on the interaction between neighboring benzyl groups in these assembled systems. These findings provide significant insight into the structure-function relationship for Fmoc-Phe-derived hydrogelators and give cues for the design of next-generation materials with desired emergent properties.

The effect of fluorine on supramolecular hydrogelation of 4-fluorobenzyl-capped diphenylalanine

Due to the replacement of only one hydrogen atom by fluorine, 4-fluorobenzyl-diphenylalanine molecules self-assemble to form a transparent hydrogel.

Design, synthesis, and study of fluorinated proteins

Highly fluorinated analogs of hydrophobic amino acids have proven to be generally effective in increasing the thermodynamic stability of proteins. These non-proteogenic amino acids can be incorporated into both α-helix and β-sheet structural motifs and generally enhance protein stability towards unfolding by heat and chemical denaturants, and retard their degradation by proteases. Recent detailed structural and thermodynamic studies have demonstrated that the increase in buried hydrophobic surface area that accompanies fluorination is primarily responsible for the stabilizing properties of fluorinated side chains. Fluorination appears to be a particularly useful strategy for increasing protein stability because fluorinated amino acids closely retain the shape of the side chain, and are thus minimally perturbing to protein structure and function. The first part of this chapter discusses some examples of highly fluorinated model proteins designed by our laboratory and protocols for their synthesis. In the second part, methods for determining their thermodynamic stability, along with conditions that have proven to be useful for crystallizing these proteins, are presented.

Anti-parallel sheet structures of side-chain-free γ-, δ-, and ε-dipeptides stabilized by benzene–pentafluorobenzene stacking

Benzene–pentafluorobenzene stacking can guide ω-amino acid dipeptides to arrange in an anti-parallel manner.

Exploring and exploiting polar-π interactions with fluorinated aromatic amino acids

Fluorination has become an increasingly attractive strategy in protein engineering for both basic research and biomedical applications. Thus researchers would like to understand the consequences of fluorination to the structure, stability, and function of target proteins. Although a substantial amount of work has focused on understanding the properties of fluorinated aliphatic amino acids, much less is known about fluorinated aromatic residues. In addition, polar-π interactions, often referred to as aromatic interactions, may play a significant role in protein folding and protein-protein interactions. Fluorination of aromatic residues presents an ideal strategy for probing polar-π interactions in proteins. This Account summarizes the recent studies of the incorporation of fluorinated aromatic amino acids into proteins. Herein we discuss the effects of fluorinating aromatic residues and rationalize them in the context of polar-π interactions. The results strongly support the proposal that polar-π interactions are energetically significant to protein folding and function. For example, an edge-face interaction of a pair of phenylalanines contributes as much as -1 kcal/mol to protein stability, while cation-π interactions can be much stronger. Furthermore, this new knowledge provides guidelines for protein engineering with fluorination. Importantly, incorporating perfluorinated aromatic residues into proteins enables novel mechanisms of molecular recognition that do not exist in native proteins, such as arene-perfluoroarene stacking. Such novel mechanisms can be used for programming protein folding specificity and engineering peptide-based materials.

Structure-Activity Relationship for Thiirane-Based Gelatinase Inhibitors

An extensive structure-activity relationship study with the template of 2-(4-phenoxyphenylsulfonylmethyl)thiirane (1), a potent and highly selective inhibitor for human gelatinases, is reported herein. Syntheses of 65 new analogs, each in multistep processes, allowed for exploration of key structural components of the molecular template. This study reveals that the presence of the sulfonylmethylthiirane and the phenoxyphenyl group were important for gelatinase inhibition. However, para- and some meta-substitutions of the terminal phenyl ring enhanced inhibitory activity, and led to improve metabolic stability. This agrees with the result from metabolism studies with compound 1 that the primary route of biotransformation is oxidation, mainly at the para position of the phenyl ring and alpha position of the sulfonyl group in the aliphatic side chain.

Fluorine: a new element in protein design

Fluorocarbons are quintessentially man-made molecules, fluorine being all but absent from biology. Perfluorinated molecules exhibit novel physicochemical properties that include extreme chemical inertness, thermal stability, and an unusual propensity for phase segregation. The question we and others have sought to answer is to what extent can these properties be engineered into proteins? Here, we review recent studies in which proteins have been designed that incorporate highly fluorinated analogs of hydrophobic amino acids with the aim of creating proteins with novel chemical and biological properties. Fluorination seems to be a general and effective strategy to enhance the stability of proteins, both soluble and membrane bound, against chemical and thermal denaturation, although retaining structure and biological activity. Most studies have focused on small proteins that can be produced by peptide synthesis as synthesis of large proteins containing specifically fluorinated residues remains challenging. However, the development of various biosynthetic methods for introducing noncanonical amino acids into proteins promises to expand the utility of fluorinated amino acids in protein design.

Experimental evaluation of CH-π interactions in a protein core

CH-π stacks up! Using the protein α(2) D as a model system, we estimate that a CH-π contact between cyclohexylalanine (Cha) and phenylalanine (F) contributes approximately -0.7 kcal  mol(-1) to the protein stability. The stacking F-Cha pairs are sequestered in the core of the protein, where water interference does not exist (see figure). Therefore, the observed energetic gain should represent the inherent magnitude and upper limit of the CH-π interactions.

Quasiracemic crystallization as a tool to assess the accommodation of noncanonical residues in nativelike protein conformations

Quasiracemic crystallization has been used to obtain high-resolution structures of two variants of the villin headpiece subdomain (VHP) that contain a pentafluorophenylalanine (F(5)Phe) residue in the hydrophobic core. In each case, the crystal contained the variant constructed from l-amino acids and the native sequence constructed from d-amino acids. We were motivated to undertake these studies by reports that racemic proteins crystallize more readily than homochiral forms and the prospect that quasiracemic crystallization would enable us to determine whether a polypeptide containing a noncanonical residue can closely mimic the tertiary structure of the native sequence. The results suggest that quasiracemic crystallization may prove to be generally useful for assessing mimicry of naturally evolved protein folding patterns by polypeptides that contain unnatural side-chain or backbone subunits.

Synthesis of tetrafluorinated aromatic amino acids with distinct signatures in 19F NMR

Fluorinated amino acids serve as powerful tools in protein chemistry. We synthesized a series of para-substituted tetrafluorophenylalanines via the regioselective S(NAr) chemistry of the commercially available pentafluorophenylalanine Boc-Z. These novel unnatural amino acids display distinct (19)F NMR signatures, making them powerful tools for analyzing protein-membrane interactions with NMR spectroscopy.

Fluorinated amino acids: compatibility with native protein structures and effects on protein-protein interactions

Fluorinated analogues of the canonical α-L-amino acids have gained widespread attention as building blocks that may endow peptides and proteins with advantageous biophysical, chemical and biological properties. This critical review covers the literature dealing with investigations of peptides and proteins containing fluorinated analogues of the canonical amino acids published over the course of the past decade including the late nineties. It focuses on side-chain fluorinated amino acids, the carbon backbone of which is identical to their natural analogues. Each class of amino acids--aliphatic, aromatic, charged and polar as well as proline--is presented in a separate section. General effects of fluorine on essential properties such as hydrophobicity, acidity/basicity and conformation of the specific side chains and the impact of these altered properties on stability, folding kinetics and activity of peptides and proteins are discussed (245 references).

Complementary π-π interactions induce multicomponent coassembly into functional fibrils

Noncovalent self-assembled materials inspired by amyloid architectures are useful for biomedical applications ranging from regenerative medicine to drug delivery. The selective coassembly of complementary monomeric units to provide ordered multicomponent fibrils is a possible strategy for enhancing the sophistication of these noncovalent materials. Herein we report that complementary π-π interactions can be exploited to promote the coassembly of phenylalanine (Phe) derivatives that possess complementary aromatic side-chain functionality. Specifically, equimolar mixtures of Fmoc-Phe and Fmoc-F(5)-Phe, which possess side-chain groups with complementary quadrupole electronics, readily coassemble to form two-component fibrils and hydrogels under conditions where Fmoc-Phe alone fails to self-assemble. In addition, it was found that equimolar mixtures of Fmoc-Phe with monohalogenated (F, Cl, and Br) Fmoc-Phe derivatives also coassembled into two-component fibrils. These results collectively indicate that face-to-face quadrupole stacking between benzyl side-chain groups does not account for the molecular recognition between Phe and halogenated Phe derivatives that promote cofibrillization but that coassembly is mediated by more subtle π-π effects arising from the halogenation of the benzyl side chain. The use of complementary π-π interactions to promote the coassembly of two distinct monomeric units into ordered two-component fibrils dramatically expands the repertoire of noncovalent interactions that can be used in the development of sophisticated noncovalent materials.

Aromatic rings in chemical and biological recognition: energetics and structures

This review describes a multidimensional treatment of molecular recognition phenomena involving aromatic rings in chemical and biological systems. It summarizes new results reported since the appearance of an earlier review in 2003 in host-guest chemistry, biological affinity assays and biostructural analysis, data base mining in the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB), and advanced computational studies. Topics addressed are arene-arene, perfluoroarene-arene, S⋅⋅⋅aromatic, cation-π, and anion-π interactions, as well as hydrogen bonding to π systems. The generated knowledge benefits, in particular, structure-based hit-to-lead development and lead optimization both in the pharmaceutical and in the crop protection industry. It equally facilitates the development of new advanced materials and supramolecular systems, and should inspire further utilization of interactions with aromatic rings to control the stereochemical outcome of synthetic transformations.