Oligoprolines as Molecular Entities for Controlling Distance in Biological and Material Sciences

Bottom-up design of peptide shapes in water using oligomers of N-methyl-l/d-alanine

De novo design of peptide shapes is of great interest in biomolecular science since the local peptide shapes formed by a short peptide chain in the proteins are often key to biological activities. Here, we show that the de novo design of peptide shapes with sub-nanometer conformational control can be realized using peptides consisting of N-methyl-l-alanine and N-methyl-d-alanine residues. The conformation of N-methyl-l/d-alanine residue is largely fixed because of the restricted bond rotation and hence can serve as a scaffold on which we can build a peptide into a designed shape. The local shape control by per-residue conformational restriction by torsional strains starkly contrasts with the global shape stabilization of proteins based on many remote interactions. The oligomers allow the bottom-up design of diverse peptide shapes with a small number of amino acid residues and would offer unique opportunities to realize the de novo design of biofunctional molecules.

An anionic and proline-rich peptide prolonged blood circulation of liposomes and evaded accelerated blood clearance after repeated administration

In recent years, polypeptides have been standing out as excellent candidates to replace polyethylene glycol (PEG) with adequate biocompatibility and biodegradability. In this study, we found that (VELPPP)3, an anionic γ-zein-based proline-rich peptide with a polyproline-II helical structure, was able to impart liposomes with considerable stability and significantly prolonged blood circulation in vivo. Furthermore, we have shown that (VELPPP)3-modified liposomes induced negligible anti-peptide IgM production, and no noticeable accelerated blood clearance after repeated or multi-dose administration. The biodistribution study suggested that compared to PEGylated liposomes, (VELPPP)3-modified liposomes showed a slight inclination of accumulation in livers, and a decreased entrapment in most of the other organs over long hours. In conclusion, (VELPPP)3 has shown considerable capacity in establishing stealth nanocarriers, providing inspiring insights into developing alternatives for PEGylation.

Sequence-controlled divergent supramolecular assembly of polyproline helices into metallo-peptide nanoparticles

The field of peptide based supramolecular biomaterials is fast evolving. These types of constructs have been shown to find applications in the fields of bioimaging, drug delivery and scaffolds for chemical reactions. However, the community typically focuses on the use of two specific classes of structured peptides: α-helices and β-sheets, clearly neglecting a unique peptide secondary structure: the polyproline helix. Herein, we report the first design, synthesis and characterization of polyproline based metallo-peptide nanoparticles. We demonstrate that rationally engineered polyproline helices can assemble in a divergent manner, into two types of nanoparticles. We also demonstrate that the primary sequence of the functionalised polyproline peptide is crucial to ensure a controlled assembly. This work clearly demonstrates that polyproline helices can be a powerful tool to achieve supramolecular assemblies of complex and responsive bioinspired nanomaterials.

Incorporation of CF3-pseudoprolines into polyproline type II foldamers confers promising biophysical features

The development and the use of fluorinated polyproline-type II (PPII) foldamers are still underexplored. Herein, trifluoromethyl pseudoprolines have been incorporated into polyproline backbones without affecting their PPII helicity. The ability of the trifluoromethyl groups to increase hydrophobicity and to act as 19F NMR probes is demonstrated. Moreover, the enzymatic stability and the non-cytotoxicity of these fluorinated foldamers make them valuable templates for use in medicinal chemistry.

Proline Analogues

Within the canonical repertoire of the amino acid involved in protein biogenesis, proline plays a unique role as an amino acid presenting a modified backbone rather than a side-chain. Chemical structures that mimic proline but introduce changes into its specific molecular features are defined as proline analogues. This review article summarizes the existing chemical, physicochemical, and biochemical knowledge about this peculiar family of structures. We group proline analogues from the following compounds: substituted prolines, unsaturated and fused structures, ring size homologues, heterocyclic, e.g., pseudoproline, and bridged proline-resembling structures. We overview (1) the occurrence of proline analogues in nature and their chemical synthesis, (2) physicochemical properties including ring conformation and cis/trans amide isomerization, (3) use in commercial drugs such as nirmatrelvir recently approved against COVID-19, (4) peptide and protein synthesis involving proline analogues, (5) specific opportunities created in peptide engineering, and (6) cases of protein engineering with the analogues. The review aims to provide a summary to anyone interested in using proline analogues in systems ranging from specific biochemical setups to complex biological systems.

Pseudodiproline (Pro-Cyp) Oligomers Fold into Helical Polyproline Type secondary structures

The synthesis and conformational properties of oligo-proline mimetics composed of dimeric and tetrameric Pro-Cyp constructs linked by a hydroxymethylene unit are reported. Oligomers were studied both in the solid state and in solution, unveiling right-handed helical conformation depending on the configuration of the vicinally substituted trans-cyclopentane carboxylic acid unit (Cyp). Unlike polyproline oligomers, the alternating synthetic Pro-Cyp counterparts are not stabilized by n-π* interactions but rely instead on the steric demands of the extended backbone conformation within the hydroxymethylene-linked Pro-Cyp repeating units.

Deducing the conformational space for an octa-proline helix

A molecular dyad, PY-P8-PER, comprising a proline octamer sandwiched between pyrene and perylene terminals has been synthesized in order to address the dynamics of electronic energy transfer (EET) along the oligo-proline chain. A simple pyrene-based control compound equipped with a bis-proline attachment serves as a reference for spectroscopic studies. The N-H NMR signal at the terminal pyrene allows distinction between cis and trans amides and, although the crystal structure for the control has the trans conformation, temperature-dependent NMR studies provide clear evidence for trans/cis isomerisation in D6-DMSO. Polar solvents tend to stabilise the trans structure for the pyrene amide group, even for longer oligo-proline units. Circular dichroism shows that the proline spacer for PY-P8-PER exists mainly in the all-trans geometry in methanol. Preferential excitation of the pyrene chromophore is possible at wavelengths in the 320-350 nm range and, for the dyad, is followed by efficacious EET to the perylene emitter. The probability for intramolecular EET, obtained from analysis of steady-state spectroscopic data, is ca. 80-90% in solvents of disparate polarity. Comparison with the Förster critical distance suggests the terminals are ca. 18 Å apart. Time-resolved fluorescence spectroscopy, in conjunction with DFT calculations, indicates the dyad exists as a handful of conformers displaying a narrow range of EET rates. Optimisation of a distributive model allows accurate simulation of the EET dynamics in terms of reasonable structures based on isomerisation of certain amide groups.

Catalytic templated length-controlled oligomerization

Templated synthesis is an intriguing strategy for the length-controlled synthesis of oligomers. Traditionally, such reactions require stoichiometric amounts of the template with respect to the product. Recently we reported catalytic macrocyclic templates that promote oligomerization of a small molecule substrate with a remarkable degree of length control. Herein we present our efforts toward creating linear templates for catalytic length-controlled oligomer synthesis.

Iridium-Catalyzed Synthesis of Chiral 1,2,3-Triazoles Units and Precise Construction of Stereocontrolled Oligomers

Iridium-catalyzed azide-thioalkyne cycloaddition reaction (IrAAC) has proved to be a powerful tool for the synthesis of fully substituted 1,2,3-triazole compounds with exclusive regioselectivity. Here we report its successful use in the precise construction of stereocontrolled oligomers that have great potential in diverse applications. Starting with the azide derived from L-prolinol and different functionalized thioalkynes, chiral 1,2,3-triazole units were fabricated with high efficiency under the IrAAC condition, which were further assembled into stereocontrolled oligotriazoles through metal-free exponential growth strategies. The structure and uniformity of these oligomers were well identified by ¹H NMR, size-exclusion chromatography, and mass spectrometry, the stereoregularity of which were studied through circular dichroism and circular polarized luminescence analysis.

Influence of Proline Chirality on Neighbouring Azaproline Residue Stereodynamic Nitrogen Preorganization

We report herein the first systematic crystal structural investigation of azaproline incorporated in homo- and heterochiral diprolyl peptides. The X-ray crystallography data of peptides 1-5 illustrates that stereodynamic nitrogen in azaproline adopted the stereochemistry of neighbouring proline residue without depending on its position in the peptide sequence. Natural bond orbital analysis of crystal structures indicates O_azPro -C'_Pro of peptides 4 and 5 participating in n→π* interaction with stabilization energy about 1.21-1.33 kcal/mol. Density functional theory calculations suggested that the endo-proline ring puckering favoured over exo-conformation by 6.72-7.64 kcal/mol. NBO and DFT data reveals that the n→π* interactions and proline ring puckering stabilize azaproline chirality with the neighbouring proline stereochemistry. The CD, solvent titration, variable-temperature and 2D NMR experimental results further supported the crystal structures conformation.

Crystal structure analysis of N-acetylated proline and ring size analogs

Crystal structures of N-acetylated proline and homologs with four- and six-membered rings (azetidine carboxylic acid and piperidine carboxylic acid) were obtained and compared. The distinctly different conformations of the four-, five-, and six-membered rings reflect Bayer strain, n → π* interaction, and allylic strain, and result in crystal lattices with a zigzag structure.

Skeletal Ring Contractions via I(I)/I(III) Catalysis: Stereoselective Synthesis of cis-α,α-Difluorocyclopropanes

The clinical success of α,α-difluorocyclopropanes, combined with limitations in the existing synthesis portfolio, inspired the development of an operationally simple, organocatalysis-based strategy to access cis-configured derivatives with high levels of stereoselectivity (up to >20:1 cis:trans). Leveraging an I(I)/I(III)-catalysis platform in the presence of an inexpensive HF source, it has been possible to exploit disubstituted bicyclobutanes (BCBs) as masked cyclobutene equivalents for this purpose. In situ generation of this strained alkene, enabled by Brønsted acid activation, facilitates an unprecedented 4 → 3 fluorinative ring contraction, to furnish cis-α,α-difluorinated cyclopropanes in a highly stereoselective manner (up to 88% yield). Mechanistic studies are disclosed together with conformational analysis (X-ray crystallography and NMR) to validate cis-α,α-difluorocyclopropanes as isosteres of the 1,4-dicarbonyl moiety. Given the importance of this unit in biology and the foundational n_o → π* interactions that manifest themselves in this conformation (e.g., collagen), it is envisaged that the title motif will find application in focused molecular design.

Memory Effect in Thermoresponsive Proline-based Polymers

We report that synthetic polymers consisting of L-proline monomer units exhibit temperature-driven aggregation in water with unprecedented hysteresis. This protein-like behavior is robust and governed by the chirality of the proline units. It paves the way to new processes, driven by either temperature or ionic strength changes, such as a simple "with memory" thermometer.

Determination of the critical chain length for macromolecular crystallization using structurally flexible polyketones

Critical chain length that divides small molecule crystallization from macromolecular crystallization is an important index in macro-organic chemistry to predict chain-length dependent properties of oligomers and polymers. However, extensive research on crystallization behavior of individual oligomers has been inhibited by difficulties in their synthesis and crystallization. Here, we report on the determination of critical chain length of macromolecular crystallization for structurally flexible polyketones consisting of 3,3-dimethylpentane-2,4-dione. Discrete polyketone oligomers were synthesized via stepwise elongation up to 20-mer. Powder and single crystal X-ray diffraction showed that the critical chain length for polyketones existed at an unexpectedly short chain length, 5-mer. While shorter oligomers adopted unique conformations and packing structures in the solid state, higher oligomers longer than 4-mer produced helical conformations and similar crystal packing. The critical chain length helped with understanding the inexplicable changes in melting point in the shorter chain length region resulting from chain conformations and packing styles.

A Peptide Nanocage Constructed by Self-Assembly of Oligoproline Conjugates

Cage-like supramolecular assemblies called molecular cages, which possess attractive functions, have been prepared. Although biomolecule-based nanocages are required for biological/medical applications such as drug delivery systems, the majority of nanocages are constructed using aromatic compounds with lower biocompatibility and biodegradability. In this study, the construction of a peptide nanocage consisting of an oligoproline conjugate is demonstrated. The conjugate was easy to prepare and had high biocompatibility. The oligoproline moiety of the conjugate had a rigid, rod-like structure suitable for the backbone of the supramolecular nanocage. The conjugates self-assembled to form peptide nanocages with a huge inner cavity.

Water-Assisted and Protein-Initiated Fast and Controlled Ring-Opening Polymerization of Proline N-Carboxyanhydride

The production of polypeptides via the ring-opening polymerization (ROP) of N-carboxyanhydride (NCA) is usually conducted under stringent anhydrous conditions. The ROP of proline NCA (ProNCA) for the synthesis of poly-_L-proline (PLP) is particularly challenging due to the premature product precipitation as polyproline type I helices, leading to slow reactions for up to one week, poor control of the molar mass and laborious workup. Here, we report the unexpected water-assisted controlled ROP of ProNCA, which affords well-defined PLP as polyproline II helices in 2–5 minutes and almost-quantitative yields. Experimental and theoretical studies together suggest the as-yet-unreported role of water in facilitating proton shift, which significantly lowers the energy barrier of the chain propagation. The scope of initiators can be expanded from hydrophobic amines to encompass hydrophilic amines and thiol-bearing nucleophiles, including complex biomacromolecules such as proteins. Protein-mediated ROP of ProNCA conveniently affords various protein-PLP conjugates via a grafting-from approach. PLP modification not only preserves the biological activities of the native proteins, but also enhances their resistance to extreme conditions. Moreover, PLP modification extends the elimination half-life of asparaginase (ASNase) 18-fold and mitigates the immunogenicity of wt ASNase >250-fold (ASNase is a first-line anticancer drug for lymphoma treatment). This work provides a simple solution to a long-standing problem in PLP synthesis, and offers valuable guidance for the development of water-resistant ROP of other proline-like NCAs. The facile access to PLP can greatly boost the application potential of PLP-based functional materials for engineering industry enzymes and therapeutic proteins.

Leveraging the n→π* Interaction in Alkene Isomerization by Selective Energy Transfer Catalysis

Examples of geometric alkene isomerization in nature are often limited to the net exergonic direction (ΔG°<0), with the antipodal net endergonic processes (ΔG°>0) comparatively under-represented. Inspired by the expansiveness of the maleate to fumarate (Z→E) isomerization in biochemistry, we investigated the inverse E→Z variant to validate nO →πC=O * interactions as a driving force for contra-thermodynamic isomerization. A general protocol involving selective energy transfer catalysis with inexpensive thioxanthone as a sensitizer (λmax =402 nm) is disclosed. Whilst in the enzymatic process nO →πC=O * interactions commonly manifest themselves in the substrate, these same interactions are shown to underpin directionality in the antipodal reaction by shortening the product alkene chromophore. The process was validated with diverse fumarate derivatives (>30 examples, up to Z:E>99:1), including the first examples of tetrasubstituted alkenes, and the involvement of nO →πC=O * interactions was confirmed by X-ray crystallography.

Deciphering the Backbone Noncovalent Interactions that Stabilize Polyproline II Conformation and Reduce cis Proline Abundance in Polyproline Tracts

Proline (Pro) has a higher propensity to adopt cis amide geometry than the other natural amino acids, and a poly-Pro (poly-P) tract can adopt either a polyproline I (PPI, all cis amide) or a polyproline II (PPII, all trans amide) helical conformation. Recent studies have revealed a reduced abundance of cis amide geometry among the inner Pro residues of a poly-P tract. However, the forces that stabilize the polyproline helices and the reason for the higher trans amide propensity of the inner Pro residues of a poly-P tract are poorly understood. Herein, we have studied both Pro and non-Pro PPII helical sequences and identified the backbone noncovalent interactions that are crucial to the higher stability of the trans Pro-amide geometry and the preference for a PPII helical conformation. We show the presence of reciprocal CO···CO interactions that extend over the whole PPII helical region. Interestingly, the CO···CO interactions strengthen with the increase in the PPII helical chain length and the inner CO groups possess stronger CO···CO interactions, which could explain the reduced cis abundance of the inner Pro residues of a poly-P tract. We also identified a much stronger (∼0.9 kcal·mol^-1) n_O → σ*_Cα-Cβ interaction between the N-terminal CO oxygen lone pair and the antibonding orbital (σ*) of their C_α-C_β bonds. As the n_O → σ*_Cα-Cβ interaction is possible only in the trans isomers of Pro, this interaction should be crucial for the stabilization of a PPII helix. Finally, an unusual n_N(amide) → σ*_C-N interaction (∼0.3 kcal·mol^-1) was observed between the peptidic nitrogen lone pair (n_N) and the antibonding orbital (σ*_C-N) of the subsequent C-terminal peptide C-N bond. We propose a cumulative effect of these interactions in the stabilization of a PPII helix.

Exploring the signaling space of a GPCR using bivalent ligands with a rigid oligoproline backbone

G protein–coupled receptors (GPCRs) are major players in cellular signal transmission. In this work, we have used rigid oligoproline backbones derivatized with two ligands at defined distances to induce GPCR dimer formation as a way to alter its signaling profile. We show that bivalent ligands at distances of 20 and 30 Å induce dimers of the GRPR receptor with different signaling responses. In addition, a nondimer–inducing bivalent ligand (with 10-Å distance between agonists) also induces different signaling patterns, most likely due to allosteric effects. These findings identify bivalent ligands with a stiff oligoproline backbone as tools to explore the natural signaling space of GPCRs.

G protein–coupled receptors (GPCRs) are one of the most important drug–target classes in pharmaceutical industry. Their diversity in signaling, which can be modulated with drugs, permits the design of more effective and better-tolerated therapeutics. In this work, we have used rigid oligoproline backbones to generate bivalent ligands for the gastrin-releasing peptide receptor (GRPR) with a fixed distance between their recognition motifs. This allows the stabilization of GPCR dimers irrespective of their physiological occurrence and relevance, thus expanding the space for medicinal chemistry. Specifically, we observed that compounds presenting agonists or antagonists at 20- and 30-Å distance induce GRPR dimerization. Furthermore, we found that 1) compounds with two agonists at 20- and 30-Å distance that induce dimer formation show bias toward Gq efficacy, 2) dimers with 20- and 30-Å distance have different potencies toward β-arrestin-1 and β-arrestin-2, and 3) the divalent agonistic ligand with 10-Å distance specifically reduces Gq potency without affecting β-arrestin recruitment, pointing toward an allosteric effect. In summary, we show that rigid oligoproline backbones represent a tool to develop ligands with biased GPCR signaling.

Design and synthesis of fluorinated peptides for analysis of fluorous effects on the interconversion of polyproline helices

The unique interaction between fluorine atoms has been exploited to alter protein structures and to develop synthetic and analytical applications. To expand such fluorous interaction for novel applications, polyproline peptides represent an excellent molecular nanoscaffold for controlling the presentation of perfluoroalkyl groups on their unique secondary structure. We develop approaches to synthesis fluorinated peptides to systematically investigate how the number, location and types of the fluorous groups on polyproline affect the conformation by monitoring the transition between the two major polyproline structures PPI and PPII. This work provides valuable information on how fluorous interaction affects the peptide structure and also benefits the design of functional fluorous molecules.

Self-Assembly and Rearrangement of a Polyproline II Helix Peptide on Gold

Polyproline peptide sequences have gained popularity as anchors for peptide-based self-assembled monolayers (SAMs) due to their attractive properties. In this work, peptides containing the polyproline II helix (PPII) conformation were designed and assembled on gold (Au). A quartz crystal microbalance with dissipation was used to characterize SAM formation kinetics and related properties. Peptides were designed with the sequence (GPPPPPG)₂C. It was discovered that a biexponential adsorption and rearrangement model describes the binding kinetics of the PPII-containing peptide on Au. In this model, an initial reversible binding step is followed by an irreversible rearrangement step, given by parameter k_t. This study found k_t to be approximately 0.00064 s^-1 for the PPII-containing peptides. Similarly, we found that the adsorption of the PPII-containing peptide on Au, given by ΔG_ads, was thermodynamically favorable (-7.8 kcal mol^-1) and comparable to other common thiol terminated SAMs on Au. Furthermore, we characterized SAM properties via QCM-D, Fourier-transform infrared (FTIR) spectroscopy, and electrochemical techniques to reveal high molecular density SAMs consisting of PPII helices. In addition, these SAMs were found to have high antifouling properties. Overall, this study characterizes the fundamental assembly mechanisms, particularly, rearrangement of PPII-containing peptides for the first time, which will be useful in the designing of future peptide-based SAMs with high surface coverage and antifouling properties.

Hybrid Cyclobutane/Proline-Containing Peptidomimetics: The Conformational Constraint Influences Their Cell-Penetration Ability

A new family of hybrid β,γ-peptidomimetics consisting of a repetitive unit formed by a chiral cyclobutane-containing trans-β-amino acid plus a N^α-functionalized trans-γ-amino-l-proline joined in alternation were synthesized and evaluated as cell penetrating peptides (CPP). They lack toxicity on the human tumoral cell line HeLa, with an almost negligible cell uptake. The dodecapeptide showed a substantial microbicidal activity on Leishmania parasites at 50 µM but with a modest intracellular accumulation. Their previously published γ,γ-homologues, with a cyclobutane γ-amino acid, showed a well-defined secondary structure with an average inter-guanidinium distance of 8–10 Å, a higher leishmanicidal activity as well as a significant intracellular accumulation. The presence of a very rigid cyclobutane β-amino acid in the peptide backbone precludes the acquisition of a defined conformation suitable for their cell uptake ability. Our results unveiled the preorganized charge-display as a relevant parameter, additional to the separation among the charged groups as previously described. The data herein reinforce the relevance of these descriptors in the design of CPPs with improved properties.

Oligodimethylsiloxane-Oligoproline Block Co-Oligomers: the Interplay between Aggregation and Phase Segregation in Bulk and Solution

Discrete block co-oligomers (BCOs) assemble into highly ordered nanostructures, which adopt a variety of morphologies depending on their environment. Here, we present a series of discrete oligodimethylsiloxane-oligoproline (oDMS-oPro) BCOs with varying oligomer lengths and proline end-groups, and study the nanostructures formed in both bulk and solution. The conjugation of oligoprolines to apolar siloxanes permits a study of the aggregation behavior of oligoproline moieties in a variety of solvents, including a highly apolar solvent like methylcyclohexane. The apolar solvent is more reminiscent of the polarity of the siloxane bulk, which gives insights into the supramolecular interactions that govern both bulk and solution assembly processes of the oligoproline. This extensive structural characterization allows the bridging of the gap between solution and bulk assembly. The interplay between the aggregation of the oligoproline block and the phase segregation induced by the siloxane drives the assembly. This gives rise to disordered, micellar microstructures in apolar solution and crystallization-driven lamellar nanostructures in the bulk. While most di- and triblock co-oligomers adopt predictable morphological features, one of them, oDMS15-oPro6-NH2, exhibits pathway complexity leading to gel formation. The pathway selection in the complex interplay between aggregation and phase segregation gives rise to interesting material properties.

Peptide-Protein Interactions: From Drug Design to Supramolecular Biomaterials

The self-recognition and self-assembly of biomolecules are spontaneous processes that occur in Nature and allow the formation of ordered structures, at the nanoscale or even at the macroscale, under thermodynamic and kinetic equilibrium as a consequence of specific and local interactions. In particular, peptides and peptidomimetics play an elected role, as they may allow a rational approach to elucidate biological mechanisms to develop new drugs, biomaterials, catalysts, or semiconductors. The forces that rule self-recognition and self-assembly processes are weak interactions, such as hydrogen bonding, electrostatic attractions, and van der Waals forces, and they underlie the formation of the secondary structure (e.g., α-helix, β-sheet, polyproline II helix), which plays a key role in all biological processes. Here, we present recent and significant examples whereby design was successfully applied to attain the desired structural motifs toward function. These studies are important to understand the main interactions ruling the biological processes and the onset of many pathologies. The types of secondary structure adopted by peptides during self-assembly have a fundamental importance not only on the type of nano- or macro-structure formed but also on the properties of biomaterials, such as the types of interaction, encapsulation, non-covalent interaction, or covalent interaction, which are ultimately useful for applications in drug delivery.

Peptide-Metal Frameworks with Metal Strings Guided by Dispersion Interactions

Despite impressive advances in the construction of metal-organic frameworks (MOFs), the formation of networks from peptidic ligands is difficult, though they are sought after for their modularity and biocompatibility. Herein we present a peptide-metal framework that consists of helical oligoproline ligands and Zn/K (or Zn/Rb). The crystalline network contains pleated nanosheets with the metal ions aligned in strings. This unprecedented architecture derives from under-appreciated London dispersion interactions between the oligoproline ligands that play in concert with the metal coordination to create the network. Hence, the secondary structure of the peptidic ligand represents an additional control element for the creation of new MOF architectures. We anticipate that our results will instruct the design of further peptidic MOFs and enable the generation of versatile biocompatible materials.

Distance-Dependent Cellular Uptake of Oligoproline-Based Homobivalent Ligands Targeting GPCRs-An Experimental and Computational Analysis

Tumor targeting with bivalent radiolabeled ligands for GPCRs is an attractive means for cancer imaging and therapy. Here, we studied and compared the distance dependence of homobivalent ligands for the human gastrin-releasing peptide receptor (hGRP-R) and the somatostatin receptor subtype II (hSstR_2a). Oligoprolines were utilized as molecular scaffolds to enable distances of 10, 20, or 30 Å between two identical, agonistic recognition motifs. In vitro internalization assays revealed that ligands with a distance of 20 Å between the recognition motifs exhibit the highest cellular uptake in both ligand series. Structural modeling and molecular dynamics simulations support an optimal distance of 20 Å for accommodating ligand binding to both binding sites of a GPCR dimer. Translation of these findings to the significantly higher complexity in vivo proved difficult and showed only for the hGRP-R increased tumor uptake of the bivalent ligand.

Chiral Cyclobutane-Containing Cell-Penetrating Peptides as Selective Vectors for Anti-Leishmania Drug Delivery Systems

Two series of new hybrid γ/γ-peptides, γ-CC and γ-CT, formed by (1S,2R)-3-amino-2,2,dimethylcyclobutane-1-carboxylic acid joined in alternation to a Nα-functionalized cis- or trans-γ-amino-l-proline derivative, respectively, have been synthesized and evaluated as cell penetrating peptides (CPP) and as selective vectors for anti-Leishmania drug delivery systems (DDS). They lacked cytotoxicity on the tumoral human cell line HeLa with a moderate cell-uptake on these cells. In contrast, both γ-CC and γ-CT tetradecamers were microbicidal on the protozoan parasite Leishmania beyond 25 μM, with significant intracellular accumulation. They were conjugated to fluorescent doxorubicin (Dox) as a standard drug showing toxicity beyond 1 μM, while free Dox was not toxic. Intracellular accumulation was 2.5 higher than with Dox-TAT conjugate (TAT = transactivator of transcription, taken as a standard CPP). The conformational structure of the conjugates was approached both by circular dichroism spectroscopy and molecular dynamics simulations. Altogether, computational calculations predict that the drug-γ-peptide conjugates adopt conformations that bury the Dox moiety into a cavity of the folded peptide, while the positively charged guanidinium groups face the solvent. The favorable charge/hydrophobicity balance in these CPP improves the solubility of Dox in aqueous media, as well as translocation across cell membranes, making them promising candidates for DDS.

Conformation and Morphology of 4-(NH2/OH)-Substituted l/d-Prolyl Polypeptides: Effect of Homo- and Heterochiral Backbones on Formation of β-Structures and Nanofibers

The relative stereochemistry of C2 and C4 in 4-substituted prolyl polypeptides plays an important role in defining the derived conformation in solution. cis-(2S,4S)-Amino/hydroxy-l-prolyl polypeptide (lC-Amp 9/lC-Hyp 9) shows a PPII conformation in phosphate buffer and a β-structure in a relatively hydrophobic solvent, trifluoroethanol (TFE). It is now demonstrated that the homochiral enantiomeric cis-substituted d-prolyl polypeptide (dC-Amp 9/dC-Hyp 9) exhibits mirror image β-structures in TFE. In the case of alternating heterochiral prolyl peptides, it is the trans-substituted [lT(2S,4R)-dT(2R,4S)] n prolyl polypeptide that shows β-structures in TFE, while the cis-substituted [lC(2S,4S)-dC(2R,4R)] n prolyl polypeptide is disordered in both phosphate buffer and TFE. The results highlight the important chirality-specific structural requirements for β-structure formation. The observed conformation in solution (circular dichroism (CD)) is also correlated with the morphology of the self-assemblies (field emission scanning electron microscopy (FESEM)), with the PPII form leading to spherical nanoparticles and β-structures leading to nanofiber formation. The results shed light on the role of relative stereochemistry at C2 and C4 in defining the polyproline peptide conformation in solution and how different conformations drive self-assemblies of peptides toward specific nanostructures.

The Diverse World of Foldamers: Endless Possibilities of Self-Assembly

Different classes of foldamers, which are synthetic oligomers that adopt well-defined conformations in solution, have been the subject of extensive studies devoted to the elucidation of the forces driving their secondary structures and their potential as bioactive molecules. Regardless of the backbone type (peptidic or abiotic), the most important features of foldamers are the high stability, easy predictability and tunability of their folding, as well as the possibility to endow them with enhanced biological functions, with respect to their natural counterparts, by the correct choice of monomers. Foldamers have also recently started playing a starring role in the self-assembly of higher-order structures. In this review, selected articles will be analyzed to show the striking number of self-assemblies obtained for foldamers with different backbones, which will be analyzed in order of increasing complexity. Starting from the simplest self-associations in solution (e.g., dimers of β-strands or helices, bundles, interpenetrating double and multiple helices), the formation of monolayers, vesicles, fibers, and eventually nanostructured solid tridimensional morphologies will be subsequently described. The experimental techniques used in the structural investigation, and in the determination of the driving forces and mechanisms underlying the self-assemblies, will be systematically reported. Where applicable, examples of biomimetic self-assembled foldamers and their interactions with biological components will be described.

Interplay of Pyrrolidine Units with Homo/Hetero Chirality and CF3-Aryl Substituents on Secondary Structures of β-Proline Tripeptides in Solution

All possible variants of β-proline functionalized tripeptides consisting of homo/hetero chiral monomeric all-cis 5-arylpyrrolidine-2,4-dicarboxylate units were synthesized for the first time by a nonpeptidic coupling method based on 1,3-dipolar cycloaddition chemistry of azomethine ylides. Secondary structures of β-proline tripeptides in solution were determined using the NMR spectroscopy data. o-(Trifluoromethyl)phenyl substituent contributes to stereoselectivity of 1,3-dipolar cycloaddition and structural features of β-proline tripeptides. A β-proline CF₃-tripeptide with alternating absolute chirality between adjacent pyrrolidine units mimics natural PPII helix secondary structure.

Shallow Distance Dependence for Proton-Coupled Tyrosine Oxidation in Oligoproline Peptides

We have explored the kinetic effect of increasing electron transfer (ET) distance in a biomimetic, proton-coupled electron-transfer (PCET) system. Biological ET often occurs simultaneously with proton transfer (PT) in order to avoid the high-energy, charged intermediates resulting from the stepwise transfer of protons and electrons. These concerted proton-electron-transfer (CPET) reactions are implicated in numerous biological ET pathways. In many cases, PT is coupled to long-range ET. While many studies have shown that the rate of ET is sensitive to the distance between the electron donor and acceptor, extensions to biological CPET reactions are sparse. The possibility of a unique ET distance dependence for CPET reactions deserves further exploration, as this could have implications for how we understand biological ET. We therefore explored the ET distance dependence for the CPET oxidation of tyrosine in a model system. We prepared a series of metallopeptides with a tyrosine separated from a Ru(bpy)32+ complex by an oligoproline bridge of increasing length. Rate constants for intramolecular tyrosine oxidation were measured using the flash-quench transient absorption technique in aqueous solutions. The rate constants for tyrosine oxidation decreased by 125-fold with three added proline residues between tyrosine and the oxidant. By comparison, related intramolecular ET rate constants in very similar constructs were reported to decrease by 4-5 orders of magnitude over the same number of prolines. The observed shallow distance dependence for tyrosine oxidation is proposed to originate in part from the requirement for stronger oxidants, leading to a smaller hole-transfer effective tunneling barrier height. The shallow distance dependence observed here and extensions to distance-dependent CPET reactions have potential implications for long-range charge transfers.

Evidence of the Reduced Abundance of Proline cis Conformation in Protein Poly Proline Tracts

Proline is found in a cis conformation in proteins more often than other proteinogenic amino acids, where it influences structure and modulates function, being the focus of several high-resolution structural studies. However, until now, technical and methodological limitations have hampered the site-specific investigation of the conformational preferences of prolines present in poly proline (poly-P) homorepeats in their protein context. Here, we apply site-specific isotopic labeling to obtain high-resolution NMR data on the cis/trans equilibrium of prolines within the poly-P repeats of huntingtin exon 1, the causative agent of Huntington's disease. Screening prolines in different positions in long (poly-P₁₁) and short (poly-P₃) poly-P tracts, we found that, while the first proline of poly-P tracts adopts similar levels of cis conformation as isolated prolines, a length-dependent reduced abundance of cis conformers is observed for terminal prolines. Interestingly, the cis isomer could not be detected in inner prolines, in line with percentages derived from a large database of proline-centered tripeptides extracted from crystallographic structures. These results suggest a strong cooperative effect within poly-Ps that enhances their stiffness by diminishing the stability of the cis conformation. This rigidity is key to rationalizing the protection toward aggregation that the poly-P tract confers to huntingtin. Furthermore, the study provides new avenues to probe the structural properties of poly-P tracts in protein design as scaffolds or nanoscale rulers.

Synthesis of Unprotected Spirocyclic β-Prolines and β-Homoprolines by Rh-Catalyzed C-H Insertion

A series of unprotected spirocyclic β-prolines and β-homoprolines are prepared by Rh-catalyzed C-H insertion. The key intermediate, a Rh nitrenoid, is generated by the N-O bond cleavage of a substituted isoxazolidin-5-one. The reaction proceeds on a gram scale with a catalyst loading of as little as 0.1 mol %, affording spirocyclic β-amino acids that are otherwise difficult to obtain. The building blocks prepared in this work will likely find applications in medicinal chemistry.

Domain-Swapping Design by Polyproline Rod Insertion

During domain swapping, proteins mutually interconvert structural elements to form a di-/oligomer. Engineering this process by design is important for creating a higher order protein assembly with minimal modification. Herein, a simple design strategy is shown for domain-swapping formation by loop deletion and insertion of a polyproline rod. Crystal structures revealed the formation of the domain-swapped dimers and polyproline portion formed a polyproline II (PPII) structure. Small-angle X-ray scattering demonstrated that an extended orientation of domain-swapped dimer was retained in solution. It is found that a multiple of three of inserting proline residue is favored for domain swapping because of the helical nature of PPII. The rigid nature of the polyproline rod enables precise control of the interdomain distance and orientation.

Templated chemistry for bioorganic synthesis and chemical biology

In light of the 2018 Max Bergmann Medal, this review discusses advancements on chemical biology-driven templated chemistry developed in the author's laboratories. The focused review introduces the template categories applied to orient functional units such as functional groups, chromophores, biomolecules, or ligands in space. Unimolecular templates applied in protein synthesis facilitate fragment coupling of unprotected peptides. Templating via bimolecular assemblies provides control over proximity relationships between functional units of two molecules. As an instructive example, the coiled coil peptide-templated labelling of receptor proteins on live cells will be shown. Termolecular assemblies provide the opportunity to put the proximity of functional units on two (bio)molecules under the control of a third party molecule. This allows the design of conditional bimolecular reactions. A notable example is DNA/RNA-triggered peptide synthesis. The last section shows how termolecular and multimolecular assemblies can be used to better characterize and understand multivalent protein-ligand interactions.

Oligoprolines guide the self-assembly of quaterthiophenes

Control over the molecular organization of π-conjugated oligothiophenes into different types of supramolecular assemblies is key to their use in organic electronics but difficult to achieve as these chromophores have a pronounced tendency to aggregate. Herein we show that oligoprolines, which do not self-assemble on their own, control the self-assembly of quaterthiophenes. Spectroscopic, microscopic, and diffraction studies with quaterthiophene-oligoproline conjugates revealed the formation of mono- or double-layered sheets or, alternatively, helically twisted ribbons - depending on the length of the oligoproline. The dimensions of the nanoscopic objects, which extend into the micrometer regime, correlate with the molecular dimensions of the quaterthiophene-oligoproline building blocks.

Strategy and Effects of Polyproline Peptide Stapling by Copper(I)-Catalyzed Alkyne-Azide Cycloaddition Reaction

Polyproline is a unique type of peptide that has a stable, robust, and well-defined helical structure in an aqueous environment. These features have allowed polyproline to be used as a nanosized scaffold for applications in chemical biology and related fields. To understand its structural properties and to expand the applications, this secondary structure was tested systematically by stapling the peptide at different locations with staples of various lengths. Using the efficient copper(I)-catalyzed alkyne-azide cycloaddition (CuAAC), we successfully prepared stapled polyproline and investigated the impact of this peptide macrocyclization through circular dichroism analysis. Whereas the stapling seems to have no significant effect on polyproline helix II (PPII) conformation in water, the location and the length of the staple affect the transformation of conformation in n-propanol. These results provide valuable information for future research using peptide stapling to manipulate polyproline conformation for various applications.

Positional Isomers of Chromophore-Peptide Conjugates Self-Assemble into Different Morphologies

Ordering π-systems into defined supramolecular structures is important for the development of organic functional materials. In recent years, peptides with defined secondary structures and/or self-assembly properties were introduced as powerful tools to order peptide-chromophore conjugates into different morphologies. This work explores whether or not the directionality of peptides can be used to control the self-assembly. The position of the π-system in conjugates between oligoprolines and perylene monoimide (PMI) chromophores was varied by attaching the PMI moiety to the second-to-last residue from the C- and N-termini, respectively. Microscopic and diffraction analysis revealed that the positional isomers form distinctly different supramolecular architectures that extend into the micrometer regime. NMR spectroscopic studies in solution phase allowed correlation of the self-assembly properties with markedly different conformational preferences of the isomeric building blocks. These insights enabled the design of building blocks with predictable self-assembly properties. Thus, the directionality of peptides offers exciting opportunities for controlling the self-assembly and electronic properties of π-systems.

Functionalized Proline-Rich Peptides Bind the Bacterial Second Messenger c-di-GMP

c-di-GMP is an attractive target in the fight against bacterial infections since it is a near ubiquitous second messenger that regulates important cellular processes of pathogens, including biofilm formation and virulence. Screening of a combinatorial peptide library enabled the identification of the proline-rich tetrapeptide Gup-Gup-Nap-Arg, which binds c-di-GMP selectively over other nucleotides in water. Computational and CD spectroscopic studies provided a possible binding mode of the complex and enabled the design of a pentapeptide with even higher binding strength towards c-di-GMP. Biological studies showed that the tetrapeptide inhibits biofilm growth by the opportunistic pathogen P. aeruginosa.

Transmembrane Polyproline Helix

The third most abundant polypeptide conformation in nature, the polyproline-II helix, is a polar, extended secondary structure with a local organization stabilized by intercarbonyl interactions within the peptide chain. Here we design a hydrophobic polyproline-II helical peptide based on an oligomeric octahydroindole-2-carboxylic acid scaffold and demonstrate its transmembrane alignment in model lipid bilayers by means of solid-state ¹⁹F NMR. As result, we provide a first example of a purely artificial transmembrane peptide with a structural organization that is not based on hydrogen-bonding.

Exploring hydrophobicity limits of polyproline helix with oligomeric octahydroindole-2-carboxylic acid

The polyproline-II helix is the most extended naturally occurring helical structure and is widely present in polar, exposed stretches and "unstructured" denatured regions of polypeptides. Can it be hydrophobic? In this study, we address this question using oligomeric peptides formed by a hydrophobic proline analogue, (2S,3aS,7aS)-octahydroindole-2-carboxylic acid (Oic). Previously, we found the molecular principles underlying the structural stability of the polyproline-II conformation in these oligomers, whereas the hydrophobicity of the peptide constructs remains to be examined. Therefore, we investigated the octan-1-ol/water partitioning and inclusion in detergent micelles of the oligo-Oic peptides. The results showed that the hydrophobicity is remarkably enhanced in longer oligomeric sequences, and the oligo-Oic peptides with 3 to 4 residues and higher are specific towards hydrophobic environments. This contrasts significantly to the parent oligoproline peptides, which were moderately hydrophilic. With these findings, we have demonstrated that the polyproline-II structure is compatible with nonpolar media, whereas additional manipulations of the terminal functionalities feature solubility in extremely nonpolar solvents such as hexane.