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This paper discusses the synergy between experimental and computational methods to determine full atomistic models of peptide-based materials. [Display omitted] • β-Peptide self-assembly leads to different sequence-dependent nanostructures. • Theoretical molecular modelling of β-peptides is challenging. • We discuss computational modelling approaches to the self-assembly of β-peptides. • Combined experimental and computational methods lead to realistic atomistic models. • The collective balance of non-covalent interactions drives peptide self-assembly. Peptide-based self-assembly has been used to produce a wide range of nanostructures. While most of these systems involve self-assembly of α-peptides, more recently β-peptides have also been shown to undergo supramolecular self-assembly, and have been used to produce materials for applications in tissue engineering, cell culture and drug delivery. In order to engineer new materials with specific structure and function, theoretical molecular modelling can provide significant insights into the collective balance of non-covalent interactions that drive the self-assembly and determine the structure of the resultant supramolecular materials under different conditions. However, this approach has only recently become feasible for peptide-based self-assembled nanomaterials, particularly those that incorporate non α-amino acids. This perspective provides an overview of the challenges associated with computational modelling of the self-assembly of β-peptides and the recent success using a combination of experimental and computational techniques to provide insights into the self-assembly mechanisms and fully atomistic models of these new biocompatible materials. [ABSTRACT FROM AUTHOR]

β-peptides are peptide-mimetics with wide biomedical and biotechnological applications. Their most peculiar feature is their readiness to fold into various secondary structures not found in their natural counterparts. Furthermore, β-amino acid insertions to natural polypeptides were found to provide unique features and also increase enzymatic stability. This is due to the additional methylene group in their backbone, which on the other hand makes it impossible to use the established algorithms and computational tools developed for α-peptides and proteins. An extension to the PyMOL v2.x molecular graphics environment is presented for β-peptides, which allows rapid graphical visualization and greatly simplified model building for computational studies, with special emphasis also put on direct formation of diverse folding states.

Complementary to hydrophobic five membered ring β-amino acids (e.g. ACPC), β-sugar amino acids (β-SAAs) have found increasing application as hydrophilic building blocks of foldamers and α/β chimeric peptides. Fmoc-protected β-SAAs [e.g. Fmoc-RibAFU(ip)-OH] are indeed useful Lego elements, ready to use for SPPS. The removal of 1,2-OH isopropylidene protecting group increasing the hydrophilicity of such SAA is presented here. We first used N3-RibAFU(ip)-OH model compound to optimize mild deprotection conditions. The formation of the 1,2-OH free product N3-RibAFU-OH and its methyl glycoside methyl ester, N3-RibAFU(Me)-OMe were monitored by RP-HPLC and found that either 50% TFA or 8 eqv. Amberlite IR-120 H+ resin in MeOH are optimal reagents for the effective deprotection. These conditions were then successfully applied for the synthesis of chimeric oligopeptide: -GG-X-GG- [X=RibAFU(ip)]. We found the established conditions to be effective and—at the same time—sufficiently mild to remove 1,2-O-isopropylidene protection and thus, it is proposed to be used in the synthesis of oligo- and polypeptides of complex sequence combination. [ABSTRACT FROM AUTHOR]

The title compound, C38H50N2O7, represents a chiral β-proline dipeptide. Corresponding stereogenic centres of constituting pyrrolidine units have opposite absolute configurations. The central amide fragment is planar within 0.1 Å and adopts a Z configuration along the N—CO bond. In the crystal, the hydrogen atoms of the methylene groups form several short intermolecular C—H...O contacts with the carbonyl oxygen atoms of an adjacent molecule. The only active amino hydrogen atom is not involved in hydrogen bonding.

4‐l‐menthyloxycarbonyl 5‐aryl prolinates were studied as organocatalysts of a novel three‐component reaction of cyclohexanone, benzoic acid, and β‐nitrostyrene. The presence of ortho‐halogen atom in 5‐aryl fragment of the catalyst is favored for driving the formation of chiral 7a‐hydroxyoctahydro‐2H‐indol‐2‐one scaffold. 5‐(o‐Chlorophenyl) prolinate selectively afforded 3‐phenyl‐7a‐hydroxyoctahydro‐2H‐indol‐2‐one with ee 63%, whereas 5‐phenyl prolinate led to conjugation of β‐nitrostyrene to cyclohexanone (the Michael adduct). Plausible chlorine effect is accounted for the specific interaction of the 5‐aryl prolinate enamine intermediate with β‐nitrostyrene in the transition state. [ABSTRACT FROM AUTHOR]

Carbapenem‐resistant Gram‐negative bacteria (GNB) are heading the list of pathogens for which antibiotics are the most critically needed. Many antibiotics are either unable to penetrate the outer‐membrane or are excluded by efflux mechanisms. Here, we report a cationic block β‐peptide (PAS8‐b‐PDM12) that reverses intrinsic antibiotic resistance in GNB by two distinct mechanisms of action. PAS8‐b‐PDM12 does not only compromise the integrity of the bacterial outer‐membrane, it also deactivates efflux pump systems by dissipating the transmembrane electrochemical potential. As a result, PAS8‐b‐PDM12 sensitizes carbapenem‐ and colistin‐resistant GNB to multiple antibiotics in vitro and in vivo. The β‐peptide allows the perfect alternation of cationic versus hydrophobic side chains, representing a significant improvement over previous antimicrobial α‐peptides sensitizing agents. Together, our results indicate that it is technically possible for a single adjuvant to reverse innate antibiotic resistance in all pathogenic GNB of the ESKAPE group, including those resistant to last resort antibiotics. [ABSTRACT FROM AUTHOR]

β-Aminopeptidases have the unique capability to hydrolyse N-terminal β-amino acids, with varied preferences for the nature of β-amino acid side chains. This unique capability makes them useful as biocatalysts for synthesis of β-peptides and to kinetically resolve β-peptides and amides for the production of enantiopure β-amino acids. To date six β-aminopeptidases have been discovered and functionally characterised, five from Gram negative bacteria and one from a fungus, Aspergillus. Here we report on the purification and characterisation of an additional four β-aminopeptidases from a Gram-positive bacterium, Mycolicibacterium smegmatis (Ms BapA), a yeast, Yarrowia lipolytica (Ylip BapA), and two β-aminopeptidases BcA5 BapA and BcC1 BapA) from Gram-negative bacteria isolated from activated sludge identified as Burkholderia sp. The genes encoding β-aminopeptidases were cloned, expressed in Escherichia coli and purified. The β-aminopeptidases were produced as inactive preproteins that underwent self-cleavage to form active enzymes comprised of two different subunits. The subunits, designated α and β, appeared to be tightly associated as the active enzyme was recovered after IMAC purification even though only the α-subunit was His6-tagged. The enzymes were shown to hydrolyse chromogenic substrates with the N-terminal L-configuration βhGly and β3hLeu with high activities. These enzymes displayed higher activity with H-βhGly-pNA than previously characterised enzymes from other microorganisms. These data indicate that the new β-aminopeptidases are fully functional, adding to the toolbox of enzymes that could be used to produce β-peptides. Overexpression studies in Pseudomonas aeruginosa also showed that the β-aminopeptidases may play a role in some cellular functions. Importance β-Aminopeptidases are unique enzymes found in a diverse range of microorganisms that can utilise synthetic β-peptides as a sole carbon source. Six β-aminopeptidases have been previously characterised with preferences for different β-amino acid substrates and have demonstrated the capability to not only catalyse the degradation of synthetic β-peptides, but also catalyse the synthesis of short β-peptides. Identification of other β-aminopeptidases adds to this toolbox of enzymes with varying β-amino acid substrate preferences and kinetics. These enzymes have potential to be utilised in the sustainable manufacture of β-amino acid derivatives and β-peptides for use in biomedical and biomaterial applications. This is important because β-amino acids and peptides confer increased proteolytic resistance to bioactive compounds and form novel structures as well as structures similar to α-peptides. The discovery of new enzymes will also provide insight into the biological importance of these enzymes in nature. [ABSTRACT FROM AUTHOR]

The increasing interest in novel foldamer constructs demands an accurate computational treatment on an extensive timescale. However, it is still a challenge to derive a force field (FF) that can reproduce the experimentally known fold while also allowing the spontaneous exploration of other structures. Here, aiming at a realistic reproduction of backbone torsional barriers, the relevant proper dihedrals of acyclic β²-, β³- and β2,3-amino acids were added to the CHARMM FF and optimized using a novel, self-consistent iterative procedure based on quantum chemical relaxed scans. The new FF was validated by molecular dynamics simulations on three acyclic peptides. While they resided most of the time in their preferred fold (>80% in helices and >50% in hairpin), they also visited other conformations. Owing to the CHARMM36m-consistent parametrization, the proposed extension is suitable for exploring new foldamer structures and assemblies, and their interactions with diverse biomolecules. [ABSTRACT FROM AUTHOR]

The title compound, C38H50N2O7, represents a chiral β-proline dipeptide. Corresponding stereogenic centres of constituting pyrrolidine units have opposite absolute configurations. The central amide fragment is planar within 0.1-Å and adopts a Z configuration along the N--CO bond. In the crystal, the hydrogen atoms of the methyl­ene groups form several short inter­molecular C-H...O contacts with the carbonyl oxygen atoms of an adjacent mol­ecule. The only active amino hydrogen atom is not involved in hydrogen bonding. [ABSTRACT FROM AUTHOR]

Synthetic β-peptides are potential functional mimetics of native α-proteins. A recently developed, novel, synthetic approach provides an effective route to the broad group of β-proline oligomers with alternating patterns of stereogenic centers. Conformation of the pyrrolidine ring, Z/E isomerism of β-peptide bonds, and hindered rotation of the neighboring monomers determine the spatial structure of this group of β-proline oligopeptides. Preferences in their structural organization and corresponding thermodynamic properties are determined by NMR spectroscopy, restrained molecular dynamics and quantum mechanics. The studied β-proline oligopeptides exist in dimethyl sulfoxide solution in a limited number of conformers, with compatible energy of formation and different spatial organization. In the β-proline tetrapeptide with alternating chirality of composing pyrrolidine units, one of three peptide bonds may exist in an E configuration. For the alternating β-proline pentapeptide, the presence of an E configuration for at least of one β-peptide bond is mandatory. In this case, three peptide bonds synchronously change their configurations. Larger polypeptides may only exist in the presence of several E configurations of β-peptide bonds forming a wave-like extended structure.

The conformational characteristics of protected homo-oligomeric Boc-[β3(R)Val]n-OMe, n = 1, 2, 3, 4, 6, 9, and 12 have been investigated in organic solvents using nuclear magnetic resonance (NMR), Fourier transform infrared (FTIR) absorption spectroscopy and circular dichroism (CD) methods. The detailed 1H NMR analysis of Boc-[β3(R)Val]12-OMe reveals that the peptide aggregates extensively in CDCl3, but is disaggregated in 20%, (v/v) dimethyl sulfoxide (DMSO) in CDCl3 and in CD3OH. Limited assignment of the N-terminus NH groups, together with solvent dependence of NH chemical shifts and temperature coefficients provides evidence for 14-helix conformation in the 12-residue peptide. FTIR analysis in CHCl3 establishes that the onset of folding and aggregation, as evidenced by NH stretching bands at 3375 cm−1 (intramolecular) and 3285 cm−1 (intermolecular), begins at the level of the tetrapeptide. The observed CD bands, 214 nm (negative) and 198 nm (positive), support 14-helix formation in the 9 and 12 residue sequences. The folding and aggregation tendencies of homo-oligomeric α-, β-, and γ- residues is compared in the model peptides Boc-[ωVal]n-NHMe, ω = α, β, and γ and n = 1, 2, and 3. Analysis of the FTIR spectra in CHCl3, establish that the tendency to aggregate at the di and tripeptide level follows the order β > α∼γ, while the tendency to fold follows the order γ > β > α. [ABSTRACT FROM AUTHOR]

Catheter-associated urinary tract infections (CAUTI) are the most common type of hospital-acquired infection, with more than 30 million catheters placed annually in the US and a 10–30% incidence of infection. Candida albicans forms fungal biofilms on the surfaces of urinary catheters and is the leading cause of fungal urinary tract infections. As a step toward new strategies that could prevent or reduce the occurrence of C. albicans -based CAUTI, we investigated the ability of antifungal β-peptide-based mimetics of antimicrobial peptides (AMPs) to kill C. albicans and prevent biofilm formation in synthetic urine. Many α-peptide-based AMPs exhibit antifungal activities, but are unstable in high ionic strength media and are easily degraded by proteases—features that limit their use in urinary catheter applications. Here, we demonstrate that β-peptides designed to mimic the amphiphilic helical structures of AMPs retain 100% of their structural stability and exhibit antifungal and anti-biofilm activity against C. albicans in a synthetic medium that mimics the composition of urine. We demonstrate further that these agents can be loaded into and released from polymer-based multilayer coatings applied to polyurethane, polyethylene, and silicone tubing commonly used as urinary catheters. Our results reveal catheters coated with β-peptide-loaded multilayers to kill planktonic fungal cells for up to 21 days of intermittent challenges with C. albicans and prevent biofilm formation on catheter walls for at least 48 h. These new materials and approaches could lead to advances that reduce the occurrence of fungal CAUTI. Statement of Significance Catheter-associated urinary tract infections are the most common type of hospital-acquired infection. The human pathogen Candida albicans is the leading cause of fungal urinary tract infections, and forms difficult to remove ‘biofilms’ on the surfaces of urinary catheters. We investigated synthetic β-peptide mimics of natural antimicrobial peptides as an approach to kill C. albicans and prevent biofilm formation in media that mimics the composition of urine. Our results reveal these mimics to retain structural stability and activity against C. albicans in synthetic urine. We also report polymer-based approaches to the local release of these agents within urinary catheter tubes. With further development, these materials-based approaches could lead to advances that reduce the occurrence of fungal urinary tract infections. [ABSTRACT FROM AUTHOR]

Aggregation, orientation and dynamics of transmembrane helices are of relevance for protein function and transmembrane signaling. To explore the interactions of transmembrane helices and the interdependence of peptide structure and lipid composition of the membranes, β-peptides were explored as model transmembrane domains. Various hydrophobic β-peptide sequences were synthesized by solid phase peptide synthesis. Conformational analyses of β-peptide helices were performed in organic solvents (methanol and 2,2,2-trifluoroethanol) and in large unilamellar liposomes (dimyristoylphosphatidylcholine, dipalmitoylphosphatidylcholine and dioleoylphosphatidylcholine) indicating 12- and 14-helix conformations, depending on β3-amino acid sequences. The intrinsic tryptophan fluorescence of β3-homotryptophan units inserted in the center or near the end of the sequence was used to verify the membrane insertion of the β-peptides. A characteristic blue shift with peripheral β3-homotryptophan compared with β-peptides with central tryptophan served as indication for a transmembrane orientation of the β-peptides within the lipid bilayer. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

Disequilibrium in the human debilitated immune system favors proliferation of invasive Candida species, a major therapeutic challenge due to development of resistance to several conventional antifungal agents (CAA) worldwide. Multiple mutations observed at specific loci that are targets for CAA are recognized as sources of drug resistance. This has prompted a shift from CAA, to diverse combination therapies, photodynamic and short peptide therapies capable of triggering specific apoptotic reactions within candidal cells. In this review, new designs and combination of short peptide (SP) with CAA as well as current application of photodynamic inactivation (PDI) against Candida species geared at generating reactive species of oxygen (ROS) and nitrogen (RNS) are discussed. It is observed that oxidative and nitrosative stresses provides a superior broad candidacidal effects for eradication of drug-resistant Candida species. The mechanism and limitations in these strategic approaches over CAA is also discussed. [ABSTRACT FROM AUTHOR]

Fungal infections are a pressing concern for human health worldwide, particularly for immunocompromised individuals. Current challenges such as the elevated toxicity of common antifungal drugs and the emerging resistance towards these could be overcome by multidrug therapy. Natural antimicrobial peptides, AMPs, in combination with other antifungal agents are a promising avenue to address the prevailing challenges. However, they possess limited biostability and susceptibility to proteases, which has significantly hampered their development as antifungal therapies. β-peptides are synthetic materials designed to mimic AMPs while allowing high tunability and increased biostability. In this work, we report for the first time the inhibition achieved in Candida albicans when treated with amixture of a β-peptide model and fluconazole or ketoconazole. This combination treatment enhanced the biological activity of these azoles in planktonic and biofilm Candida, and also in a fluconazole-resistant strain. Furthermore, the in vitro cytotoxicity of the dual treatment was evaluated towards the human hepatoma cell line, HepG2, a widely used model derived from liver tissue, which is primarily affected by azoles. Analyses based on the LA-based method and the mass-action law principle, using a microtiter checkerboard approach, revealed synergism of the combination treatment in the inhibition of planktonic C. albicans. The dual treatment proved to be fungicidal at 48 and 72h. Interestingly, it was also found that the viability of HepG2 was not significantly affected by the dual treatments. Finally, a remarkable enhancement in the inhibition of the highly azole-resistant biofilms and fluconazole resistant C. albicans strain was obtained. [ABSTRACT FROM AUTHOR]

Peptide mimics, possessing excellent biocompatibility and protease stability, have attracted broad attention and research in the biomedical field. β-Peptides and β-peptoids, as two types of vital peptide mimics, have demonstrated great potential in the field of foldamers, antimicrobials and protein binding, etc. Currently, the main synthetic strategies for β-peptides and β-peptoids include solid-phase synthesis and polymerization. Among them, polymerization in one-pot can minimize the repeated separation and purification used in solid-phase synthesis, and has the advantages of high efficiency and low cost, and can synthesize β-peptides and β-peptoids with high molecular weight. This review summarizes the polymerization methods for β-peptides and β-peptoids. Moreover, future developments of the polymerization method for the synthesis of β-peptides and β-peptoids will be discussed., (© 2022 Wiley-VCH GmbH.)

In the present study, the coordination abilities of Ac-TLEGTKKGHKLHLβDY-NH2 peptide (the analogue of SPARC 114-128 fragment containing β-Asp127 residue) are discussed. The analysis is provided based on the results of potentiometric and spectroscopic measurements supported by quantum-chemical calculations. Presented results clearly show that the β-Asp amino acid residue may influence the efficiency of metal ion binding despite the fact that it is not directly involved in metal ion binding. Moreover, in order to further characterize experimentally observed species, we performed quantum-chemical calculations for structures mimicking SPARC 114-128 fragment as a step towards a better understanding of structural and energetical aspects related to the coordination abilities of the analogue of SPARC fragment. [ABSTRACT FROM AUTHOR]

Tetrameric H10/12 helix stabilization was achieved by the application of aromatic side-chains in β-peptide oligomers by intramolecular backbone-side chain CH-π interactions. Because of the enlarged hydrophobic surface of the oligomers, a further aim was the investigation of the self-assembly in a polar medium for the β-peptide H10/12 helices. NMR, ECD, and molecular modeling results indicated that the oligomers formed by cis-[1 S,2 S]- or cis-[1 R,2 R]-1-amino-1,2,3,4-tetrahydronaphthalene-2-carboxylic acid (ATENAC) and cis-[1 R,2 S]- or cis-[1 S,2 R]-2-aminocyclohex-3-enecarboxylic acid (ACHEC) residues promote stable H10/12 helix formation with an alternating backbone configuration even at the tetrameric chain length. These results support the view that aromatic side-chains can be applied for helical structure stabilization. Importantly, this is the first observation of a stable H10/12 helix with tetrameric chain-length. The hydrophobically driven self-assembly was achieved for the helix-forming oligomers, seen as vesicles in transmission electron microscopy images. The self-association phenomenon, which supports the helical secondary structure of these oligomers, depends on the hydrophobic surface area, because a higher number of aromatic side-chains yielded larger vesicles. These results serve as an essential element for the design of helices relating to the H10/12 helix. Moreover, they open up a novel area for bioactive foldamer construction, while the hydrophobic area gained through the aromatic side-chains may yield important receptor-ligand interaction surfaces, which can provide amplified binding strength. [ABSTRACT FROM AUTHOR]

Rainbow of pyrrolidines: Red, orange, yellow, green, blue (indigo, violet). [ABSTRACT FROM AUTHOR]

To determine local chirality driven conformational preferences of small aminocyclobutane-1-carboxylic acid derivatives, X-(ACBA)-Y, their matrix-isolation IR spectra were recorded and analyzed. For the very first time model systems of this kind were deposited in a frozen (~10 K) noble gas matrix to reduce line width and thus, the recorded sharp vibrational lines were analyzed in details. For cis- (S,R)- 1 monomer two ' zigzag' conformers composed of either a six or an eight-membered H-bonded pseudo ring was identified. For trans- (S,S)- 2 stereoisomer a zigzag of an eight-membered pseudo ring and a helical building unit were determined. Both findings are fully consistent with our computational results, even though the relative conformational ratios were found to vary with respect to measurements. For the dimers ( S,R,S,S)- 3 and ( S,S,S,R)- 4 as many as four different cis,trans and three different trans,cis conformers were localized in their matrix-isolation IR (MI-IR) spectra. These foldamers not only agree with the previous computational and NMR results, but also unambiguously show for the first time the presence of a structure made of a cis,trans conformer which links a ' zigzag' and a helical foldamer via a bifurcated H-bond. The present work underlines the importance of MI-IR spectroscopy, applied for the first time for triamides to analyze the conformational pool of small biomolecules. We have shown that the local chirality of a β-amino acid can fully control its backbone folding preferences. Unlike proteogenic α-peptides, β- and especially (ACBA) type oligopeptides could thus be used to rationally design and influence foldamer's structural preferences. [ABSTRACT FROM AUTHOR]

Abstract: The prion protein coordinates copper with high affinity in the regions encompassing residues 92–99 (GGGTHSQW) and 106–115 (KTNMKHMAGA). Cu(II) binding to these sites involves the coordination of the His96/His111 imidazole ring and backbone deprotonated amides that precede the His residue. Such a coordination arrangement involves the formation of hexa- and penta-membered cycles that provide further stabilization of the metal–peptide complex. The purpose of the present study is to introduce a methylene group in the peptide backbone, to evaluate the impact of increasing the size of these cycles in Cu(II) binding. Thus, a β-alanine residue was inserted at different positions preceding the His residue in these prion fragments, and their Cu(II) coordination properties were assessed by UV–Visible absorption, circular dichroism, and electron paramagnetic resonance. Spectroscopic data show that the insertion of a methylene group leads to a completely different Cu(II) coordination that involves the His96/His111 imidazole ring and nitrogen or oxygen atoms provided by the peptide backbone towards the C-terminal. This study clearly shows that two main factors determine the nature of Cu(II)–peptide complexes involving an anchoring His residue and deprotonated amides from the backbone chain: i) the stabilization of Cu(II)–peptide complexes due to the formation of cyclic structures (i.e. chelate effect) and ii) the nature of the residues associated to the deprotonated amide groups that participate in metal ion coordination. [Copyright &y& Elsevier]

Crystals of the dimeric β-peptides 13 and 20, derived from (1 R,2 S)-2-aminocyclopentanecarboxylic acid and (1 S,2 R,3 S)-2-amino-3-methylcyclopentanecarboxylic acid, respectively, were synthesised and studied by X-ray diffraction in order to establish their solid state secondary structural characteristics. Compound 13 crystallises in the monoclinic space group P 2 with cell parameters of a = 5.2682(1) Å, b = 9.1211(2) Å, c = 22.4467(6) Å, β = 91.3855(9)°, V = 1078.29(4) Å and Z = 2. Compound 20 crystallizes in the orthorhombic space group P 2 2 2 with cell parameters of a = 5.0968(1) Å, b = 11.5546(2) Å, c = 43.5414(8) Å, V = 2564.22(8) Å and Z = 4. In both cases adjacent molecules are linked by a series of N-H···O=C hydrogen bonds to form β-sheet like structures. Graphical Abstract: The structures of two dipeptides derived from the β-amino acids (1 R,2 S)-2-aminocyclopentanecarboxylic acid and (1 S,2 R,3 S)-2-amino-3-methylcyclopentanecarboxylic acid have been analysed by X-ray diffraction.[Figure not available: see fulltext.] [ABSTRACT FROM AUTHOR]

Microfluidic devices are emerging as true alternatives to traditional batch processes, as evidenced by recent applications in important synthetic transformations. Besides biologically important oligomers such as β-peptides and oligosaccharides, pharmaceutically active substances have been the target of the most recent investigations. Furthermore, synthetic processes posing challenges to process chemists such as highly exothermic or explosive reactions and reactions that are difficult to control on large scale (such as radical transformations) have been of particular interest. This account briefly introduces the concepts of continuous-flow microreactors, and reviews our investigations on the application of microfluidic devices in synthetic transformations such as glycosylations, amide bond formations mediated by trimethylaluminum, radical-based transformations, and deoxyfluorinations. 1 Introduction 2 Classical Chemical Transformations 2.1 Proof-of-Principle Studies 2.2 Trimethylaluminum-Mediated Amide Bond Formations 2.3 Deoxyfluorinations with (Diethylamino)sulfur Trifluoride 3 Synthesis of Biopolymers 3.1 Synthesis of Carbohydrates 3.1.1 Glycosylation Reactions 3.1.2 Synthesis of Oligosaccharides 3.2 Synthesis of β-Peptides 4 Free-Radical-Based Reactions 4.1 Dehalogenations and Deoxygenations 4.2 Hydrosilylations 5 Conclusions [ABSTRACT FROM AUTHOR]

Abstract: The synthesis of some representative compounds of a new class of cyclobutane-containing β-peptides starting from (−)-verbenone as a chiral precursor is presented. In these products, the cyclobutane moiety is not a part of the peptide backbone but a bulky substituent at the β3-position. These compounds have been carefully characterized and studied on the basis of the combined use of several experimental techniques together with molecular modeling by means of theoretical calculations. In the solid state, the non-cyclic β-peptides adopt a hairpin-like molecular folding ruled by intermolecular hydrogen bonds in the crystal packing. [Copyright &y& Elsevier]

The use of peptides as drugs in pharmaceutical applications is hindered by their susceptibility to proteolysis and therefore low bioavailability. β-Peptides that contain an additional methylene group in the backbone, are gaining recognition from a pharmaceutical stand point as they are considerably more resilient to proteolysis and metabolism. Recently, we reported two new classes of β-peptides, β3- and β2-peptides derived froml-aspartic acid andl-diaminopropionic acid, respectively. Here, we report the proteolytic stability of these β-peptidic compounds and a mixed α /β-peptide against three enzymes (pronase, trypsin and elastase), as well as, human serum. The stability of these peptides was compared to an α-peptide. Peptides containing β-linkages were resistant to all conditions. The mixed α /β-peptide, however, exhibited proteolysis in the presence of trypsin and pronase but not elastase. The rate of degradation of the mixed α /β-peptide was slower than that would be expected for an α-peptide. In addition, these β-peptides were not toxic to HeLa and COS-1 cell lines as observed by MTT cytotoxicity assay. These results expand the scope of mixed α /β-peptides containing β-amino acids or small β-peptide fragments as therapeutic peptides. [ABSTRACT FROM AUTHOR]

Abstract: Ten C-glycosyl β2- and β/β 2-peptides with three to eight amino acid residues have been prepared. Solution and solid-phase peptide syntheses were employed to assemble β2-amino acids in which C-glycosylic substituents are attached to the C-2 position of β-amino acids. Conformational analysis of the C-glycosyl β2-peptides using NMR and CD spectra indicates that the tripeptide can form a helical secondary structure. Besides, helix directions of the C-glycosyl β/β2-peptides are governed by the configuration at the α-carbon of the peptide backbone that originates from the stereocenter of the C-glycosyl β2-amino acids. [Copyright &y& Elsevier]

Abstract: We previously described a series of 314-helical β-peptides that bind the hDM2 protein and inhibit its interaction with a p53-derived peptide in vitro. Here we present a detailed characterization of the interaction of these peptides with hDM2 and report two new β-peptides in which non-natural side chains have been substituted into the hDM2-recognition epitope. These peptides feature both improved affinity and inhibitory potency in fluorescence polarization and ELISA assays. Additionally, one of the new β-peptides also binds the hDM2-related protein, hDMX, which has been identified as another key therapeutic target for activation of the p53 pathway in tumors. [Copyright &y& Elsevier]

We have studied two different β-peptides in methanol using explicit solvent molecular dynamics simulations and the GROMOS 53A6 force field: a heptapeptide (peptide 1) expected to form a left-handed 314-helix, and a hexapeptide (peptide 2) expected to form a β-hairpin in solution. Our analysis has focused on identifying and analyzing the stability of the dominant secondary structure conformations adopted by the peptides, as well as on comparing the experimental NOE distance upper bounds and 3J-coupling values with their counterparts calculated on the basis of the simulated ensembles. Moreover, we have critically compared the present results with the analogous results obtained with the GROMOS 45A3 (peptide 1) and 43A1 (peptide 2) force fields. We conclude that within the limits of conformational sampling employed here, the GROMOS 53A6 force field satisfactorily reproduces experimental findings regarding the behavior of short β-peptides, with accuracy that is comparable to but not exceeding that of the previous versions of the force field.[Figure not available: see fulltext.] [ABSTRACT FROM AUTHOR]

Abstract: β-Peptides made from L-aspartic acid monomers form a new class of β3-peptides. Here we report the first three-dimensional NMR solution structure of a β3-hexapeptide (1) from L-aspartic acid monomers in 2,2,2-trifluoroethanol (TFE). We show that 1 forms a right-handed 14-helical structure in TFE. α-peptides from naturally occurring L-amino acids adopt a right-handed α-helix whereas β3-peptides formed from β3-amino acids derived from naturally occurring L-amino acids form left-handed 14-helices. The right-handed 14-helical conformation of 1 is a better mimic of α-peptide conformations. Using the NMR structure of 1 in TFE, we further study the conformation of 1 in water, as well as two similar β3-peptides (2 and 3) in water and TFE by molecular dynamics (MD) simulations. NMR and MD results suggest loss of secondary structure of 1 in water and show that it forms a fully extended structure. 2 and 3 contain residues with oppositely charged side chains that engage in salt-bridge interactions and dramatically stabilize the 14-helical conformation in aqueous media. [Copyright &y& Elsevier]

The highly selective cross-aldol addition of hydroxyacetone (HA) to p-nitro and m-nitrobenzaldehyde is reported; the reaction is catalyzed by three different di- or tripeptides all containing D-Pro in the N-terminal position and one or two residues of β3-homophenylglycine (β3-hPhg): H-D-Pro-(R)-β3-hPhg-OBn, H-D-Pro-(R)-β3-hPhg-(S)-β3-hPhg-OBn and H-D-Pro-[(S)-β3-hPhg]2-OBn. Several reaction conditions have been tested, always in the absence of a protecting group on the HA hydroxyl. This reaction affords the desired compounds with complete regioselectivities being the other regioisomer completely avoided. Furthermore high enantioselectivities and satisfactory diastereoselectivities, always favouring the syn diastereoisomers, were obtained. The stereochemistry of the diols was further confirmed by the analysis of the 1H NMR spectrum of the corresponding carbonates, obtained by reaction of the syn/anti mixtures with triphosgene in presence of dimethylamino-pyridine (DMAP). [ABSTRACT FROM AUTHOR]

Abstract: The reaction of chiral (2S)-enolates of dioxolan-4-ones, derived from lactic and mandelic acids, with (S R )-tert-butyl sulfinyl ketimines, derived from butan-2-one, pentan-2-one, and decan-2-one, afforded conformationally restrained β2,2,3,3-isoserines bearing two adjacent quaternary stereogenic centers in the form of N-sulfinyl protected 1′-amino-dioxolan-4-ones. The selective acid-induced removal of the sulfinyl protecting group provided the corresponding 1′-aminodioxolanones, whose base-induced cyclization afforded the corresponding chiral tetra-substituted 3-hydroxy-β-lactams. The synthesis of a dipeptide by reaction coupling between the 1′-aminodioxolanone (2S,5R,1′R)-19 and N,N-dimethylglycine was successfully achieved. [Copyright &y& Elsevier]

We previously discovered that BapA, a bacterial β-peptidyl aminopeptidase, is able to hydrolyze two otherwise metabolically inert β-peptides [Geueke B, Namoto K, Seebach D & Kohler H-PE (2005) J Bacteriol 187, 5910–5917]. Here, we describe the purification and characterization of two distinct bacterial β-peptidyl aminopeptidases that originated from different environmental isolates. Both bapA genes encode a preprotein with a signal sequence and were flanked by ORFs that code for enzymes with similar predicted functions. To form the active enzymes, which had an (αβ)4 quaternary structure, the preproteins needed to be cleaved into two subunits. The two β-peptidyl aminopeptidases had 86% amino acid sequence identity, hydrolyzed a variety of β-peptides and mixed β/α-peptides, and exhibited unique substrate specificities. The prerequisite for peptides being accepted as substrates was the presence of a β-amino acid at the N-terminus; peptide substrates with an N-terminal α-amino acid were not hydrolyzed at all. Both enzymes cleaved the peptide bond between the N-terminal β-amino acid and the amino acid at the second position of tripeptidic substrates of the general structure H-βhXaa-Ile-βhTyr-OH according to the following preferences with regard to the side chain of the N-terminal β-amino acid: aliphatic and aromatic > OH-containing > hydrogen, basic and polar. Experiments with the tripeptides H-d-βhVal-Ile-βhTyr-OH and H-βhVal-Ile-βhTyr-OH demonstrated that the two BapA enzymes preferred the peptide with thel-configuration of the N-terminal β-homovaline residue as a substrate. [ABSTRACT FROM AUTHOR]

A convenient method for the stereoselective syntheses of β-amino acids with α-substitutions has been developed. This synthetic route involves the preparation of isoxazolidinones through hydroxylamine addition to unsaturated esters and subsequent hydrogenation. This procedure is also useful for the stereoselective syntheses of α-deuterated β-amino acids. [ABSTRACT FROM AUTHOR]

The history of peptide chemistry in our group is described. It all started with the cyclic undecapeptide cyclosporin, the immunosuppressive compound, which is commercialised as Sandimmune®/Neoral® by Sandoz/Novartis, and which has revolutionized transplant medicine. The discovery that cyclosporin can be deprotonated to a hexalithio derivative, and thus C-alkylated on a sarcosine moiety, led us into a research project on peptide modifications. We defined structural prerequisites for the use of peptide enolates and for electrolytic decarboxylation of peptides. Parallel to these activities, the group was engaged in developing synthetic methodologies aimed at stereoselective preparations of α-, β-, and γ-amino acid derivatives (cf. diastereoselective alkylations, self regeneration of stereogenic centers, axially chiral enolates). A third avenue into peptide chemistry originated from our investigations on the biopolymer PHB (poly-3-hydroxybutanoic acid); the question arose ‘what happens upon replacement of chain-bound O by NH in the polyester?’ A brief summary is given of the results obtained in our ensuing discovery tour of β-peptides built of homologated proteinogenic amino acids. They form secondary structures with short chain lengths and they have unexpected physiological properties, rendering them candidates for peptidic drugs. The synthesis of β3-peptides is straightforward, and in the meantime most of the Fmoc-protected building blocks are commercial. The β2-homoamino acids are less readily available. Their preparation and the assembly of a β2-eicosapeptide with the twenty proteinogenic side chains are discussed herein. The reasons for the chosen sequence and the strategy of what turned out to be a 159-step synthesis are described. Full experimental details are given for the preparation of the dimeric Fmoc-β2hXaa(PG)-β2hXaa(PG)-OH building blocks used, for their solid-phase coupling to two β2-decapeptide segments, for the thioligation, and for the purification, isolation and spectroscopic characterization of the resulting 20mer. An outlook to future projects in the exciting field of β- and γ-peptide chemistry and biology is given. [Copyright &y& Elsevier]

This review briefly surveys the conformational properties of guest ω-amino acid residues when incorporated into host α-peptide sequences. The results presented focus primarily on the use of β- and γ-residues in α ω sequences. The insertion of additional methylene groups into peptide backbones enhances the range of accessible conformations, introducing additional torsional variables. A nomenclature system, which permits ready comparisons between α-peptides and hybrid sequences, is defined. Crystal structure determination of hybrid peptides, which adopt helical and β-hairpin conformations permits the characterization of backbone conformational parameters for β- and γ-residues inserted into regular α-polypeptide structures. Substituted β- and γ-residues are more limited in the range of accessible conformation than their unsubstituted counterparts. The achiral β, β-disubstituted γ-amino acid, gabapentin, is an example of a stereochemically constrained residue in which the torsion angles about the C β–C γ ( θ1) and C α–C β ( θ2) bonds are restricted to the gauche conformation. Hybrid sequences permit the design of novel hydrogen bonded rings in peptide structures. [ABSTRACT FROM AUTHOR]

As one of the most important families of non-natural polymers with the propensity to form well-defined secondary structures, the β-peptides are attracting increasing attention. The compounds incorporating β-amino acid residues have found various applications in medicinal chemistry and biochemistry. The conformational pool of β-peptides comprises several periodic folded conformations, which can be classified as helices, and nonpolar and polar strands. The latter two are prone to form pleated sheets. The numerous studies that have been performed on the side-chain dependence of the stability of the folded structures allow certain conclusions concerning the principles of design of the β-peptide foldamers. The folding propensity is influenced by local torsional, side-chain to backbone and long-range side-chain interactions. Although β-peptide foldamers are sensitive to solvent, the systematic choice of the side-chain pattern and spatiality allows the design of the desired specific secondary structure. The application of β-peptide foldamers may open up new directions in the synthesis of highly organized artificial tertiary structures with biochemical functions. [ABSTRACT FROM AUTHOR]

α-Aspartyl-containing cyclic pentapeptides were synthesised in high yields using astrategy that maintained fluorenylmethyl protection on the aspartic acid side chain during chainassembly, resin cleavage and cyclisation of the linear precursors. Tetra-n-butylammoniumfluoride treatment of the fluorenylmethyl-protected cyclic peptides catalysed imide formation,whereas piperidine-induced deprotection resulted in good yields of the target cyclic peptides. [ABSTRACT FROM AUTHOR]

β-Aminopeptidases have the unique capability to hydrolyze N-terminal β-amino acids, with varied preferences for the nature of β-amino acid side chains. This unique capability makes them useful as biocatalysts for synthesis of β-peptides and to kinetically resolve β-peptides and amides for the production of enantiopure β-amino acids. To date, six β-aminopeptidases have been discovered and functionally characterized, five from Gram-negative bacteria and one from a fungus, Aspergillus Here we report on the purification and characterization of an additional four β-aminopeptidases, one from a Gram-positive bacterium, Mycolicibacterium smegmatis (BapA Ms ), one from a yeast, Yarrowia lipolytica (BapA Ylip ), and two from Gram-negative bacteria isolated from activated sludge identified as Burkholderia spp. (BapA BcA5 and BapA BcC1 ). The genes encoding β-aminopeptidases were cloned, expressed in Escherichia coli , and purified. The β-aminopeptidases were produced as inactive preproteins that underwent self-cleavage to form active enzymes comprised of two different subunits. The subunits, designated α and β, appeared to be tightly associated, as the active enzyme was recovered after immobilized-metal affinity chromatography (IMAC) purification, even though only the α-subunit was 6-histidine tagged. The enzymes were shown to hydrolyze chromogenic substrates with the N-terminal l-configurations β-homo-Gly (βhGly) and β 3 -homo-Leu (β 3 hLeu) with high activities. These enzymes displayed higher activity with H-βhGly- p -nitroanilide (H-βhGly- p NA) than previously characterized enzymes from other microorganisms. These data indicate that the new β-aminopeptidases are fully functional, adding to the toolbox of enzymes that could be used to produce β-peptides. Overexpression studies in Pseudomonas aeruginosa also showed that the β-aminopeptidases may play a role in some cellular functions. IMPORTANCE β-Aminopeptidases are unique enzymes found in a diverse range of microorganisms that can utilize synthetic β-peptides as a sole carbon source. Six β-aminopeptidases have been previously characterized with preferences for different β-amino acid substrates and have demonstrated the capability to catalyze not only the degradation of synthetic β-peptides but also the synthesis of short β-peptides. Identification of other β-aminopeptidases adds to this toolbox of enzymes with differing β-amino acid substrate preferences and kinetics. These enzymes have the potential to be utilized in the sustainable manufacture of β-amino acid derivatives and β-peptides for use in biomedical and biomaterial applications. This is important, because β-amino acids and β-peptides confer increased proteolytic resistance to bioactive compounds and form novel structures as well as structures similar to α-peptides. The discovery of new enzymes will also provide insight into the biological importance of these enzymes in nature., (© Crown copyright 2019.)

Peptide self-assembly represents a powerful bottom-up approach to the fabrication of nanomaterials. β 3 -Peptides are non-natural peptides composed entirely of β-amino acids, which have an extra methylene in the backbone, and we reported fibers derived from the self-assembly of β 3 -peptides that adopt 14-helical structures. β 3 -Peptide assemblies represent a class of stable nanomaterials that can be used to generate bio- and magneto-responsive materials with proteolytic stability. However, the three-dimensional structure of many of these materials remains unknown. To develop structure-based criteria for the design of β 3 -peptide-based biomaterials with tailored function, we investigated the structure of a tri-β 3 -peptide nanoassembly by molecular dynamics simulations and X-ray fiber diffraction analysis. Diffraction data was collected from aligned fibrils formed by Ac-β 3 [LIA] in water and used to inform and validate the model structure. Models with 3-fold radial symmetry resulted in stable fibers with a triple-helical coiled-coil motif and measurable helical pitch and periodicity. The fiber models revealed a hydrophobic core and twist along the fiber axis arising from a maximization of contacts between hydrophobic groups of adjacent tripeptides on the solvent-exposed fiber surface. These atomic structures of macroscale fibers derived from β 3 -peptide-based materials provide valuable insight into the effects of the geometric placement of the side chains and the influence of solvent on the core fiber structure which is perpetuated in the superstructure morphology.