Evaluation of β‐Amino Acid Replacements in Protein Loops: Effects on Conformational Stability and Structure

β‐Amino acids have a backbone that is expanded by one carbon atom relative to α‐amino acids, and β residues have been investigated as subunits in protein‐like molecules that adopt discrete and predictable conformations. Two classes of β residue have been widely explored in the context of generating α‐helix‐like conformations: β³‐amino acids, which are homologous to α‐amino acids and bear a side chain on the backbone carbon adjacent to nitrogen, and residues constrained by a five‐membered ring, such the one derived from trans‐2‐aminocyclopentanecarboxylic acid (ACPC). Substitution of α residues with their β³ homologues within an α‐helix‐forming sequence generally causes a decrease in conformational stability. Use of a ring‐constrained β residue, however, can offset the destabilizing effect of α→β substitution. Here we extend the study of α→β substitutions, involving both β³ and ACPC residues, to short loops within a small tertiary motif. We start from previously reported variants of the Pin1 WW domain that contain a two‐, three‐, or four‐residue β‐hairpin loop, and we evaluate α→β replacements at each loop position for each variant. By referral to the ?,ψ angles of the native structure, one can choose a stereochemically appropriate ACPC residue. Use of such logically chosen ACPC residues enhances conformational stability in several cases. Crystal structures of three β‐containing Pin1 WW domain variants show that a native‐like tertiary structure is maintained in each case.     

Structure‐Guided Rational Design of α/β‐Peptide Foldamers with High Affinity for BCL‐2 Family Prosurvival Proteins

We have used computational methods to improve the affinity of a foldamer ligand for its target protein. The effort began with a previously reported α/β‐peptide based on the BH3 domain of the proapoptotic protein Puma; this foldamer binds tightly to Bcl‐x_L but weakly to Mcl‐1. The crystal structure of the Puma‐derived α/β‐peptide complexed to Bcl‐x_L was used as the basis for computational design of variants intended to display improved binding to Mcl‐1. Molecular modelling suggested modification of three α residues of the original α/β backbone. Individually, each substitution caused only a modest (4‐ to 15‐fold) gain in affinity; however, together the three substitutions led to a 250‐fold increase in binding to Mcl‐1. These modifications had very little effect on affinity for Bcl‐x_L. Crystal structures of a number of the new α/β‐peptides bound to either Mcl‐1 or Bcl‐x_L validated the selection of each substitution. Overall, our findings demonstrate that structure‐guided rational design can be used to improve affinity and alter partner selectivity of peptidic ligands with unnatural backbones that bind to specific protein partners.     

Ac‐LPFFD‐Th: A Trehalose‐Conjugated Peptidomimetic as a Strong Suppressor of Amyloid‐β Oligomer Formation and Cytotoxicity

The inhibition of amyloid formation is a promising therapeutic approach for the treatment of neurodegenerative diseases. Peptide‐based inhibitors, which have been widely investigated, are generally derived from original amyloid sequences. Most interestingly, trehalose, a nonreducing disaccharide of α‐glucose, is effective in preventing the aggregation of numerous proteins. We have determined that the development of hybrid compounds could provide new molecules with improved properties that might synergically increase the potency of their single moieties. In this work, the ability of Ac‐LPFFD‐Th, a C‐terminally trehalose‐conjugated derivative, to slow down the Aβ aggregation process was investigated by means of different biophysical techniques, including thioflavin T fluorescence, dynamic light scattering, ESI‐MS, and NMR spectroscopy. Moreover, we demonstrate that Ac‐LPFFD‐Th modifies the aggregation features of Aβ and protects neurons from Aβ oligomers' toxic insult.     

Highly Diverse Protein Library Based on the Ubiquitous (β/α)8 Enzyme Fold Yields Well‐Structured Proteins through in Vitro Folding Selection

Proper protein folding is a prerequisite for protein stability and enzymatic activity. Although directed evolution can be a powerful tool to investigate enzymatic function and to isolate novel activities, well‐designed libraries of folded proteins are essential. In vitro selection methods are particularly capable of searching for enzymatic activities in libraries of trillions of protein variants, yet high‐quality libraries of well‐folded enzymes with such high diversity are lacking. We describe the construction and detailed characterization of a folding‐enriched protein library based on the ubiquitous (β/α)₈ barrel fold, which is found in five of the six enzyme classes. We introduced seven randomized loops on the catalytic face of the monomeric, thermostable (β/α)₈ barrel of glycerophosphodiester phosphodiesterase (GDPD) from Thermotoga maritima. We employed in vitro folding selection based on protease digestion to enrich intermediate libraries containing three to four randomized loops for folded variants, and then combined them to assemble the final library (10¹⁴ DNA sequences). The resulting library was analyzed by using the in vitro protease assay and an in vivo GFP‐folding assay; it contains ～10¹² soluble monomeric protein variants. We isolated six library members and demonstrated that these proteins are soluble, monomeric and show (β/α)₈‐barrel fold‐like secondary and tertiary structure. The quality of the folding‐enriched library improved up to 50‐fold compared to a control library that was assembled without the folding selection. To the best of our knowledge, this work is the first example of combining the ultra‐high throughput mRNA display method with selection for folding. The resulting (β/α)₈ barrel libraries provide a valuable starting point to study the unique catalytic capabilities of the (β/α)₈ fold, and to isolate novel enzymes.     

Conversion of Low‐Affinity Peptides to High‐Affinity Peptide Binders by Using a β‐Hairpin Scaffold‐Assisted Approach

Affinity maturation of protein‐targeting peptides is generally accomplished by homo‐ or heterodimerization of known peptides. However, applying a heterodimerization approach is difficult because it is not clear a priori what length or type of linker is required for cooperative binding to a target. Thus, an efficient and simple affinity maturation method for converting low‐affinity peptides into high‐affinity peptides would clearly be advantageous for advancing peptide‐based therapeutics. Here, we describe the development of a novel affinity maturation method based on a robust β‐hairpin scaffold and combinatorial phage‐display technology. With this strategy, we were able to increase the affinity of existing peptides by more than four orders of magnitude. Taken together, our data demonstrate that this scaffold‐assisted approach is highly efficient and effective in generating high‐affinity peptides from their low‐affinity counterparts.     

Linear and Cyclic Depsipeptidomimetics with β‐Lactam Cores: A Class of New αvβ3 Integrin Receptor Inhibitors

The α_vβ₃ integrin receptor plays an important role in tumor metastasis and tumor‐induced angiogenesis. The inhibition of this receptor with diverse ligands, antibodies, or cyclic peptides is a promising research field for the treatment of a variety of tumors. The replacement of Phe‐(Me)Val dipeptide by a β‐lactam ring in Cilengitide has led to new products that show higher inhibitory activity than the parent cyclopeptide. In particular, substitution of a peptide bond β‐lactam‐NH‐Asp linkage by a β‐lactam‐O‐Asp ester linkage increases the activity of the new cyclodepsipeptide. In the same way it has been found that open‐chain compounds of the form Asp‐β‐lactam‐Arg can interact with the receptor and inhibit its activity moderately. The integrin inhibitory activity of the synthesized compounds has been established by using the CGH array, a method that appears to be a more reliable trial than the classical adhesion test.     

Atomic‐Resolution Structure of a Class C β‐Lactamase and Its Complex with Avibactam

β‐Lactamases (BLs) are important antibiotic‐resistance determinants that significantly compromise the efficacy of valuable β‐lactam antibacterial drugs. Thus, combinations with BL inhibitor were developed. Avibactam is the first non‐β‐lactam BL inhibitor introduced into clinical practice. Ceftazidime–avibactam represents one of the few last‐resort antibiotics available for the treatment of infections caused by near‐pandrug‐resistant bacteria. TRU‐1 is a chromosomally encoded AmpC‐type BL of Aeromonas enteropelogenes, related to the FOX‐type BLs and constitutes a good model for class C BLs. TRU‐1 crystals provided ultrahigh‐resolution diffraction data for the native enzyme and for its complex with avibactam. A comparison of the native and avibactam‐bound structures revealed new details in the conformations of residues relevant for substrate and/or inhibitor binding. Furthermore, a comparison of the TRU‐1 and Pseudomonas aeruginosa AmpC avibactam‐bound structures revealed two inhibitor conformations that were likely to correspond to two different states occurring during inhibitor carbamylation/recyclization.     

Base‐Catalyzed Condensation of 2‐Hydroxybenzaldehydes with α,β‐Unsaturated Aldehydes – Scope and Limitations

The base‐catalyzed condensation of α,β‐unsaturated carbonyl compounds with 2‐hydroxybenzaldehydes yielding tetrahydroxanthones and dihydrobenzopyrans has been investigated. A novel access to highly functionalized dihydrobenzopyrans via a mild generation of the dienol of senecialdehyde and subsequent conjugated aldol reaction has been reported.     

A Highly Diastereoselective Tertiary Amine‐Catalyzed Cascade Michael–Michael–Henry Reaction between Nitromethane,Activated Alkenes and α,β‐Unsaturated Carbonyl Compounds

A new tertiary amine‐catalyzed cascade Michael–Michael–Henry reaction between nitromethane, a doubly activated alkene and an α,β‐unsaturated carbonyl compound is described, which provides a convenient and efficient synthesis for densely functionalized cyclohexanes and some bicyclic compounds in moderate to excellent yields with high diastereoselectivity.     

γ‐ and δ‐tocopherols are more effective than α‐tocopherol on the autoxidation of a 10% rapeseed oil triacylglycerol‐in‐water emulsion with and without a radical initiator

The antioxidative effects of γ‐ and mainly δ‐tocopherol in a multiphase system were hardly considered up to now. The aim of this study was i) to assess the effects and ii) to follow the degradation of α‐, γ‐ and δ‐tocopherol in concentrations of 0.01%, 0.05%, 0.1% and 0.25% during the oxidation of a 10% purified rapeseed oil triacylglycerol‐in‐water emulsion at 40 °C in the dark for 15 wk in a system containing a low oxygen concentration. Oxidation experiments were performed weekly by assessing the formation of hydroperoxides and hexanal, and the stability of the tocopherols was determined using high‐performance liquid chromatography. Storage tests were conducted with and without the addition of 0.01% α, α′‐azoisobutyronitrile (AIBN), which is a known radical initiator. α‐Tocopherol increased the formation of hydroperoxides in both tests as well as the generation of hexanal when the radical initiator was added; furthermore it was the least stable. γ‐Tocopherol delayed the formation of hexanal and prolonged the stability of the emulsion in a dose‐dependant manner. δ‐Tocopherol was the most stable and also the most effective in delaying lipid oxidation in the emulsions. Each concentration that was tested reduced the rate of hydroperoxide and especially hexanal formation. Hexanal was only formed to a slight extent after 15 wk of oxidation in the test with AIBN and the lowest dose of 0.01% δ‐tocopherol. For all tocopherols, strong correlations were found between tocopherol stability and the extent of oxidation. Results suggest that i) mainly δ‐tocopherol, but also γ‐tocopherol even less pronounced, are very good antioxidants in order to stabilize and prolong the shelf life of oil‐in‐water emulsions, ii) the antioxidative effects were intensified with increasing amounts.     

Organocatalytic Asymmetric Aldol Reaction of Ketones with β,γ‐Unsaturated α‐Keto Esters: An Efficient Access to Chiral Tertiary Alcohol Skeletons

This update describes a highly efficient organocatalytic aldol reaction of ketones and β,γ‐unsaturated α‐keto esters for constructing the chiral tertiary alcohol motif. With the application of 9‐amino(9‐deoxy)epi‐Cinchona alkaloid and an acidic additive as catalysts, both acyclic and cyclic ketones react with β,γ‐unsaturated α‐keto esters smoothly to afford aldol adducts in good to excellent yields and asymmetric induction. This protocol offers a new pathway for the construction of adjacent chiral carbon centers and the synthesis of chiral β‐hydroxy carbonyl compounds.     

Synthesis and Pharmacological Evaluation of α4β2 Nicotinic Ligands with a 3‐Fluoropyrrolidine Nucleus

Nicotinic acetylcholine receptors (nAChRs) play an important role in many central nervous system disorders such as Alzheimer’s and Parkinson’s diseases, schizophrenia, and mood disorders. The α₄β₂ subtype has emerged as an important target for the early diagnosis and amelioration of Alzheimer’s disease symptoms. Herein we report a new class of α₄β₂ receptor ligands characterized by a basic pyrrolidine nucleus, the basicity of which was properly decreased through the insertion of a fluorine atom at the 3‐position, and a pyridine ring carrying at the 3‐position substituents known to positively affect affinity and selectivity toward the α₄β₂ subtype. Derivatives 3‐(((2S,4R)‐4‐fluoropyrrolidin‐2‐yl)methoxy)‐5‐(phenylethynyl)pyridine ( 11 ) and 3‐((4‐fluorophenyl)ethynyl)‐5‐(((2S,4R)‐4‐fluoropyrrolidin‐2‐yl)methoxy)pyridine ( 12 ) were found to be the most promising ligands identified in this study, showing good affinity and selectivity for the α₄β₂ subtype and physicochemical properties predictive of a relevant central nervous system penetration.     

Discovery of α‐Substituted Imidazole‐4‐acetic Acid Analogues as a Novel Class of ρ1 γ‐Aminobutyric Acid Type A Receptor Antagonists with Effect on Retinal Vascular Tone

The ρ‐containing γ‐aminobutyric acid type A receptors (GABA_ARs) play an important role in controlling visual signaling. Therefore, ligands that selectively target these GABA_ARs are of interest. In this study, we demonstrate that the partial GABA_AR agonist imidazole‐4‐acetic acid (IAA) is able to penetrate the blood–brain barrier in vivo; we prepared a series of α‐ and N‐alkylated, as well as bicyclic analogues of IAA to explore the structure–activity relationship of this scaffold focusing on the acetic acid side chain of IAA. The compounds were prepared via IAA from l ‐histidine by an efficient minimal‐step synthesis, and their pharmacological properties were characterized at native rat GABA_ARs in a [³H]muscimol binding assay and at recombinant human α₁β₂γ_2S and ρ₁ GABA_ARs using the FLIPR? membrane potential assay. The (+)‐α‐methyl‐ and α‐cyclopropyl‐substituted IAA analogues ((+)‐ 6 a and 6 c , respectively) were identified as fairly potent antagonists of the ρ₁ GABA_AR that also displayed significant selectivity for this receptor over the α₁β₂γ_2S GABA_AR. Both 6 a and 6 c were shown to inhibit GABA‐induced relaxation of retinal arterioles from porcine eyes.     

Acid‐Catalyzed Synthesis of α,β‐Disubstituted Conjugated Enones by a Meyer–Schuster‐Type Rearrangement in Allenols

A novel, direct and simple methodology to gain access to α,β‐disubstituted conjugated enones from α‐allenols in a sustainable metal catalysis context, considering the inexpensiveness and environmentally friendliness of iron(III) species and protons, has been developed.