Azetidine-Derived Amino Acids versus Proline Derivatives. Alternative Trends in Reverse Turn Induction

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.

A review on the effect of prolyl isomerization on immune response aberration and hypersensitivity reactions: A unifying hypothesis

Little is known about the causes and mechanisms of ectopic immune responses, including different types of hypersensitivity, superantigens, and cytokine storms. Two of the most questionable phenomena observed in immunology are why the intensity and extent of immune responses to different antigens are different, and why some self-antigens are attacked as foreign. The secondary structure of the peptides involved in the immune system, such as the epitope-paratope interfaces plays a pivotal role in the resulting immune responses. Prolyl cis/trans isomerization plays a fundamental role in the form of the secondary structure and the folding of proteins. This review covers some of the emerging evidence indicating the impact of prolyl isomerization on protein conformation, aberration of immune responses, and the development of hypersensitivity reactions.

Recent strategies used in the synthesis of saturated four-membered heterocycles

The importance and prevalance of O-, N-, and S-atom containing saturated four-membered ring motifs in biologically active molecules and potential therapeutics continues to drive efforts in their efficient synthetic preparation. In this review, general and recent strategies for the synthesis of these heterocycles are presented. Due to the limited potential bond disconnections, retrosynthetic strategies are broadly limited to cyclizations and cycloadditions. Nonetheless, diverse approaches for accessing cyclization precursors have been developed, ranging from nucleophilic substitution to C-H functionalization. Innovative methods for substrate activation have been developed for cycloadditions under photochemical and thermal conditions. Advances in accessing oxetanes, azetidines, and thietanes remain active areas of research with continued breakthroughs anticipated to enable future applications.

Uncommon Four-Membered Building Blocks - Cyclobutenes, Azetines and Thietes

Strained ring systems have gained considerable importance over the last few years for their implication in natural product syntheses or in drug discovery programs. We present herein a recollection of our work on the construction and functionalization of unsaturated four-membered carbo- and heterocycles in the context of the literature, as well as their applications in further reactions.

Stereoselective Access to Azetidine-Based α-Amino Acids and Applications to Small Peptide Synthesis

Non-natural azetidine-based amino acids (Aze) present interesting features in protein engineering. A simple organometallic route toward unsaturated carboxylic acid precursors is presented. Subsequent metal-catalyzed asymmetric reduction allowed for the synthesis of a new library of 2-azetidinylcarboxylic acids, which were finally employed in the formation of small peptide chains.

A novel peptide conformation: the γ-bend ribbon

Unlike the extensively investigated relationship between the peptide β-bend ribbon and its prototypical 310-helix conformation, the corresponding relationship between the narrower γ-bend ribbon and its regular γ-helix counterpart still remains to be studied, as the latter 3D-structures have not yet been experimentally authenticated. In this paper, we describe the results of the first characterization, both in the crystal state and in solution, of the γ-bend ribbon conformation using X-ray diffraction and FT-IR absorption, electronic CD and 2D-NMR spectroscopies applied to an appropriate set of synthetic, homo-chiral, sequential dipeptide oligomers based on (S)-Ala and the known γ-bend inducer, Cα-tetrasubstituted, N-alkylated α-amino acid residue (S)-Cα-methyl-azetidine-carboxylic acid.

Different Expression Levels of Human Mutant Ubiquitin B+1 (UBB+1) Can Modify Chronological Lifespan or Stress Resistance of Saccharomyces cerevisiae

The ubiquitin-proteasome system (UPS) is the main pathway responsible for the degradation of misfolded proteins, and its dysregulation has been implicated in several neurodegenerative diseases, including Alzheimer's disease (AD). UBB⁺¹, a mutant variant of ubiquitin B, was found to accumulate in neurons of AD patients and it has been linked to UPS dysfunction and neuronal death. Using the yeast Saccharomyces cerevisiae as a model system, we constitutively expressed UBB⁺¹ to evaluate its effects on proteasome function and cell death, particularly under conditions of chronological aging. We showed that the expression of UBB⁺¹ caused inhibition of the three proteasomal proteolytic activities (caspase-like (β1), trypsin-like (β2) and chymotrypsin-like (β5) activities) in yeast. Interestingly, this inhibition did not alter cell viability of growing cells. Moreover, we showed that cells expressing UBB⁺¹ at lower level displayed an increased capacity to degrade induced misfolded proteins. When we evaluated cells during chronological aging, UBB⁺¹ expression at lower level, prevented cells to accumulate reactive oxygen species (ROS) and avert apoptosis, dramatically increasing yeast life span. Since proteasome inhibition by UBB⁺¹ has previously been shown to induce chaperone expression and thus protect against stress, we evaluated our UBB⁺¹ model under heat shock and oxidative stress. Higher expression of UBB⁺¹ caused thermotolerance in yeast due to induction of chaperones, which occurred to a lesser extent at lower expression level of UBB⁺¹ (where we observed the phenotype of extended life span). Altering UPS capacity by differential expression of UBB⁺¹ protects cells against several stresses during chronological aging. This system can be valuable to study the effects of UBB⁺¹ on misfolded proteins involved in neurodegeneration and aging.

Exploiting structural and conformational effects for a site-selective lithiation of azetidines

Interest in molecular structures bearing four-membered heterocycles (FMHs) is growing due to the possibility to explore new regions of the chemical space and get new lead molecules. Our interest in the development of divergent synthesis of functionalized FMHs, prompted us to disclose factors affecting the reactivity of nitrogen-bearing FMHs towards metalating agents. Our investigations demonstrated that structural factors and conformational preferences need to be considered in planning a site-selective functionalization of azetidines. It will be showed how such factors could have pivotal importance in the reactivity of FMHs.

Straightforward synthesis of novel enantiopure α-trifluoromethylated azetidine 2-carboxylic acid and homoserines

The straightforward syntheses of enantiopure (2R)-2-trifluoromethyl-2-carboxyazetidine and (R)- and (S)-trifluoromethylhomoserines are reported. The key step is a Strecker-type reaction on a common chiral CF3-containing bicyclic oxazolidine intermediate obtained by a condensation reaction of (R)-phenylglycinol and ethyl-4,4,4-trifluoroacetoacetate (ETFAA).

Single and multiple peptide γ-turns: literature survey and recent progress

Published data on peptide isolated and repetitive γ-turns are reviewed. Advancements in our laboratories on these 3D-structures are also presented.

Easy access to constrained peptidomimetics and 2,2-disubstituted azetidines by the unexpected reactivity profile of α-lithiated N-Boc-azetidines

The unprecedented reactivity profile of lithiatedN-Boc-2-arylazetidines gave access either to new azetidine-based peptidomimetics or to the regioselective functionalization of the azetidine ring.

NXO beta structure mimicry: an ultrashort turn/hairpin mimic that folds in water

An NXO building block derived tetrapeptide mimic emulates a natural proline-glycine β-turn/hairpin in polar media, including water at room temperature.

Parameterization of the proline analogue Aze (azetidine-2-carboxylic acid) for molecular dynamics simulations and evaluation of its effect on homo-pentapeptide conformations

We have parameterized and evaluated the proline homologue Aze (azetidine-2-carboxylic acid) for the gromos56a3 force-field for use in molecular dynamics simulations using GROMACS. Using bi-phasic cyclohexane/water simulation systems and homo-pentapeptides, we measured the Aze solute interaction potential energies, ability to hydrogen bond with water, and overall compaction, for comparison to Pro, Gly, and Lys. Compared to Pro, Aze has a slightly higher H-bonding potential, and stronger electrostatic but weaker non-electrostatic interactions with water. The 20-ns simulations revealed the preferential positioning of Aze and Pro at the interface of the water and cyclohexane layers, with Aze spending more time in the aqueous layer. We also demonstrated through simulations of the homo-pentapeptides that Aze has a greater propensity than Pro to undergo trans→cis peptide bond isomerization, which results in a severe 180° bend in the polypeptide chain. The results provide evidence for the hypothesis that the misincorporation of Aze within proline-rich regions of proteins could disrupt the formation of poly-proline type II structures and compromise events such as recognition and binding by SH3-domains.

Cyclic amino acid linkers stabilizing key loops of brain derived neurotrophic factor

Based on β-turn-like BDNF loops 2 and 4, involved in receptor interaction, cyclic peptide replicas were designed, synthesized and tested. In addition to the native turn residues, the cyclic peptides include a linker unit between the N- and C-termini, selected by molecular modeling among various non-proteinogenic cyclic amino acids. NMR conformational studies showed that most of the cyclic peptides were able to adopt turn-like structures. Several of the analogues displayed significant inhibition of the BDNF-induced TrkB receptor phosphorylation, and hence could be useful templates for developing improved antagonists for this receptor.

Synthesis and SAR studies on azetidine-containing dipeptides as HCMV inhibitors

SAR studies on an azetidine-containing dipeptide prototype inhibitor of HCMV are described. Three series of structurally modified analogues, involving substitutions at the N- and C-terminus, and at the C-terminal side-chain were synthesized and evaluated for antiviral activity. Aliphatic or no substituents at the C-carboxamide group, an aliphatic C-terminal side-chain, as well as a benzyloxycarbonyl moiety at the N-terminus were absolute requirements for anti-HCMV activity. The conformational restriction induced by the 2-azetidine residue into the dipeptide derivatives, identified by ¹H NMR as a γ-type reverse turn, seems to have influence on the activity of these molecules.

Misincorporation of the proline homologue Aze (azetidine-2-carboxylic acid) into recombinant myelin basic protein

We have evaluated the effects of the proline homologue Aze (1) (azetidine-2-carboxylic acid) on growth of Escherichia coli strains used to over-express recombinant forms of murine myelin basic protein (rmMBP), and on the degree of misincorporation. Addition of Aze to minimal media resulted in severe diminution of growth rate, but rmMBP could still be produced and purified. Mass spectrometry indicated that a detectable proportion of the rmMBP produced had incorporated Aze instead of proline (Pro), to a maximum of three of eleven possible sites. Molecular modelling of a proline-rich region of rmMBP illustrated that the misincorporation of Aze at any site would cause a severe bend in the polypeptide chain, and that multiple Pro-->Aze substitutions would completely disrupt a poly-proline type II structure that has been conjectured to be functionally significant.

Synthesis and evaluation of new endomorphin analogues modified at the Pro(2) residue

Six new endomorphin analogues, incorporating constrained amino acids in place of native proline have been synthesized. Residues of (S)-azetidine-2-carboxylic acid (Aze), 3,4-dehydro-(S)-proline (Delta(3)Pro), azetidine-3-carboxylic acid (3Aze) and dehydro-alanine (DeltaAla) have been used to prepare [Delta(3)Pro(2)]EM-2 (1), [Aze(2)]EM-1 (2), [Aze(2)]EM-2 (3), [3Aze(2)]EM-1 (4), [3Aze(2)]EM-2 (5) and [DeltaAla(2)]EM-2 (6). Binding assays and functional bioactivities for mu- and delta-receptors are reported. The highest affinity, bioactivity and selectivity are shown by peptides 2 and 3 containing the Aze residue.