An examination of the steric effects of 5-tert-butylproline on the conformation of polyproline and the cooperative nature of type II to type I helical interconversion

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.

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.

A Proline Mimetic for the Design of New Stable Secondary Structures: Solvent-Dependent Amide Bond Isomerization of (S)-Indoline-2-carboxylic Acid Derivatives

A thorough experimental and computational study on the conformational properties of (S)-indoline-2-carboxylic acid derivatives has been conducted. Methyl (S)-1-acetylindoline-2-carboxylate, both a mimetic of proline and phenylalanine, shows a remarkable tendency toward the cis amide isomer when dissolved in polar solvents. This behavior is opposite to the general preference of proline for the trans isomer, making indoline-2-carboxylic acid a good candidate for the design of different secondary structures and new materials.

A Temperature-Driven, Reversible, Helical-Handedness Inversion in Peptaibol Analogues Tuned by the C-Terminal Capping Moiety

Trichogin is a natural peptide endowed with antimicrobial and antitumor activity. A member of the peptaibol family, trichogin possesses a C-terminal amino alcohol. In the past, this moiety was substituted for a methyl ester for synthetic purposes and it was observed that this apparently slight modification caused significant changes in the peptide bioactivity. With the aim of understanding the reasons behind such observations, a detailed spectroscopic study on a number of trichogin analogues has been performed. Herein, data obtained from synchrotron radiation circular dichroism, NMR spectroscopy, and fluorescence spectroscopy in organic solvents at cryogenic temperatures are compared with those independently acquired by means of EPR spectroscopy at 80 K. It is unambiguously revealed that the presence of a reversible, temperature-driven, screw-sense interconversion from a right- to left-handed helix is determined by the C-terminal capping moiety. Data demonstrate, for the first time, the key role of a C-terminal methyl ester in promoting peptide screw-sense inversion.

Variation in the Yaa position of collagen peptides containing azaGlycine

Herein, we report the systematic investigation of amino acid variation in the Yaa position of collagen peptides containing an adjacent azaGlycine residue. We demonstrate the reliability of azaGlycine as a glycine replacement and provide a sequence independent strategy for stabilizing the triple helical assembly of collagen peptides.

Synthetic alienation of microbial organisms by using genetic code engineering: Why and how?

The main goal of synthetic biology (SB) is the creation of biodiversity applicable for biotechnological needs, while xenobiology (XB) aims to expand the framework of natural chemistries with the non-natural building blocks in living cells to accomplish artificial biodiversity. Protein and proteome engineering, which overcome limitation of the canonical amino acid repertoire of 20 (+2) prescribed by the genetic code by using non-canonic amino acids (ncAAs), is one of the main focuses of XB research. Ideally, estranging the genetic code from its current form via systematic introduction of ncAAs should enable the development of bio-containment mechanisms in synthetic cells potentially endowing them with a "genetic firewall" i.e. orthogonality which prevents genetic information transfer to natural systems. Despite rapid progress over the past two decades, it is not yet possible to completely alienate an organism that would use and maintain different genetic code associations permanently. In order to engineer robust bio-contained life forms, the chemical logic behind the amino acid repertoire establishment should be considered. Starting from recent proposal of Hartman and Smith about the genetic code establishment in the RNA world, here the authors mapped possible biotechnological invasion points for engineering of bio-contained synthetic cells equipped with non-canonical functionalities.

cis-trans-Amide isomerism of the 3,4-dehydroproline residue, the 'unpuckered' proline

Proline (Pro) is an outstanding amino acid in various biochemical and physicochemical perspectives, especially when considering the cis-trans isomerism of the peptidyl-Pro amide bond. Elucidation of the roles of Pro in chemical or biological systems and engineering of its features can be addressed with various Pro analogues. Here we report an experimental work investigating the basic physicochemical properties of two Pro analogues which possess a 3,4-double bond: 3,4-dehydroproline and 4-trifluoromethyl-3,4-dehydroproline. Both indicate a flat pyrroline ring in their crystal structures, in agreement with previous theoretical calculations. In solution, the peptide mimics exhibit an almost unchanged equilibrium of the trans/cis ratios compared to that of Pro and 4-trifluoromethylproline derivatives. Finally we demonstrate that the 3,4-double bond in the investigated structures leads to an increase of the amide rotational barriers, presumably due to an interplay with the transition state.

Estimating the "steric clash" at cis peptide bonds

To account for the scarcity of cis peptide bonds in proteins, especially in nonproline (or secondary amide) cases, a steric-clash argument is often put forward, in a scheme where the R lateral chains are facing parallel one another, and the backbone is kept in an "all- trans"-like arrangement. Although such a steric conflict can be partly relieved through proper adjustment of the backbone dihedral angles, one can try to estimate its associated energy cost. To this end, quantum-chemistry approaches using a differential-torsion protocol and bond-separation-energy analyses are applied to N-ethyl propionamide CH3-CH2-CO-NH-CH2-CH3, regarded as a model capable of exhibiting C beta...C beta interaction as in alanine succession. The calculations provide an increment of 9 kcal/mol, quite close to that obtained in the nearly isostere (gsg) rotamer of n-hexane (10 kcal/mol), suggesting the local effects induced by methyl-methyl contact are similar in both cases. Analogous treatments on larger radicals as encountered in leucine or phenylalanine dimers do not change this increment much, which therefore defines the basic reference per-plaque quota to be overcome along all- cis chains. Explicit modeling indicated it can be reduced by up to a factor of 4.

Stereoselective Synthesis of (Z)-Alkene-Containing Proline Dipeptide Mimetics

In peptides and proteins, the peptide bond between an amino acid and proline exists as an equilibrium mixture of the cis-imide and trans-imide due to the low energy barrier in their interconversion. This feature greatly influences the structure and function of the proline-containing peptides and proteins. Therefore, restricting the amide bond with an (E)- or (Z)-alkene should provide a promising method for elucidating the structure-activity relationships of the peptide and the proteins. In this report, the regio- and stereoselective synthesis of cis-alanylproline (Ala-Pro) type (Z)-alkene dipeptide mimetic is described. The key steps of this synthesis are to introduce a C3 unit onto a gamma-phosphoryloxy-alpha,beta-unsaturated-delta-lactam with an organocopper-mediated anti-S(N)2' reaction and subsequently construct a five-membered proline-like cyclic structure with an intramolecular Suzuki coupling reaction. Hydrolysis of the amide bond in the resulting bicyclic lactam yields the desired cis-Ala-Pro type (Z)-alkene dipeptide isostere. The presented synthetic methodology should be applicable to the general syntheses of other cis-aminoacylproline type (Z)-alkene dipeptide mimetics.

β-Pseudopeptide foldamers. The homo-oligomers of (4R)-(2-oxo-1,3-oxazolidin-4-yl)-acetic acid (D–Oxac)

A total synthesis in solution and a conformational analysis of the homo-oligomers of (4R)-(2-oxo-1,3-oxazolidin-4-yl)-acetic acid (D-Oxac) to the tetramer level are described. As the D-Oxac building block contains both an oxazolidin-2-one and a beta-amino acid group, it may represent a new type of conformationally constrained tool for the construction of beta-pseudopeptide foldamers. A conformational investigation using NMR and an extensive, unconstrained analysis with a Monte Carlo search to the octamer level, both in water and in chloroform, showed that these homo-oligomers tend to fold in a regular helical structure in a competitive solvent, such as water. Since aqueous solutions are of major relevance for biological systems, these molecules are good candidates for application to these environments.

Conformational Behavior of β-Proline Oligomers

Conformations of the monomer, dimer, and hexamer of beta-proline ((S) pyrrolidine-3-carboxylic acid) were determined using ab initio molecular orbital calculations at the RHF/6-31G level of theory. The calculated minima are in good agreement with experimental data for the system and imply that the conformations could be controlled through chemical modification at Calpha, Cgamma, or Cdelta. The monomer and dimer are small and flexible with many low-energy minima. In the hexamer, two forms of regular secondary structure are preferred: left-handed helices with cis-peptide bonds and right-handed helices with trans-peptide bonds. This is similar to the behavior of alpha-proline helices, except that the relationship between the peptide rotamer and the handedness of the helix is reversed. Therefore, helices of the enantiomer of beta-proline ((R)-pyrrolidine-3-carboxylic acid) should exhibit the same behavior as alpha-proline helices. Through understanding the conformational behavior of beta-proline in various environments, it may be possible to use these protein mimics to inhibit various protein-protein recognition events. To estimate these effects, SCRF energies for the conformers were determined in dielectrics corresponding to water, methanol, and chloroform. It appears that the cis helices are more favorably solvated than the trans helices, but the cause is not clear.

Regio- and stereoselective synthesis of (E)-alkene trans-Xaa-Pro dipeptide mimetics utilizing organocopper-mediated anti-S(N)2' reactions

Proline dipeptides (Xaa-Pro) exist as an equilibrium mixture of cis- and trans-rotamers, which depends on the energy barriers for imide isomerization. This conformation mixture contributes to both structure and function of proline-containing peptides and proteins. Structural motifs resembling these cis- or trans-conformers have served as useful tools for elucidating contributions of proline residues in the physicochemical and biological profiles of structures which contain them. Among such motifs are alkene dipeptide isosteres which mimic cis- or trans-imide using (Z)- or (E)-alkene, respectively. In this report, the first regio- and stereoselective syntheses of (E)-alkene dipeptide isosteres (20, 31, and 35) corresponding to trans-proline dipeptides are described. Key to the synthesis of these mimetics is the anti-S(N)2' reaction of vinyl aziridines such as 15 or vinyl oxazolidinones such as 28 and 32 with organocopper reagents "RCu" (R = CH(2)SiMe(2)(Oi-Pr)). Reaction of cis-vinylaziridine 15 derived from L-serine with organocopper reagent gave a precursor of the trans-L-Ser-D-Pro type alkene isosteres 20, accompanied by an S(N)2 side product. One limitation with the use of such aziridine-mediated methodology is formation of the corresponding trans-aziridine 22, which leads to L-L type isosteres, that is unstable and obtainable only in low yield. On the other hand, both isomers of oxazolidinone derivatives can be easily obtained from N-Boc-protected amino alcohols. The reaction of trans- 28 or cis-oxazolidinone derivative 32 with organocopper reagents proceeds quantitatively with high regio- and diastereoselectivities in anti-S(N)2' fashion. Subsequent oxidative treatment of the newly introduced isopropoxydimethylsilylmethyl group yields trans-L-Ser-L-Pro 31 or trans-L-Ser-D-Pro type isosteres 35, respectively. Of note, synthesized isostere 31 can also be converted to trans-phosphoSer-Pro 42 and trans-Cys-Pro mimetics 44. The present synthetic methodology affords trans-Xaa-Pro alkene-type dipeptide isosteres in high yield with relatively simple manipulation.

An oligomeric ser-pro dipeptide mimetic assuming the polyproline II helix conformation

A hexapeptide assembled from dipeptide building blocks assumes the secondary structure of the polyproline II (PPII) helix. Side chain-to-backbone hydrogen bonds stabilize peptide torsions next to the fused ring systems. The solution structure of the polyhydroxylated peptide was studied by spectroscopic methods.

Effect of sequence on peptide geometry in 5-tert-butylprolyl type VI beta-turn mimics

The influence of sequence on turn geometry was examined by incorporating (2S,5R)-5-tert-butylproline (5-(t)BuPro) into a series of dipeptides and tetrapeptides. (2S,5R)-5-tert-Butylproline and proline were respectively introduced at the C-terminal residue of N-acetyl dipeptide N'-methylamides 1 and 2. The conformational analysis of these analogues was performed using NMR and CD spectroscopy as well as X-ray diffraction to examine the factors that control the prolyl amide (in this text, the term "prolyl amide" refers to the tertiary amide composed of the pyrrolidine nitrogen of the prolyl residue and the carbonyl of the N-terminal residue) equilibrium and stabilize type VI beta-turn conformation. The high cis-isomer population with aromatic residues N-terminal to proline was shown to result from a stacking interaction between the partial positive charged prolyl amide nitrogen and the aromatic pi-system as seen in the crystal structure of 1c. The effect of sequence on the prolyl amide equilibrium of 5-(t)BuPro-tetrapeptides (Ac-Xaa-Yaa-5-(t)BuPro-Zaa-XMe, 13 and 14) was studied by varying the amino acids at the Xaa, Yaa, and Zaa positions. High (>80%) cis-isomer populations were obtained with alkyl groups at the Xaa position, an aromatic residue at the Yaa position, and either an alanine or a lysine residue at the Zaa position of the 5-(t)BuPro-tetrapeptide methyl esters in water. Tetrapeptides Ac-Ala-Phe-5-(t)BuPro-Zaa-OMe (Zaa = Ala, Lys), 14d and 14f, with high cis-isomer content adopted type VIa beta-turn conformations as shown by their NMR and CD spectra. Although a pattern of amide proton temperature coefficient values indicative of a hairpin geometry was observed in peptides 14d and 14f, the value magnitudes did not indicate strong hydrogen bonding in water.

Synthesis, conformation and biological activity of linear and cyclic Thr6-bradykinin analogues containing N-benzylglycine in place of phenylalanine

Three linear Thr6-bradykinin analogues in which either one or both the two phenylalanine residues in the peptide sequence have been substituted by N-benzylglycine (BzlGly) and their head-to-tail cyclic analogues were synthesized and tested on an isolated rat duodenum preparation. The linear (BzlGly5,Thr6-BK, BzlGly8,Thr6-BK and BzlGly(5,8),Thr6-BK) and the cyclic (cyclo BzlGly5,Thr6-BK, cyclo BzlGly8,Thr6-BK and cyclo BzlGly(5,8),Thr6-BK) peptoid-like analogues were characterized by amino acid analysis, optical rotation, analytical HPLC and MALDI-TOF mass spectroscopy. The conformational features of both the linear and cyclic derivatives were investigated by FT-IR and CD measurements. Preliminary molecular mechanics calculations were also performed on some synthetic peptides. Pharmacological screening using the relaxation of the isolated rat duodenum preparation showed that incorporation of N-benzylglycine at positions 5 and/or 8 in the linear Thr6-BK causes a substantial decrease in potency. Comparable incorporation in cyclo Thr6-BK, at position 8, or 5 and 8, resulted in nearly inactive analogues. However, cyclo BzlGly5,Thr6-BK showed a potency which is of the same order of magnitude as for cyclo-BK and cyclo Thr6-BK.

The hunchback and its neighbours: proline as an environmental modulator

The unique ability of Pro or Pro-rich repeats to affect the stability and function of proteins has recently been highlighted by biophysical studies on fragments from prions, signalling domains and muscle proteins. Pro-rich regions have been observed to either occupy disordered states or adopt various helical structures; some are also able to undergo an environmental-dependent transformation between these states. Such a transformation could explain some of the inherent functional properties of the parent proteins and, additionally, can be efficiently exploited to generate novel temperature- and pH-switches in more conventional globular proteins.

Design, synthesis, and conformational analysis of azacycloalkane amino acids as conformationally constrained probes for mimicry of peptide secondary structures

Conformationally constrained amino acid and dipeptide units can serve in mimics of specific secondary structures for studying relationships between peptide conformation and biological activity. A variety of mimics are required to study systematically the structure-activity relationships in biologically relevant peptides. We present our efforts on the design, synthesis, and conformational analysis of a series of rigid surrogates of amino acid and dipeptide units for application within constrained peptide analogues, and for employment as inputs for combinatorial science. Conceived to be general and versatile, our methodology has delivered a variety of azacycloalkane and azabicycloalkane amino acids in enantiomerically pure form, via practical methods, from readily available and inexpensive starting materials.

Influence of N-terminal residue stereochemistry on the prolyl amide geometry and the conformation of 5-tert-butylproline type VI beta-turn mimics

The effects of N-terminal amino acid stereochemistry on prolyl amide geometry and peptide turn conformation were investigated by coupling both L- and D-amino acids to (2S, 5R)-5-tert-butylproline and L-proline to generate, respectively, N-(acetyl)dipeptide N'-methylamides 1 and 2. Prolyl amide cis- and trans-isomers were, respectively, favored for peptides 1 and 2 as observed by proton NMR spectroscopy in water, DMSO and chloroform. The influence of solvent composition on amide proton chemical shift indicated an intramolecular hydrogen bond between the N'-methylamide proton and the acetamide carbonyl for the major conformer of dipeptides (S)-1, that became less favorable in (R)-1 and 2. The coupling constant (3J(NH,alpha)) values for the cis-isomer of (R)-1 indicated a phi2 dihedral angle value characteristic of a type VIb beta-turn conformation in solution. X-ray crystallographic analysis of N-acetyl-D-leucyl-5-tert-butylproline N'-methylamide (R)-lb showed the prolyl residue in a type VIb beta-turn geometry possessing an amide cis-isomer and psi3-dihedral angle having a value of 157 degrees, which precluded an intramolecular hydrogen bond. Intermolecular hydrogen bonding between the leucyl residues of two turn structures within the unit cell positioned the N-terminal residue in a geometry where their phi2 and psi2 dihedral angle values were not characteristic of an ideal type VIb turn. The circular dichroism spectra of tert-butylprolyl peptides (S)- and (R)-1b were found not to be influenced by changes in solvent composition from water to acetonitrile. The type B spectrum exhibited by (S)-1b has been previously assigned to a type VIa beta-turn conformation [Halab L, Lubell WD. J. Org. Chem. 1999; 64: 3312-3321]. The type C spectrum exhibited by the (R)-lb has previously been associated with type II' beta-turn and alpha-helical conformations in solution and appears now to be also characteristic for a type VIb geometry.

Racemization in the use of N-(9-(9-phenylfluorenyl))serine-derived cyclic sulfamidates in the synthesis of delta-keto alpha-amino carboxylates and prolines

[reaction: see text]Ring opening of enantiopure N-(9-(9-phenylfluorenyl)serine-derived cyclic sulfamidates with beta-keto esters, beta-keto ketones, and dimethyl malonate gave a variety of gamma-substituted amino acid analogues in racemic form. Investigation of the mechanism for racemization revealed that beta-elimination occurred to form a dehydroalanine intermediate that underwent subsequent Michael addition.