A Novel Acid-Catalyzed Isomerization of Aib-Containing Thiodipeptides

The use of amino thioacids in the `azirine/oxazolone method' led to completely epimerized Aib-containing endothiodipeptides (Aib=2-aminoisobutyric acid). It could be established that the epimerization occurred during the acidic hydrolysis of the primarily formed dipeptide thioanilides in which the thiocarbonyl group was shifted from the last to the penultimate amino-acid residue. Several conditions for the hydrolysis were tested, and, in some of them, the degree of epimerization could be reduced. By treatment of the Aib-containing dipeptide thioanilides 21 with ZnCl₂ in AcOH followed by HCl in AcOH, the isomeric endothiodipeptide anilides 25 were formed, i.e., the thiocarbonyl group was again shifted from the last to the penultimate amino acid residue. Under optimized reaction conditions, this novel isomerization proceeded in high yields and without any epimerization. Two conceivable mechanisms are proposed in Scheme 12. X-Ray diffraction analyses were performed for Z−Gly−Aib-Ψ(CS)−N(Me)Ph ( 21f ) and the isomeric Z−Gly-Ψ(CS)−Aib−N(Me)Ph ( 25f ).     

N‐(tert‐Butoxycarbonyl)‐α‐aminoisobutyryl‐α‐aminoisobutyric acid methyl ester: two polymorphic forms in the space group P21/n

The title compound (systematic name: methyl 2‐{2‐[(tert‐butoxycarbonyl)amino]‐2‐methylpropanamido}‐2‐methylpropanoate), C₁₄H₂₆N₂O₅, (I), crystallizes in the monoclinic space group P2₁/n in two polymorphic forms, each with one molecule in the asymmetric unit. The molecular conformation is essentially the same in both polymorphs, with the α‐aminoisobutyric acid (Aib) residues adopting ϕ and ψ values characteristic of α‐helical and mixed 3₁₀‐ and α‐helical conformations. The helical handedness of the C‐terminal residue (Aib2) is opposite to that of the N‐terminal residue (Aib1). In contrast to (I), the closely related peptide Boc‐Aib‐Aib‐OBn (Boc is tert‐butoxycarbonyl and Bn is benzyl) adopts an α_L‐P_II backbone conformation (or the mirror image conformation). Compound (I) forms hydrogen‐bonded parallel β‐sheet‐like tapes, with the carbonyl groups of Aib1 and Aib2 acting as hydrogen‐bond acceptors. This seems to represent an unusual packing for a protected dipeptide containing at least one α,α‐disubstituted residue.     

Formation of 1,3‐Thiazol‐5(4H)‐imines and 1,3‐Oxazol‐5(4H)‐imines in Aib‐Containing Thiopeptides

When tripeptides of type Axx^t‐Aib‐Axx‐OH were coupled with amino acid methyl esters by means of commonly used coupling reagents, the formation of 1,3‐thiazol‐5(4H)‐imines and 1,3‐oxazol‐5(4H)‐imines was observed. With the aim of understanding which structure elements are required for this reaction, several model peptides have been prepared according to our recently described methodology, a modification of the ‘azirine/oxazolone method', followed by selective isomerization of the peptide thioamides. In addition, attempts to prepare peptides that contain more than one C=S group by the same methodology also led to the formation of 1,3‐thiazol‐5(4H)‐imine‐containing derivatives. An additional C=S group can be introduced into the peptide, when the 1,3‐thiazol‐5(4H)‐imines were treated with H₂S, although mixtures of epimers were obtained. The structures of an endothiohexapeptide, two 1,3‐thiazol‐5(4H)‐ones, and two peptides containing a 1,3‐thiazol‐5(4H)‐imine moiety have been established by X‐ray crystal‐structure analysis.     

The first N‐terminal unprotected (Gly‐Aib)n peptide: H‐Gly‐Aib‐Gly‐Aib‐OtBu

Glycine (Gly) is incorporated in roughly half of all known peptaibiotic (nonribosomally biosynthesized antibiotic peptides of fungal origin) sequences and is the residue with the greatest conformational flexibility. The conformational space of Aib (α‐aminoisobutyric acid) is severely restricted by the second methyl group attached to the C_α atom. Most of the crystal structures containing Aib are N‐terminal protected. Deprotection of the N‐ or C‐terminus of peptides may alter the hydrogen‐bonding scheme and/or the structure and may facilitate crystallization. The structure reported here for glycyl‐α‐aminoisobutyrylglycyl‐α‐aminoisobutyric acid tert‐butyl ester, C₁₆H₃₀N₄O₅, describes the first N‐terminal‐unprotected (Gly‐Aib)_n peptide. The achiral peptide could form an intramolecular hydrogen bond between the C=O group of Gly1 and the N—H group of Aib4. This hydrogen bond is found in all tetrapeptides and N‐terminal‐protected tripeptides containing Aib, apart from one exception. In the present work, this hydrogen bond is not observed (N...O = 5.88 Å). Instead, every molecule is hydrogen bonded to six other symmetry‐related molecules with a total of eight hydrogen bonds per molecule. The backbone conformation starts in the right‐handed helical region (and the left‐handed helical region for the inverted molecule) and reverses the screw sense in the last two residues.     

Synthesis and Use of 2H‐Azirin‐3‐amines as Dipeptide Synthons

The synthesis of the new 2H‐azirin‐3‐amines (‘3‐amino‐2H‐azirines') 11, 20, 28 , and 33 as dipeptide synthons is described. The reactions of the starting amides with Lawesson reagent gave the corresponding thioamides, and consecutive treatment with COCl₂, 1,4‐diazabicyclo[2.2.2]octane (DABCO), and NaN₃ led to the desired products. It is shown that these 2H‐azirin‐3‐amines can conveniently be used as building blocks of the dipeptides Aib‐(Me)Axx (Axx=alanine, valine), Aib‐Homoproline, and Iva‐Pro in the synthesis of several model peptides. However, some limitations apply for the synthesis of such 2H‐azirin‐3‐amines. The starting material for the azirine synthesis, the corresponding thioamides, cannot generally be synthesized, and the 2H‐azirin‐3‐amines could not be obtained in all cases from the thioamides prepared.     

Novel N‐(2,2‐Dimethyl‐2H‐azirin‐3‐yl)‐L‐prolinates as Aib‐Pro Synthons

The syntheses of phenacyl N‐(2,2‐dimethyl‐2H‐azirin‐3‐yl)‐L ‐prolinate and allyl N‐(2,2‐dimethyl‐2H‐azirin‐3‐yl)‐L ‐prolinate are reported. Reactions of these 2H‐azirin‐3‐amine derivatives with Z‐protected amino acids have shown them to be suitable synthons for the Aib‐Pro unit in peptide synthesis. After incorporation into the peptide by means of the ‘azirine/oxazolone method’, the C‐termini of the resulting peptides were deprotected selectively with Zn in AcOH or by a mild Pd⁰‐promoted procedure, respectively.     

Benzyl tert‐but­oxy­carbonyl‐α‐amino­isobutyrate

The small synthetic peptide, benzyl 2‐(tert‐but­oxy­carbonyl‐amino)­isobutyrate, C₁₆H₂₃NO₄, has the α‐helical conformation [|?| = 55.8 (2)° and |ψ| = 37.9 (2)°] observed in peptide fragments of peptaibols containing the α‐amino­isobutyric acid (Aib) residue. The structure shows no intramolecular hydrogen bonding, which would disrupt the limited conformational freedom associated with this amino acid. Two weak intermolecular hydrogen contacts are observed.     

A Novel 2H‐Azirin‐3‐amine as a Dipeptide (Aib‐Hyp) Synthon

The synthesis of methyl (2S,4R)‐4‐(benzyloxy)‐N‐(2,2‐dimethyl‐2H‐azirin‐3‐yl)prolinate ( 10 ), a novel 2H‐azirin‐3‐amine (`3‐amino‐2H‐azirine'), is described (Scheme 1). The reaction of methyl (2S,4R)‐N‐(2‐methylpropanoyl)‐4‐(benzyloxy)prolinate ( 7 ) with Lawesson reagent gave methyl (2S,4R)‐4‐(benzyloxy)‐N‐[2‐(methylthio)propanoyl]prolinate ( 8 ) and consecutive treatment with COCl₂, 1,4‐diazabicyclo[2.2.2]octane (DABCO), and NaN₃ led to 10 . The use of 10 as a building block of the dipeptide Aib‐Hyp (Aib=2‐aminoisobutyric acid, Hyp=(2S,4R)‐4‐hydroxyproline) is demonstrated by the syntheses of several model peptides (Scheme 2 and Table). The benzyl protecting group of the 4‐OH function in Hyp in the model peptides has been removed in good yields.     

The achiral tetrapeptide Z‐Aib‐Aib‐Aib‐Gly‐OtBu

The title achiral peptide N‐benzyloxycarbonyl‐α‐aminoisobutyryl‐α‐aminoisobutyryl‐α‐aminoisobutyrylglycine tert‐butyl ester or Z‐Aib‐Aib‐Aib‐Gly‐OtBu (Aib is α‐aminoisobutyric acid, Z is benzyloxycarbonyl, Gly is glycine and OtBu indicates the tert‐butyl ester), C₂₆H₄₀N₄O₇, is partly hydrated (0.075H₂O) and has two different conformations which together constitute the asymmetric unit. Both molecules form incipient 3₁₀‐helices. They differ in the relative orientation of the N‐terminal protection group and at the C‐terminus. There are two 4→1 intramolecular hydrogen bonds.     

An oxazol‐5(4H)‐one from benzyloxy­carbonyl‐(Aib)4‐OH

Benzyl N‐[8‐(4,4‐dimethyl‐5‐oxo‐4,5‐dihydrooxazol‐2‐yl)‐2,5,5,8‐tetra­methyl‐3,6‐dioxo‐4,7‐diazanon‐2‐yl]­carbamate, C₂₄H₃₄N₄O₆, an oxazol‐5(4H)‐one from N‐α‐benzyloxycarbonyl‐(Aib)₄‐OH (Aib = α‐amino­isobutyryl) represents the longest peptide oxazolone so far characterized by X‐ray diffraction. The overall geometry of the oxazolone ring compares well with literature data. The Aib(1) and Aib(2) residues are folded into a type III β‐bend, while the conformation adopted by Aib(3), preceding the oxazolone moiety, is semi‐extended. The disposition of the oxazolone ring relative to the preceding residue is stabilized by C—­H?N and C—H?O intramolecular interactions.     

Efficient Access to Enantiopure γ4‐Amino Acids with Proteinogenic Side‐Chains and Structural Investigation of γ4‐Asn and γ4‐Ser in Hybrid Peptide Helices

Hybrid peptides composed of α‐ and β‐amino acids have recently emerged as new class of peptide foldamers. Comparatively, γ‐ and hybrid γ‐peptides composed of γ⁴‐amino acids are less studied than their β‐counterparts. However, recent investigations reveal that γ⁴‐amino acids have a higher propensity to fold into ordered helical structures. As amino acid side‐chain functional groups play a crucial role in the biological context, the objective of this study was to investigate efficient synthesis of γ⁴‐residues with functional proteinogenic side‐chains and their structural analysis in hybrid‐peptide sequences. Here, the efficient and enantiopure synthesis of various N‐ and C‐terminal free‐γ⁴‐residues, starting from the benzyl esters (COOBzl) of N‐Cbz‐protected (E)‐α,β‐unsaturated γ‐amino acids through multiple hydrogenolysis and double‐bond reduction in a single‐pot catalytic hydrogenation is reported. The crystal conformations of eight unprotected γ⁴‐amino acids (γ⁴‐Val, γ⁴‐Leu, γ⁴‐Ile, γ⁴‐Thr(OtBu), γ⁴‐Tyr, γ⁴‐Asp(OtBu), γ⁴‐Glu(OtBu), and γ‐Aib) reveals that these amino acids adopted a helix favoring gauche conformations along the central C^γ? C^β bond. To study the behavior of γ⁴‐residues with functional side chains in peptide sequences, two short hybrid γ‐peptides P1 (Ac‐Aib‐γ⁴‐Asn‐Aib‐γ⁴‐Leu‐Aib‐γ⁴‐Leu‐CONH₂) and P2 (Ac‐Aib‐γ⁴‐Ser‐Aib‐γ⁴‐Val‐Aib‐γ⁴‐Val‐CONH₂) were designed, synthesized on solid phase, and their 12‐helical conformation in single crystals were studied. Remarkably, the γ⁴‐Asn residue in P1 facilitates the tetrameric helical aggregations through interhelical H bonding between the side‐chain amide groups. Furthermore, the hydroxyl side‐chain of γ⁴‐Ser in P2 is involved in the interhelical H bonding with the backbone amide group. In addition, the analysis of 87 γ⁴‐residues in peptide single‐crystals reveal that the γ⁴‐residues in 12‐helices are more ordered as compared with the 10/12‐ and 12/14‐helices.     

Synthesis of Poly‐Aib Oligopeptides and Aib‐Containing Peptides via the ‘Azirine/Oxazolone Method’, and Their Crystal Structures

The protected poly‐Aib oligopeptides Z‐(Aib)_n‐N(Me)Ph with n=2–6 were prepared according to the ‘azirine/oxazolone method’, i.e., by coupling amino or peptide acids with 2,2,N‐trimethyl‐N‐phenyl‐2H‐azirin‐3‐amine ( 1a ) as an Aib synthon (Scheme 2). Following the same concept, the segments Z‐(Aib)₃‐OH ( 9 ) and H‐L ‐Pro‐(Aib)₃‐N(Me)Ph ( 20 ) were synthesized, and their subsequent coupling with N,N′‐dicyclohexylcarbodiimide (DCC)/ZnCl₂ led to the protected heptapeptide Z‐(Aib)₃‐L ‐Pro‐(Aib)₃‐N(Me)Ph ( 21 ; Scheme 3). The crystal structures of the poly‐Aib oligopeptide amides were established by X‐ray crystallography confirming the 3₁₀‐helical conformation of Aib peptides.     

Conformational Study of Heteropentapeptides Containing an α‐Ethylated α,α‐Disubstituted Amino Acid: (S)‐Butylethylglycine (=2‐Amino‐2‐ethylhexanoic Acid) within a Sequence of Dimethylglycine (=2‐Aminoisobutyric Acid) Residues

Heteropentapeptides containing the α‐ethylated α,α‐disubstituted amino acid (S)‐butylethylglycine and four dimethylglycine residues, i.e., CF₃CO‐[(S)‐Beg]‐(Aib)₄‐OEt ( 4 ) and CF₃CO‐(Aib)₂‐[(S)‐Beg]‐(Aib)₂‐OEt ( 7 ), were synthesized by conventional solution methods. In the solid state, the preferred conformation of 4 was shown to be both a right‐handed (P) and a left‐handed (M) 3₁₀‐helical structure, and that of 7 was a right‐handed (P) 3₁₀‐helical structure. IR, CD, and ¹H‐NMR spectra revealed that the dominant conformation of both 4 and 7 in solution was the 3₁₀‐helical structure. These conformations were also supported by molecular‐mechanics calculations.     

The Propensity of α‐Aminoisobutyric Acid (=2‐Methylalanine; Aib) to Induce Helical Secondary Structure in an α‐Heptapeptide: A Computational Study

We present a molecular‐dynamics simulation study of an α‐heptapeptide containing an α‐aminoisobutyric acid (=2‐methylalanine; Aib) residue, Val¹‐Ala²‐Leu³‐Aib⁴‐Ile⁵‐Met⁶‐Phe⁷, and a quantum‐mechanical (QM) study of simplified models to investigate the propensity of the Aib residue to induce 3₁₀/α‐helical conformation. For comparison, we have also performed simulations of three analogues of the peptide with the Aib residue being replaced by L ‐Ala, D ‐Ala, and Gly, respectively, which provide information on the subtitution effect at C(α) (two Me groups for Aib, one for L ‐Ala and D ‐Ala, and zero for Gly). Our simulations suggest that, in MeOH, the heptapeptide hardly folds into canonical helical conformations, but appears to populate multiple conformations, i.e., C₇ and 3₁₀‐helical ones, which is in agreement with results from the QM calculations and NMR experiments. The populations of these conformations depend on the polarity of the solvent. Our study confirms that a short peptide, though with the presence of an Aib residue in the middle of the chain, does not have to fold to an α‐helical secondary structure. To generate a helical conformation for a linear peptide, several Aib residues should be present in the peptide, either sequentially or alternatively, to enhance the propensity of Aib‐containing peptides towards the helical conformation. A correction of a few of the published NMR data is reported.     

The Structural Characterization of Folded Peptides Containing the Conformationally Constrained β‐Amino Acid Residue β2,2Ac6c

Backbone alkylation has been shown to result in a dramatic reduction in the conformational space that is sterically accessible to α‐amino acid residues in peptides. By extension, the presence of geminal dialkyl substituents at backbone atoms also restricts available conformational space for β and γ residues. Five peptides containing the achiral β^2,2‐disubstituted β‐amino acid residue, 1‐(aminomethyl)cyclohexanecarboxylic acid (β^2,2Ac₆c), have been structurally characterized in crystals by X‐ray diffraction. The tripeptide Boc‐Aib‐β^2,2Ac₆c‐Aib‐OMe ( 1 ) adopts a novel fold stabilized by two intramolecular H‐bonds (C₁₁ and C₉) of opposite directionality. The tetrapeptide Boc‐[Aib‐β^2,2Ac₆c]₂‐OMe ( 2 ) and pentapeptide Boc‐[Aib‐β^2,2Ac₆c]₂‐Aib‐OMe ( 3 ) form short stretches of a hybrid αβ C₁₁ helix stabilized by two and three intramolecular H‐bonds, respectively. The structure of the dipeptide Boc‐Aib‐β^2,2Ac₆c‐OMe ( 5 ) does not reveal any intramolecular H‐bond. The aggregation pattern in the crystal provides an example of an extended conformation of the β^2,2Ac₆c residue, forming a ‘polar sheet’ like H‐bond. The protected derivative Ac‐β^2,2Ac₆c‐NHMe ( 4 ) adopts a locally folded gauche conformation about the C_β? C_α bonds (θ=?55.7°). Of the seven examples of β^2,2Ac₆c residues reported here, six adopt gauche conformations, a feature which promotes local folding when incorporated into peptides. A comparison between the conformational properties of β^2,2Ac₆c and β^3,3Ac₆c residues, in peptides, is presented. Backbone torsional parameters of H‐bonded αβ/βα turns are derived from the structures presented in this study and earlier reports.     

The ‘Azirine/Oxazolone Method’ on Solid Phase: Introduction of Various α,α‐Disubstituted α‐Amino Acids

Peptides containing various α,α‐disubstituted α‐amino acids, such as α‐aminoisobutyric acid (Aib), 1‐aminocyclopentane‐1‐carboxylic acid, α‐methylphenylalanine, and 3‐amino‐3,4,5,6‐tetrahydro‐2H‐pyran‐3‐carboxylic acid have been synthesized from the N‐ to the C‐terminus by the ‘azirine/oxazolone method’ under solid‐phase conditions. In this convenient method for the synthesis of sterically demanding peptides on solid‐phase, 2H‐azirin‐3‐amines are used to introduce the α,α‐disubstituted α‐amino acids without the need for additional reagents. Furthermore, the synthesis of poly(Aib) sequences has been explored.     

The peptide Z‐Aib‐Aib‐Aib‐L‐Ala‐OtBu

The title peptide, N‐benzyloxycarbonyl‐α‐aminoisobutyryl‐α‐aminoisobutyryl‐α‐aminoisobutyryl‐L‐alanine tert‐butyl ester or Z‐Aib‐Aib‐Aib‐L‐Ala‐OtBu (Aib is α‐aminoisobutyric acid, Z is benzyloxycarbonyl and OtBu indicates the tert‐butyl ester), C₂₇H₄₂N₄O₇, is a left‐handed helix with a right‐handed conformation in the fourth residue, which is the only chiral residue. There are two 4→1 intramolecular hydrogen bonds in the structure. In the lattice, molecules are hydrogen bonded to form columns along the c axis.     

Identification of the Enzymes Mediating the Maturation of the Seryl‐tRNA Synthetase Inhibitor SB‐217452 during the Biosynthesis of Albomycins

Albomycin δ₂ is a sulfur‐containing sideromycin natural product that shows potent antibacterial activity against clinically important pathogens. The l ‐serine‐thioheptose dipeptide partial structure, known as SB‐217452, has been found to be the active seryl‐tRNA synthetase inhibitor component of albomycin δ₂. Herein, it is demonstrated that AbmF catalyzes condensation between the 6′‐amino‐4′‐thionucleoside with the d ‐ribo configuration and seryl‐adenylate supplied by the serine adenylation activity of AbmK. Formation of the dipeptide is followed by C3′‐epimerization to produce SB‐217452 with the d ‐xylo configuration, which is catalyzed by the radical S‐adenosyl‐l ‐methionine enzyme AbmJ. Gene deletion suggests that AbmC is involved in peptide assembly linking SB‐217452 with the siderophore moiety. This study establishes how the albomycin biosynthetic machinery generates its antimicrobial component SB‐217452.     

New Optically Active 2H‐Azirin‐3‐amines as Synthons for Enantiomerically Pure 2,2‐Disubstituted Glycines

The synthesis of novel 2,2‐disubstituted 2H‐azirin‐3‐amines with a chiral amino group is described. Chromatographic separation of the diastereoisomer mixture yielded the pure diastereoisomers (1′R,2R)‐ 4a – e and (1′R,2S)‐ 4a – e (Scheme 1, Table 1), which are synthons for the (R)‐ and (S)‐isomers of isovaline, 2‐methylvaline, 2‐cyclopentylalanine, 2‐methylleucine, and 2‐(methyl)phenylalanine, respectively. The configuration at C(2) of the synthons was determined by X‐ray crystallography relative to the known configuration of the chiral auxiliary group. The reaction of 4 with thiobenzoic acid, benzoic acid, and the dipeptide Z‐Leu‐Aib‐OH ( 12 ) yielded the monothiodiamides 10 , the diamides 11 (Scheme 2, Table 3), and the tripeptides 13 (Scheme 3, Table 4), respectively.     

Synthesis,and Helix or Hairpin‐Turn Secondary Structures of ‘Mixed’ α/β‐Peptides Consisting of Residues with Proteinogenic Side Chains and of 2‐Amino‐2‐methylpropanoic Acid (Aib)

Twelve peptides, 1 – 12 , have been synthesized, which consist of alternating sequences of α‐ and β‐amino acid residues carrying either proteinogenic side chains or geminal dimethyl groups (Aib). Two peptides, 13 and 14 , containing 2‐methyl‐3‐aminobutanoic acid residues or a ‘random mix’ of α‐, β²‐, and β³‐amino acid moieties were also prepared. The new compounds were fully characterized by CD (Figs. 1 and 2), and ¹H‐ and ¹³C‐NMR spectroscopy, and high‐resolution mass spectrometry (HR‐MS). In two cases, 3 and 14 , we discovered novel types of turn structures with nine‐ and ten‐membered H‐bonded rings forming the actual turns. In two other cases, 8 and 11 , we found 14/15‐helices, which had been previously disclosed in mixed α/β‐peptides containing unusual β‐amino acids with non‐proteinogenic side chains. The helices are formed by peptides containing the amino acid moiety Aib in every other position, and their backbones are primarily not held together by H‐bonds, but by the intrinsic conformations of the containing amino acid building blocks. The structures offer new possibilities of mimicking peptide–protein and protein–protein interactions (PPI).