Synthesis of a Novel Tricyclic Dipeptide Template and Its Incorporation into a Cyclic Peptide Mimetic Containing an NPNA Motif

A novel tricyclic dipeptide template, formally derived by coupling (2S,4S)-4-aminoproline (Pro(NH₂)) and (S)-2-(carboxymethyl)proline (Pro(CH₂COOH)) as a diketopiperazine, has been synthesized in a form suitable for solid-phase peptide synthesis using Fmoc chemistry. This template was incorporated into the cyclic molecule cyclo(-Ala¹-Asn²-Pro³-Asn⁴-Ala⁵-Ala⁶-Temp-) (Temp = template), whose conformation in H₂O was studied by NMR methods. Average solution structures derived by restrained simulated annealing point to a highly populated βI-turn within the Asn-Pro-Asn-Ala motif and also indicate which conformations are likely to be preferred by the template.     

cis,cis‐Ceratospong­amide N,N‐di­methyl­acet­amide hemisolvate in the presence of twinning

Ceratospong­amide (CS) is a potent inhibitor of secreted phospho­lipase A₂, and cis,cis and trans,trans isomers, related with respect to the two proline amide bonds, are known. Crystals of cis,cis‐CS were grown from N,N‐di­methyl­acet­amide solution, giving the title compound, the cyclic ester of isoleucyl­oxazolinyl­phenyl­alanyl­prolyl­thia­zolyl­phenyl­alanyl­pro­line [cyclo(‐Ile–Oxz–Phe–Pro–Thz–Phe–Pro‐)] N,N‐di­methyl­acet­amide hemisolvate, C₄₁H₄₉N₇O₆S·0.5C₄H₉NO. The structure is the third example of cis,cis‐CS to be investigated and comprises twinned crystals, in which the a and b axes are interchanged. The ratio of co‐existing twin crystals is approximately 50%. The peptide has a `saddle‐like' structure and is very similar to previously reported structures of cis,cis‐CS, which implies that the structure of cis,cis‐CS is very stable in spite of differences in crystallization conditions.     

Crystal and NMR Structures of a Peptidomimetic β‐Turn That Provides Facile Synthesis of 13‐Membered Cyclic Tetrapeptides

Herein we report the unique conformations adopted by linear and cyclic tetrapeptides (CTPs) containing 2‐aminobenzoic acid (2‐Abz) in solution and as single crystals. The crystal structure of the linear tetrapeptide H₂N‐d ‐Leu‐d ‐Phe‐2‐Abz‐d ‐Ala‐COOH ( 1 ) reveals a novel planar peptidomimetic β‐turn stabilized by three hydrogen bonds and is in agreement with its NMR structure in solution. While CTPs are often synthetically inaccessible or cyclize in poor yield, both 1 and its N ‐Me‐d ‐Phe analogue ( 2 ) adopt pseudo‐cyclic frameworks enabling near quantitative conversion to the corresponding CTPs 3 and 4 . The crystal structure of the N ‐methylated peptide ( 4 ) is the first reported for a CTP containing 2‐Abz and reveals a distinctly planar 13‐membered ring, which is also evident in solution. The N ‐methylation of d ‐Phe results in a peptide bond inversion compared to the conformation of 3 in solution.     

Two New Cyclic Tetrapeptides of Streptomyces rutgersensis T009 Isolated from Elaphodus davidianus Excrement

Two new cyclic tetrapeptides, cyclo(l ‐Val‐l ‐Leu‐l ‐Val‐l ‐Ile) ( 1 ) and cyclo(l ‐Leu‐l ‐Leu‐l ‐Ala‐l ‐Ala) ( 2 ), and 15 known compounds, cyclo(Gly‐l ‐Leu‐Gly‐l ‐Leu) ( 3 ), cyclo(l ‐Ser‐l ‐Phe) ( 4 ), cyclo(l ‐Leu‐l ‐Ile) ( 5 ), cyclo(l ‐Tyr‐l ‐Phe) ( 6 ), cyclo(Gly‐l ‐Trp) ( 7 ), cyclo(l ‐Leu‐l ‐Tyr) ( 8 ), cyclo(Gly‐l ‐Phe) ( 9 ), cyclo(l ‐Phe‐trans‐4‐hydroxy‐l ‐Pro) ( 10 ), cyclo(l ‐Leu‐l ‐Leu) ( 11 ), cyclo(l ‐Val‐l ‐Phe) ( 12 ), cyclo(l ‐Val‐l ‐Leu) ( 13 ), cyclo(l ‐Ile‐l ‐Ile) ( 14 ), cyclo(l ‐Tyr‐l ‐Tyr) ( 15 ), turnagainolide A ( 16 ), and bacimethrin ( 17 ) were isolated from the fermentation broth of Streptomyces rutgersensis T009 obtained from Elaphodus davidianus excrement. Their structures were identified on the basis of spectroscopic analysis. Meanwhile, the absolute configurations of the amino acid residues of compounds 1 and 2 were determined by advanced Marfey method. Compound 3 was obtained from a natural source for the first time. The X‐ray single crystal diffraction data of bacimethrin ( 17 ) were also reported for the first time. Compounds 1  –  17 exhibited no antimicrobial activities with the MICs > 100 μg/ml.     

Synthesis and Pharmacological Studies on a Cyclooligopeptide from Marine Bacteria

A natural proline‐rich tetrapeptide cyclo‐prolyl‐leucyl‐prolyl‐phenylalanyl was prepared employing solution‐phase method of peptide synthesis through coupling of dipeptide fragments Boc‐l‐Pro‐l‐Leu‐OH and l‐Pro‐l‐Phe‐OMe which utilizes diisopropylcarbodiimide (DIPC) as coupling agent and N‐methylmorpholine (NMM) as the base. Deprotection of linear tetrapeptide unit followed by its cyclization provided a cyclopeptide, identical in all aspects to the natural molecule. Pharmacological evaluation showed cytotoxic, antifungal and antihelmintic potential of synthesized peptide against Dalton's Lymphoma Ascites (DLA) and Ehrlich's Ascites Carcinoma (EAC) cell lines, pathogenic dermatophytes and earthworms.     

Synthesis and Solution Conformation of β‐Hairpin Mimetics Utilizing a Template Derived from (2S,3R,4R)‐Diaminoproline

A novel template was synthesized for stabilizing β‐hairpin conformations in cyclic peptide mimetics. The template is a diketopiperazine derived formally from L ‐aspartic acid and (2S,3R,4R)‐diaminoproline, the latter being available by an efficient synthetic route from vitamin C. The template was incorporated by solid‐phase peptide synthesis into a cyclic loop mimetic containing the sequence (‐Ala‐Asn‐Pro‐Asn‐Ala‐Ala‐template‐). This mimetic was shown by NMR to adopt a stable β‐hairpin conformation in (D₆)DMSO solution. The template may prove to be generally useful for creating small‐molecule mimetics of hairpin loops on proteins of diverse function.     

cis‐Peptide Bonds: A Key for Intestinal Permeability of Peptides?

Recent structural studies on libraries of cyclic hexapeptides led to the identification of common backbone conformations that may be instrumental to the oral availability of peptides. Furthermore, the observation of differential Caco‐2 permeabilities of enantiomeric pairs of some of these peptides strongly supports the concept of conformational specificity driven uptake and also suggests a pivotal role of carrier‐mediated pathways for peptide transport, especially for scaffolds of polar nature. This work presents investigations on the Caco‐2 and PAMPA permeability profiles of 13 selected N‐methylated cyclic pentaalanine peptides derived from the basic cyclo(‐D ‐Ala‐Ala₄‐) template. These molecules generally showed moderate to low transport in intestinal epithelia with a few of them exhibiting a Caco‐2 permeability equal to or slightly higher than that of mannitol, a marker for paracellular permeability. We identified that the majority of the permeable cyclic penta‐ and hexapeptides possess an N‐methylated cis‐peptide bond, a structural feature that is also present in the orally available peptides cyclosporine A and the tri‐N‐methylated analogue of the Veber–Hirschmann peptide. Based on these observations it appears that the presence of N‐methylated cis‐peptide bonds at certain locations may promote the intestinal permeability of peptides through a suitable conformational preorganization.     

Synthesis of Cyclohexapeptides Containing Pro and Aib Residues

Cyclization reactions on hexapeptides containing several α‐aminoisobutyric acid (=2‐amino‐2‐methylpropanoic acid; Aib) residues and the turn‐promoting glycine (Gly) and proline (Pro) residues were investigated. Eight linear hexapeptides were synthesized, and their cyclization was attempted with various coupling reagents. The macrolactamization step proved to be difficult since only three hexapeptides could be cyclized. Two of these latter peptides were the linear precursors of the same cyclic hexapeptide, cyclo(Aib‐Aib‐Phe‐Pro‐Aib‐Gly) ( 1 ). Surprisingly, they gave 1 in almost the same yield. Thus, 1 was obtained in 35% yield upon ring closure at the Phe/Pro site by using DEPBT as the coupling reagent, whereas the cyclization at the Aib/Phe site led to 1 in 28 and 34% yield by using PyAOP and DEPC, respectively (DEPBT=3‐[(diethoxyphosphoryl)oxy]‐1,2,3‐benzotriazin‐4(3H)‐one, PyAOP=(1H‐7‐azabenzotriazol‐1‐yloxy)tripyrrolidin‐1‐ylphosphonium hexafluorophosphate, DEPC=diethyl phosphorocyanidate). Another cyclic hexapeptide, cyclo(Aib‐Aib‐Gly‐Aib‐Pro‐Gly) ( 2 ) was prepared in 34% yield when DEPC was used in the cyclization step. The solid‐state conformation of 1 was established by X‐ray crystallography.     

cyclo(‐Cha–Oxz–d‐Val–Thz–Ile–Oxz–d‐Val–Thz‐) N,N‐di­methyl­acetamide dihydrate: a square form of cyclo­hexyl­alanine‐incorporated ascidiacycl­amide having the strongest cytotoxicity

The title compound, 1‐cyclo­hexyl­methyl‐1‐de(1‐methyl­propyl)­asci­dia­cycl­amide N,N‐di­methyl­acet­amide di­hy­drate, C₃₉H₅₆N₈O₆S₂·C₄H₉NO·2H₂O, a cyclo­hexyl­alanine‐incorporated ascidiacycl­amide analogue ([Cha]ASC), shows a square form similar to natural ASC. On the other hand, CD (circular dichroism) spectra showed [Cha]ASC to have a folded structure in solution, making it the second known analogue to show a discrepancy between its crystal and solution structures. Moreover, the cytotoxicity of [Cha]ASC (ED₅₀ = 5.6 µg ml⁻¹) was approximately two times stronger than that of natural ASC or a related phenyl­alanine‐incorporated analogue, viz. cyclo(‐Phe–Oxz–d ‐Val–Thz–Ile–Oxz–d ‐Val–Thz‐) ([Phe]ASC), and was confirmed to be associated with the square form. However, [Phe]ASC was previously shown to be folded in the crystal structure, which suggests that the difference between the aromatic and aliphatic rings affects the molecular folding of the ASC mol­ecule.     

Synthesis of Aib‐ and Phe(2Me)‐Containing Cyclopentapeptides

Some recently described pentapeptides containing the α,α‐disubstituted α‐amino acids Aib and Phe(2Me) have been cyclized in DMF solution using diphenyl phosphorazidate (DPPA), O‐(1H‐benzotriazol‐1‐yl)‐N,N,N′,N′‐tetamethyluronium tetrafluoroborate/1‐hydroxybenzotriazole (TBTU/HOBt), and diethyl phosphorocyanidate (DEPC), respectively, to give the corresponding cyclopentapeptides in fair‐to‐good yields. In the case of peptides with L ‐amino acids, and (R)‐ and (S)‐Phe(2Me), the yields differed significantly in favor of the L /(R) combination. The conformations in the crystals of cyclo(Gly‐Aib‐(R,S)‐Phe(2Me)‐Aib‐Gly) and cyclo(Gly‐(R)‐Phe(2Me)‐Pro‐Aib‐Gly) have been determined by X‐ray crystallography, leading to quite different results. In the latter case, the conformation in solution has been elucidated by NMR studies.     

Proton magnetic resonance studies of actinomycin-related peptides containing N-methyl groups

The PMR spectra of several cyclic and acyclic dipeptide derivatives representing portions of the actinomycin structure have been studied. In the spectra of the acyclic compounds temperature-dependent duplicity resulted from the equilibration of conformers possessing cis and trans peptide bonds. The lanthanide shift reagent Eu(FOD)₃ was utilized to distinguish N-methyl groups in the two conformations and observations were made on the steric dependence of the observed shifts. The origin of the wide variation in chemical shift of N-methylvalyl α-protons is discussed in relation to the conformation of actinomycin.     

Cyclopeptides and Amides from Pseudostellaria heterophylla (Caryophyllaceae)

From the roots of Pseudostellaria heterophylla, three cyclopeptides and three amides were isolated, besides heterophyllin A and B. Their structures were determined as cyclo (Ala‐Gly‐Pro‐Val‐Tyr‐) (heterophyllin J; 1 ), cyclo (Ala‐Gly‐Pro‐Tyr‐Leu‐) (pseudostellarin A; 2 ), cyclo (Gly‐Gly‐Gly‐Pro‐Pro‐Phe‐Gly‐Ile‐) (pseudostellarin B; 3 ), methyl γ‐hydroxypyroglutamate ( 4 ), methyl pyroglutamate ( 5 ), and pyroglutamic acid ( 6 ) on the basis of spectral data, especially 2D‐NMR data. Among them, compounds 1 and 4 are new compounds.     

Conformational Analysis of the Cyclic Pentadepsipeptide Cyclo(Tro‐Aib‐Aib‐Aib‐Aib) in the Solid State and in Solution

The cyclic 16‐membered pentadepsipeptide cyclo(Tro‐Aib‐Aib‐Aib‐Aib) ( 1 ) was crystallized from MeOH/AcOEt/CH₂Cl₂, and its structure was established by X‐ray crystallography (Fig. 1). There are two symmetry‐independent molecules with different conformations in the asymmetric unit. Two intramolecular H‐bonds stabilize two β‐turns in each molecule. On the other hand, two of the four Aib residues are forced to assume a nonfavorable nonhelical conformation in each of the symmetry‐independent molecules (Table 1). The conformational study in CDCl₃ solution by NMR spectroscopy and molecular dynamics (MD) simulations indicate that the averaged structure (Fig. 3) is almost the same as in the solid state.     

Microwave‐Assisted Synthesis of β‐Lactams and Cyclo‐β‐dipeptides

Different cyclo‐β‐dipeptides were prepared from corresponding N‐substituted β‐alanine derivatives under mild conditions using PhPOCl₂ as activating agent in benzene and Et₃N as base. To evaluate β³‐substituent influence, the amino acids 7 – 26 were synthesized, and a β‐lactam formation reaction was carried out instead of cyclo‐β‐dipeptide formation. The crystal structures of three derivatives of cyclo‐β‐peptides and one β‐lactam are presented.     

Designed Beta‐Turn Mimic Based on the Allylic‐Strain Concept: Evaluation of Structural and Biological Features by Incorporation into a Cyclic RGD Peptide (Cyclo(‐L‐arginylglycyl‐L‐α‐aspartyl‐))

The (3R,5S,6E,8S,10R)‐11‐amino‐3,5,8,10‐tetramethylundec‐6‐enoic acid (ATUA; 1 ), which was designed as a βII′‐turn mimic according to the concepts of allylic strain and 2,4‐dimethylpentane units, was incorporated into a cyclic RGD peptide. The three‐dimensional structure of cyclo(‐RGD‐ATUA‐) (=cyclo(‐Arg‐Gly‐Asp‐ATUA‐)) 4 in H₂O was determined by NMR techniques, distance geometry calculations and molecular‐dynamics simulations. The RGD sequence of 4 shows high conformational flexibility but some preference for an extended conformation. The structural features of the RGD sequence of 4 were compared with the RGD moiety of cyclo(‐RGDfV‐) (=cyclo(‐Arg‐Gly‐Asp‐D ‐Phe‐Val‐)). In contrast to cyclo(‐RGDfV‐), which is a highly active αvβ3 antagonist and selective against αIIbβ3, cyclo(‐RGD‐ATUA‐) shows a lower activity and selectivity. The structure of the ATUA residue in the cyclic peptide resembles a βII′‐turn‐like conformation. Its middle part, adjacent to the C?C bond, strongly prefers the designed and desired structure.     

β‐Turn Analogues in Model αβ‐Hybrid Peptides: Structural Characterization of Peptides Containing β2,2Ac6c and β3,3Ac6c Residues

The effect of gem‐dialkyl substituents on the backbone conformations of β‐amino acid residues in peptides has been investigated by using four model peptides: Boc‐Xxx‐β^2,2Ac₆c(1‐aminomethylcyclohexanecarboxylic acid)‐NHMe (Xxx=Leu ( 1 ), Phe ( 2 ); Boc=tert‐butyloxycarbonyl) and Boc‐Xxx‐β^3,3Ac₆c(1‐aminocyclohexaneacetic acid)‐NHMe (Xxx=Leu ( 3 ), Phe ( 4 )). Tetrasubstituted carbon atoms restrict the ranges of stereochemically allowed conformations about flanking single bonds. The crystal structure of Boc‐Leu‐β^2,2Ac₆c‐NHMe ( 1 ) established a C₁₁ hydrogen‐bonded turn in the αβ‐hybrid sequence. The observed torsion angles (α(?≈?60°, ψ≈?30°), β(?≈?90°, θ≈60°, ψ≈?90°)) corresponded to a C₁₁ helical turn, which was a backbone‐expanded analogue of the type III β turn in αα sequences. The crystal structure of the peptide Boc‐Phe‐β^3,3Ac₆c‐NHMe ( 4 ) established a C₁₁ hydrogen‐bonded turn with distinctly different backbone torsion angles (α(?≈?60°, ψ≈120°), β(?≈60°, θ≈60°, ψ≈?60°)), which corresponded to a backbone‐expanded analogue of the type II β turn observed in αα sequences. In peptide 4 , the two molecules in the asymmetric unit adopted backbone torsion angles of opposite signs. In one of the molecules, the Phe residue adopted an unfavorable backbone conformation, with the energetic penalty being offset by a favorable aromatic interaction between proximal molecules in the crystal. NMR spectroscopy studies provided evidence for the maintenance of folded structures in solution in these αβ‐hybrid sequences.     

Cocrystal of cis‐ and trans‐N‐phenylformamide

N‐Phenylformamide, C₇H₇NO, crystallizes with two molecules in the asymmetric unit which have different conformations of the formylamino group, one being cis and the other trans. This is the first example of an arylformamide crystal containing both conformational isomers and it may thus be considered a cocrystal of the two conformers. The two molecules in the unit cell are linked through N—H...O hydrogen bonding to two other molecules, thereby forming hydrogen‐bonded tetramers within the crystal structure.     

β-Loop, γ-loop,and helical peptide conformations in cyclopeptides containing a steroidal pseudo-amino acid

The steroidal pseudo-amino acids 3ã-amino-5β-cholan-24-oic acid ( 2a ), 12ã-acetoxy-3ã-ammonia-5β-cholan-24-oic acid ( 2b ), and 7ã,12ã-diacetoxy-3ã-amino-5β-cholan-24-oic acid ( 2c ) are used as rigid spacers in the backbone of the cyclic peptides cyclo(– 2a –Phe-Phe–)₂ ( 1a ), cyclo(– 2b –Phe-Phe–)₂ ( 1b ), and cyclo(–2c-Phe-Phe–)₂ ( 1c ). A homogeneous β-loop conformation is found in the peptide chains of 1a and 1b , while 1c exists as a mixture of ã-helical and γ-loop conformations. The structure and homogeneity of the conformations are established by several NMR techniques and are supported by molecular-dynamics calculations. The peptide conformations depend on the distance and attraction of the two large and lipophilic steroidal parts of the cyclic molecules.     

Synthesis,Conformation, and Interactions with Small Molecules of Bis (Cyclic Dipeptides)

Bis (cyclic dipeptides), cyclo and S, S ′-bis(cyclo(hemiCys-Pro)), were synthesized. These bis (cyclic dipeptides) very efficiently formed complexes with Ba²⁺ and Na⁺ owing to intramolecular cooperation of two cyclicdipeptide moieties, the bis-effect. Cyclo stacked sodium 8-anilino-1-naphthalensulfonate in aqueous solution. These properties of complexation were controlled by the nature of the bridge connecting two cyclic dipeptide moieties. The geometry of the complex between S, S′-bis (cyclo (hemiCys-Pro)) and metal ion was investigated with the help of circular dichroism, nuclear magnetic resonance, and Raman spectroscopy.