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.     

Synthesis of Conformationally Restricted Cyclic Hexadepsipeptides via Direct Amide Cyclization

Ring closure by direct amide cyclization was used in the synthesis of 19‐membered cyclic depsipeptides 27 (Schemes 1 and 3). The linear hexapeptide precursors 4 , containing the β‐hydroxy acid 3‐hydroxy‐2‐phenylpropanoic acid (Tro), and five α‐amino acids of the type Aib, Gly, and Pro, were prepared according to Scheme 2. The α,α‐disubstituted α‐amino acid Aib was incorporated into the peptide chain via the azirine/oxazolone method, and Gly and Pro were introduced by using the TBTU/HOBt coupling method. The cyclic depsipeptides 27a – 27f were obtained in reasonable‐to‐excellent yields (Scheme 3 and Table 1).     

Studies on Synthesis of a Cycloheptapeptide and Effects of Different Metal Ions on the Cyclization

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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.     

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.     

Synthesis of a Derivative of the Peptaibol‐Antibiotic Trichovirin I 1B by Means of the ‘Azirine/Oxazolone Method’

According to the earlier published synthesis of the C‐terminal nonapeptide of Trichovirin I 1B, Z‐Ser(^tBu)‐Val‐Aib‐Pro‐Aib‐Leu‐Aib‐Pro‐Leuol ( 5 ), the complete tetradecapeptide Z‐Aib‐Asn(Trt)‐Leu‐Aib‐Pro‐Ser(^tBu)‐Val‐Aib‐Pro‐Aib‐Leu‐Aib‐Pro‐Leuol ( 11b ), a protected Trichovirin I 1B, has now been prepared by means of the ‘azirine/oxazolone method’. With the exception of the N‐terminal Aib(1), all Aib residues were introduced by the coupling of the corresponding amino or peptide acids with 2,2‐dimethyl‐2H‐azirine‐3‐(N‐methyl‐N‐phenylamine) ( 1a ) and methyl N‐(2,2‐dimethyl‐2H‐azirin‐3‐yl)‐L ‐prolinate ( 3a ) as the Aib and Aib‐Pro synthons, respectively. Single crystals of two segments, i.e., the N‐terminal hexapeptide Z‐Aib‐Asn(Trt)‐Leu‐Aib‐Pro‐Ser(^tBu)‐OMe ( 23 ) and the C‐terminal octapeptide Z‐Val‐Aib‐Pro‐Aib‐Leu‐Aib‐Pro‐Leuol ( 17 ), were obtained and their structures have been established by X‐ray crystallography. Following the same strategy, the C‐terminal nonapeptide of Trichovirin I 4A, Z‐Ala‐Val‐Aib‐Pro‐Aib‐Leu‐Aib‐Pro‐Leuol ( 26 ), was also synthesized and characterized by X‐ray crystallography.     

Synthesis and conformational analysis of 18-membered Aib-containing cyclohexapeptides

The synthesis and conformational analysis of two Aib-containing cyclic hexapeptides, cyclo(Gly-Aib-Leu-Aib-Phe-Aib) 1 and cyclo(Leu-Aib-Phe-Gly-Aib-Aib) 2, is described. The linear precursors of 1 and 2 were prepared using solution phase techniques, and the cyclization efficiency of three different coupling reagents (HATU, PyAOP, DEPC) was examined. The success of the cyclization was found to be reagent dependent. Solid-state conformational analysis of 1 and 2 was performed by X-ray crystallography and has revealed some unusual features as all three Aib residues of 1 assume nonhelical conformations. Furthermore, the residue Aib⁴ adopts an extended conformation (?=−175.9(3)°, ψ=+178.6(2)°), which is, to the best of our knowledge, the first observation of an Aib residue adopting an extended conformation in a cyclopeptide. The structure of 1 is also a rare example in which an Aib residue occupies the (i+1) position of a type II′ β-turn, stabilized by a bifurcated hydrogen bond. The cyclic peptide 2 adopts a more regular conformation in the solid state, consisting of two fused β-turns of type I/I′, stabilized by a pair of intramolecular hydrogen bonds. In addition, the conformational study of the cyclic peptide 1 in DMSO-d₆ by NMR spectroscopy and molecular dynamics simulations revealed a structure, which is very similar to its structure in the crystalline state.     

Synthesis of Cyclopentapeptides with Three to Five Aib Units

Four new Aib‐containing cyclopentapeptides have been synthesized by cyclization of the corresponding linear pentapeptides using the diethyl phosphorocyanidate (DEPC)/EtN(ⁱPr)₂ method. The linear precursors were prepared via the ‘azirine/oxazolone method’, i.e., the Aib units were introduced by the reaction of amino acids or peptide acids with a 2,2‐dimethyl‐2H‐azirin‐3‐amine, followed by selective hydrolysis of the terminal amide function. Most remarkably, cyclo[(Aib)₅] exists in CDCl₃ solution in a symmetrical conformation, i.e., no intramolecular H‐bonds are detectable.     

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.     

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.     

Effective synthesis of cyclic peptide yunnanin C and analogues via Ser/Thr ligation (STL)-mediated peptide cyclization

Cyclic peptide yunnanin C isolated from the root of Stellaria yunnanensis was efficiently synthesized in which the linear peptide was prepared by Boc-SPPS and the cyclization was realized by serine/threonine ligation (STL)-mediated cyclization. In addition, nine yunnanin C analogues, including mutations of Tyr7Gly, Tyr7Val, Tyr7Pro, Tyr7Phe, Ser1Thr, Pro2Val, Gly5Pro, Phe6Ala and Ile4Ala, were prepared in the same fashion. Here, we demonstrated that STL-mediated peptide cyclization could be an effective approach to construct cyclic peptides. Except that proline at the C-terminus could retard the cyclization process, cyclization of yunnanin C analogues with various C-terminal amino acids proceeded with fast cyclization rate (<4 h) and only trace amount of dimers (<5%) at a working concentration of 5 mM.     

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.     

Synthesis of Aib‐Pro Oligopeptides by Repeated Azirine Coupling with the Aib‐Pro Synthon

A new synthesis of (Aib‐Pro)_n oligopeptides (n=2, 3, and 4) via azirine coupling by using the dipeptide synthon methyl N‐(2,2‐dimethyl‐2H‐azirin‐3‐yl)‐L ‐prolinate ( 1b ; Fig. 1) is presented. The most important feature of the employed protocol is that no activation of the acid component is necessary, i.e., no additional reagents are required, and the coupling reaction is performed under mild conditions at room temperature. As an attempt to provide an answer to the question of the preferred conformation of the prepared molecules, we carried out experiments by using NMR techniques and X‐ray crystallography. For example, in the case of the hexapeptide 11 , it was possible to compare the conformations in the crystalline state and in solution. After the selective hydrolysis of the methyl ester p‐BrBz‐(Aib‐Pro)₄‐OMe ( 13 ) under basic conditions, the corresponding octapeptide acid was obtained, which was then converted into the octapeptide amide p‐BrBz‐(Aib‐Pro)₄‐NHC₆H₁₃ ( 15 ) by using standard coupling conditions and activating reagents (HOBt/TBTU/DIEA) of the peptide synthesis. The conformation of this compound, as well as those of the tetrapeptides 14 and 18 , was also established by X‐ray crystallography and in solution by NMR techniques. In the crystalline state, a β‐bend ribbon structure is the preferred conformation, and similar conformations are formed in solution.     

The ‘Azirine/Oxazolone Approach’ to the Synthesis of Aib‐Pro Endothiopeptides

The reaction of methyl N‐(2,2‐dimethyl‐2H‐azirin‐3‐yl)‐L ‐prolinate ( 2a ) with thiobenzoic acid at room temperature gave the endothiopeptide Bz‐AibΨ[CS]‐Pro‐OMe ( 7 ) in high yield. In an analogous manner, (benzyloxy)carbonyl (Z)‐protected proline was transformed into the thioacid, which was reacted with 2a to give the endothiotripeptide Z‐Pro‐AibΨ[CS]‐Pro‐OMe ( 12 ). The corresponding thioacid of 7 was prepared in situ via saponification, formation of a mixed anhydride, and treatment with H₂S. A second reaction with 2a led to the endodithiotetrapeptide 9 , but extensive epimerization at Pro² was observed. Similarly, saponification of 12 and coupling with either 2a or H‐Phe‐OMe and 2‐(1H‐benzotriazol‐1‐yl)‐1,1,3,3‐tetramethyluronium tetrafluoroborate/1‐hydroxy‐1H‐benzotriazole (TBTU/HOBt) gave the corresponding endothiopeptides as mixtures of two epimers. The synthesis of the pure diastereoisomer BzΨ[CS]‐Aib‐Pro‐AibΨ[CS]‐N(Me)Ph ( 21 ) was achieved via isomerization of 7 to BzΨ[CS]‐Aib‐Pro‐OMe ( 16 ), transformation into the corresponding thioacid, and reaction with N,2,2‐trimethyl‐N‐phenyl‐2H‐azirin‐3‐amine ( 1a ). The structures of 12 and 21 were established by X‐ray crystallography.     

β‐Hairpins Generated from Hybrid Peptide Sequences Containing both α‐ and β‐Amino Acids

The incorporation of the β‐amino acid residues into specific positions in the strands and β‐turn segments of peptide hairpins is being systematically explored. The presence of an additional torsion variable about the C(α) C(β) bond (θ) enhances the conformational repertoire in β‐residues. The conformational analysis of three designed peptide hairpins composed of α/β‐hybrid segments is described: Boc‐Leu‐Val‐Val‐^DPro‐β Phe ‐Leu‐Val‐Val‐OMe ( 1 ), Boc‐Leu‐Val‐β Val ‐^DPro‐Gly‐β Leu ‐Val‐Val‐OMe ( 2 ), and Boc‐Leu‐Val‐β Phe ‐Val‐^DPro‐Gly‐Leu‐β Phe ‐Val‐Val‐OMe ( 3 ). 500‐MHz ¹H‐NMR Analysis supports a preponderance of β‐hairpin conformation in solution for all three peptides, with critical cross‐strand NOEs providing evidence for the proposed structures. The crystal structure of peptide 2 reveals a β‐hairpin conformation with two β‐residues occupying facing, non‐H‐bonded positions in antiparallel β‐strands. Notably, βVal(3) adopts a gauche conformation about the C(α) C(β) bond (θ=+65°) without disturbing cross‐strand H‐bonding. The crystal structure of 2 , together with previously published crystal structures of peptides 3 and Boc‐β Phe ‐β Phe ‐^DPro‐Gly‐β Phe ‐β Phe ‐OMe, provide an opportunity to visualize the packing of peptide sheets with local ‘polar segments' formed as a consequence of reversal peptide‐bond orientation. The available structural evidence for hairpins suggests that β‐residues can be accommodated into nucleating turn segments and into both the H‐bonding and non‐H‐bonding positions on the strands.     

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.     

Cyclic RGD Peptides Containing Azabicycloalkane Reverse‐Turn Mimics

The Fmoc‐protected lactams 3 and 4 were used to prepare cyclo(Arg‐Gly‐Asp‐lactam) 1 and cyclo(Arg‐Gly‐Asp‐Phe‐lactam) 2 , which contain the Arg‐Gly‐Asp (RGD) recognition motif. Their solid‐phase synthesis, conformational analysis, and binding to purified α_Vβ₃ and α_Vβ₅ integrins are reported. Compound 1 was found to act as an active and selective inhibitor of the α_Vβ₅ integrin.     

Conformational studies on peptides containing α,α-disubstituted α-amino acids: chiral cyclic α,α-disubstituted α-amino acid as an α-helical inducer

Four types of α,α-disubstituted amino acids {i.e., α-aminoisobutyric acid (Aib), 1-aminocyclopentanecarboxylic acid (Ac(5)c), (3S,4S)-1-amino-(3,4-dimethoxy)cyclopentanecarboxylic acid [(S,S)-Ac(5)c(dOM)] and its enantiomer (R,R)-Ac(5)c(dOM)} were introduced into l-leucine-based hexapeptides and nonapeptides. The dominant conformations of eight peptides: Cbz-(L-Leu-L-Leu-dAA)(2)-OMe [dAA = 1: Aib; 2: Ac(5)c; 3: (S,S)-Ac(5)c(dOM); 4: (R,R)-Ac(5)c(dOM)] and Boc-(L-Leu-L-Leu-dAA)(3)-OMe [dAA = 5: Aib; 6: Ac(5)c; 7: (S,S)-Ac(5)c(dOM); 8: (R,R)-Ac(5)c(dOM)], were investigated by IR, CD spectra and X-ray crystallographic analysis. The CD spectra revealed that Aib hexapeptide 1 and Ac(5)c hexapeptide 2 formed right-handed (P) 3(10)-helices, while Ac(5)c(dOM) hexapeptides 3 and 4 formed a mixture of (P) 3(10)- and α-helices. The Aib nonapeptide 5 formed a (P) 3(10)-helix, the Ac(5)c nonapeptide 6 formed a mixture of (P) 3(10)- and α-helices, and the Ac(5)c(dOM) nonapeptides 7 and 8 formed (P) α-helices. X-Ray crystallographic analysis revealed that the Aib hexapeptide 1 formed a (P) 3(10)-helix, while (S,S)-Ac(5)c(dOM) hexapeptide 3 formed a (P) α-helix. In addition, the Ac(5)c nonapeptide 6 and (R,R)-Ac(5)c(dOM) nonapeptide 8 formed (P) α-helices. The Aib and achiral Ac(5)c residues have the propensity to form 3(10)-helices in short peptides, whereas the chiral Ac(5)c(dOM) residues have a penchant for forming α-helices.     

Solid-phase synthesis of cyclic hexapeptides wollamides A,B and desotamide B

Solid-phase synthesis of antibacterial cyclohexapeptides including wollamides A, B and desotamide B has been developed. Briefly, the protected linear hexapeptides were assembled on 2-chlorotrityl chloride resin using standard Fmoc chemistry and diisopropylcarbodiimide/hydroxybenzotriazole coupling reagents, cleaved off-resin with hexafluoroisopropanol/dichloromethane to keep side-chain protecting groups intact, and cyclized in solution. Final global removal of all protecting groups using a cocktail of trifluoroacetic acid/triisopropylsilane/dichloromethane afforded the desired cyclic hexapeptides, which were characterized by ¹H, ¹³C NMR, and HRMS. Subsequent investigation of macrocyclization parameters such as terminal residues, coupling reagents, and cyclization concentration revealed the optimized conditions for the synthesis of this class of cyclic hexapeptides.     

Novel immonium type peptide coupling reagent: 5‐(1H‐benzotriazol‐1‐yloxy)‐3,4‐dihydro‐1‐methyl 2H‐pyrrolium hexachloroantimonate (BDMP® )

A novel immonium type coupling reagent, 5‐(1H‐benzotriazol‐1‐yloxy)‐3,4‐dihydro‐1‐methyl 2H‐pyrrolium hexachloroantimonate (BDMP) has been designed, synthesized and utilized to synthesize oligopeptides and biologically active peptide both in solution and solid phase with satisfactory yield, low racemization and fast reaction rate. The estimation of racemization and the influence of several reaction parameters were studied by HPLC method using the model reaction: Z‐Gly‐Phe‐OH + Val‐OMe·HCl·Z‐Gly‐D/L‐Phe‐Val‐OMe. It was shown that the reactivity of BDMP was much higher and the racemization was much lower than those of HOBt‐based ‘onium’ reagents, even though its analogues BOMI. To further verified me effectiveness of BDMP, Leu‐enkephalin was synthesized both in solution and solid phase using BDMP as coupling reagent. The proposed mechanism was also speculated.