Solid-state conformation of diastereomeric -Pro-Pro-(Aib)4 sequences

The crystal structures of two diastereomeric -Pro-Pro-(Aib)₄- sequences, Cbz-l-Pro-l-Pro-(Aib)₄-OMe (1) and Cbz-d-Pro-l-Pro-(Aib)₄-OMe (2), have been determined by X-ray crystallographic analysis. The crystals of the two compounds were characterized by the following parameters: (1) monoclinic, P2₁, a=10.543 Å, b=8.103 Å, c=22.642 Å, β=97.679, Z=2, R₁=0.104, and R_w=0.327; (2) orthorhombic, P2₁2₁2₁, a=10.470 Å, b=10.953 Å, c=32.405 Å, Z=4, R₁=0.040, and R_w=0.046. In the asymmetric unit of 1, the homochiral l-Pro¹-l-Pro² adopts a polyproline II structure, which induces a left-handed (M) 3₁₀-helical structure in the following -(Aib)₄- sequence. The preferred conformation of diastereomeric 2, which contains heterochiral d-Pro¹-l-Pro² segments, was similar to that of 1 with differences at the N-terminal d-Pro residue.     

Studies of β-turn opening with model peptides containing non-coded α-amino isobutyric acid

Single crystal X-ray diffraction studies show that among the three terminally protected model tripeptides I-III, Boc-Ile-Aib-Xx-OMe (Xx in peptide I: Val; II: Leu; III: Phe) with a centrally placed non-coded amino acid Aib (Aib: α-amino isobutyric acid), peptide I displays a conformational preference for β-turn, peptide II forms a hydrated β-turn representing the solvent mediated intermediate for the interconversion between β-turn and β-strand and peptide III adopts a completely unfolded β-strand like structure. By varying the steric bulk of the third residue, Xx(3), various conformations related to the structural interconversion between the β-turn and β-strand have been isolated. The peptide conformations in the solution phase have been probed by solvent dependent NMR titration and CD spectroscopy. Morphological studies with scanning electron microscopy (SEM) reveal that among the three peptides only peptide III can form filamentous fibrils in the solid state.     

Solid-phase synthesis of backbone-cyclized β-helical peptides

This paper describes the synthesis and purification of two 22-residue cyclic peptides, cyclo{[(l-Val-d-Val)₄-(l-Val-d-Pro-Gly)]₂-} 3 and cyclo{[(d-Leu-l-Leu)₄-(d-Leu-l-Pro-Gly)]₂-} 4, that were designed to fold into double-stranded antiparallel β-helical structures. Due to intramolecular hydrogen bonding and the conformational constraints imposed by the two reverse-turn segments (d-Pro-Gly and l-Pro-Gly, respectively), the linear precursors to 3 and 4 (lin-3 and lin-4) were expected to adopt preorganized conformations that would bring the N and C termini close together and thereby favor ring closure. Precursors lin-3 and lin-4 were constructed by stepwise Boc solid-phase peptide synthesis using the commercially available alkanesulfonamide ‘safety-catch’ linker and cyclized head-to-tail via the method of cleavage-by-cyclization. The crude cyclic peptides were highly hydrophobic and contained minor impurities that could not be removed solely by reversed-phase HPLC (RP-HPLC); however, two-step purification—first by RP-HPLC with i-PrOH/water gradients, followed by gel-permeation chromatography (GPC) on Sephadex LH-20 with CHCl₃/MeOH—afforded both peptides in pure form (≥95% by ¹H NMR) and in acceptable yield (23%). Subsequent ¹H NMR experiments supported the expected structures of 3 and 4. The successful formation of the 66-membered rings of 3 and 4 is consistent with the notion of conformational preorganization in the linear precursors; furthermore, the protocols for synthesis and purification described should prove useful for preparing additional cyclic β-helical peptides, including longer peptides and peptides having polar residues.     

Lewis acid-catalyzed synthesis of dodecamethoxycalix[4]arene from 1,3,5-trimethoxybenzene and its conformational behavior and host-guest property

Lewis acid-catalyzed condensation of 1,2- and 1,3-dimethoxybenzenes with paraformaldehyde afforded an ortho-bridged cyclic trimer (1) and a meta-bridged cyclic tetramer (2), respectively. Furthermore, condensation of 1,3,5-trimethoxybenzene with paraformaldehyde in the presence of Lewis acid catalyst successfully rendered the first dodecamethoxy-substituted calix[4]arene (3) with high yield. From X-ray crystallography, it was found that 3 formed the partial cone conformation. The conformational behavior of 3 in the solution was investigated by variable temperature ¹H NMR measurements. The partial cone structure observed in the solid state was retained in the solution at low temperatures. Furthermore, because of the slow conformational exchanges of 3 on the NMR time scale, bimodal conformational exchanges were found. The host-guest property of 3 with the electron accepting guest, tetracyanoethylene (TCNE) was examined by UV-Vis measurements, and the ability to associate with the 3-TCNE complex was three times higher than that of the 2-TCNE complex. The observation is due to the superior electron donating property and slow conformational exchanges of 3 compared with those of analogous 2.     

Cyclic tetrapeptides from marine bacteria associated with the seaweed Diginea sp. and the sponge Halisarca ectofibrosa

A Pseudomonas sp. was cultured which was associated with the Japanese seaweed Diginea sp. Crude extracts prepared from this bacterial culture were found to inhibit the growth of other marine bacterial strains. From this bacterial culture, two new peptides cyclo-[phenylalanyl-prolyl-leucyl-prolyl] (3) and cyclo-[isoleucyl-prolyl-leucyl-alanyl] (4) have been isolated together with two known peptides (1) and (2). The crude extract from a culture of Pseudoalteromonas sp. associated with the Thai sponge Halisarca ectofibrosa was found to inhibit the growth of Bacillus subtilis and Vibrio anguillarum. Isolation studies yielded a fraction containing two peptides that were identified as cyclo-[phenylalanyl-leucyl]₂ (5) and cyclo-[leucyl-isoleucyl]₂ (6) by means of LC-MS and 2D NMR data. Absolute stereochemistry was confirmed by the synthesis of cyclo-[l-phenylalanyl-l-leucyl]₂. Peptides (1)-(3) were also isolated from this bacterial strain. None of the individual peptides isolated in this study showed antibiotic activity.     

Nucleation of β-hairpin structure in a pyrrole amino acid containing peptide

Synthesis and conformational studies of two short peptides containing pyrrole amino acids (1, Paa), Boc-Paa-Paa-d-Pro-Gly-Xaa-Paa-Paa-OMe (2: Xaa=Ala; 3: Xaa=Val), were carried out in which it was established that replacement of Ala in 2 with a Val residue helps peptide 3 to adopt a well-defined β-hairpin conformation in a nonpolar solvent, like CDCl₃.     

An innovative approach to the synthesis of annelated [a]diaza-anthracenones through tandem cyclization

An innovative route for the synthesis of a novel class of 4-aryl-11-oxo-1,2,3,11-tetrahydro-1,3a-diazacyclopenta[a]anthracene-6-carbonitriles 5a-h and 5-aryl-12-oxo-1,3,4,12-tetrahydro-2H-1,4a-diazabenzo[a]anthracene-7-carbonitriles 5i-k has been developed by ring transformation of suitably functionalized 2H-pyran-2-ones 1 with α-oxoketene cyclic aminals 2 to give compounds 4 followed by photo-induced cyclization.     

Conformational behavior of dithia[n.3.3](1,3,5)cyclophanes and dithia[n.3.3](1,2,6)cyclophanes

The conformational behavior of a series of crown-fused dithia[n.3.3](1,2,6)cyclophanes (126-CPs) and dithia[n.3.3](1,3,5)cyclophanes (135-CPs) was investigated by variable-temperature ¹H and ¹³C NMR spectroscopy, X-ray crystallography and density functional theory (DFT) calculations. Single crystal X-ray structure analysis showed that two thia-bridges in 126-CPs adopted a pseudochair-pseudochair (cc) conformation and the cyclophane decks underwent a ring-tilting motion in the case of [10.3.3](1,2,6)cyclophane (1a). In contrast, the thia-bridges in 135-CPs took both cc and pseudoboat-pseudochair (bc) conformations, and the ring-tilting process was also found in [10.3.3](1,3,5)cyclophane (2a). Variable temperature ¹H NMR study revealed that there was no wobbling-motion for two thia-bridges in 126-CPs while thia-bridges in 135-CPs experienced a wobbling-process with a conformational barrier of 9.21 and 8.80 kcal mol⁻¹, respectively, for 2a and [13.3.3](1,3,5)cyclophane (2b). DFT calculations for the two cyclophanes series revealed that 126-CPs preferred a cc conformation which was consistent with the experimental observation; similarly, 135-CPs took a preferential cc conformation, agreeing with 2a having a predominant cc conformer (cc:bc ratio=70:30), but not 2b having a predominant bc conformer (cc:bc ratio=15:85) in the solid state.     

Total synthesis of ulongamide A, a cyclic depsipeptide isolated from marine cyanobacteria Lyngbya sp.

A total synthesis of ulongamide A (1), a cytotoxic natural cyclic depsipeptide, was achieved by a convergent route involving coupling of the fragments 7 and 8 to the pentapeptide 24, and subsequent cyclization thereof after prior removal of the t-Boc protecting groups.     

Nucleation of the β-hairpin structure in a linear hybrid peptide containing α-, β- and γ-amino acids

Synthesis and conformational studies of a short linear peptide containing a pyrrole amino acid (1, Paa) and a furan amino acid (2, Faa), namely Boc-hGly-Faa-d-Pro-Gly-Paa-hGly-Faa-OMe (3), were carried out in which it was established that peptide 3 adopted a well-defined β-hairpin structure in DMSO-d₆.     

A new approach to cyclic hydroxamic acids: Intramolecular cyclization of N-benzyloxy carbamates with carbon nucleophiles

N-Alkyl-N-benzyloxy carbamates, 2, undergo facile intramolecular cyclization with a variety of carbon nucleophiles to give functionalized five- and six-membered protected cyclic hydroxamic acids, 3, in good to excellent yields. This method can be extended to prepare seven-membered cyclic hydroxamic acids in moderate yields. The sulfone intermediates 3 from this study can be alkylated while the corresponding phosphonates have been shown to undergo HWE reaction. The α,β-unsaturated synthon, 8, prepared by thermal elimination of sulfoxide 3m, undergoes Michael addition with secondary amines. The usefulness of this approach to prepare polydentate chelators has been demonstrated by the synthesis of bis cyclic hydroxamic acids 12, 14, and 15.     

Stereoselective synthesis of 2-methylenepyrrolizidines by tandem cyclization of N-propargylaminyl radicals

Tandem cyclization of N-propargylaminyl radicals, generated by N-chlorination of (E)-alk-4-enylamines 2a-d and 2f followed by treatment with tributyltin radical, afforded 2-methylenepyrrolizidines 3a-d and 3f in a highly stereoselective manner. A similar radical cyclization of (Z)-N-propargyl-1-methyl-5-phenylpent-4-enylamine (2e) gave pyrrolizidine 3b having the same stereochemistry as that obtained from the E isomer 2b.     

Easy access to 4-nitrothiochroman S,S-dioxides via ring-enlargement from 3-nitrobenzo[b]thiophene

The (E)-2-aryl-1-[2-(methylthio)phenyl]-1-nitroethylenes 5 can easily be oxidized to the relevant sulfones 6 and effectively subjected to cyclization via an intramolecular Michael addition after metallation with lithium bis(trimethylsilyl)amide in THF. After quenching with ammonium chloride the 3-aryl-4-nitrothiochroman S,S-dioxides 2 are obtained as diastereomeric mixtures in good to excellent yields. Both yields and stereochemistry of the ring-closure step appear to be influenced by steric effects of the 3-aryl moiety. As sulfides 5 derive from an initial ring opening of 3-nitrobenzo[b]thiophene (1), the overall 1 to 2 process can be considered as an effective 5 to 6 ring enlargement of the sulfur heterocycle. A conformational ¹H NMR and molecular-mechanics investigation on the isolated diastereomeric 2 has also been accomplished.     

Efficient synthesis of trypsin inhibitor SFTI-1 via intramolecular ligation of peptide hydrazide

Cyclic peptide trypsin inhibitor SFTI-1 was synthesized via intramolecular ligation of a linear peptide hydrazide with high yield. This cyclization strategy did not cause epimerization at the C-terminal Arg residue. CD spectrum and NMR spectroscopy analysis demonstrated that well-folded SFTI-1 could be obtained via standard oxidative folding process. Thus, we present a simple and cost-efficient strategy for the synthesis of SFTI-1.     

The synthesis of compounds related to the indole-indoline core of the vinca alkaloids (+)-vinblastine and (+)-vincristine

A series of α′-aryl-α′-carbomethoxycycloalk-2-en-1-ones, 16, has been prepared using the Pinhey arylation methodology for introducing the aromatic residue. Subjection of these compounds to Johnson iodination and Pd[0]-catalyzed Ullmann cross-coupling of the resulting α-iodocycloalkenones 11 with 2-iodonitrobenzene (5, X = I) then affords α,α′-diaryl-α′-carbomethoxycycloalk-2-en-1-ones of the general form 10. Reductive cyclization of this last type of compound gives the corresponding indoles 9a-f (n = 1-3), some of which resemble the indole-indoline cores of the clinically important alkaloids (+)-vinblastine (1) and (+)-vincristine (2).     

9,21,22-Triaza-2,11-dithia[3.3](2,6)pyridino(2,9)phenanthrolinophane: a five-donor macrocycle functioning as a bidentate ligand

9,21,22-Triaza-2,11-dithia[3.3](2,6)pyridino(2,9)phenanthrolinophane 4 was prepared from a cyclization reaction of 2,6-bis(mercaptomethyl)pyridine 5 and 2,9-bis(bromomethyl)phenanthroline 6. Results from ¹H NMR analysis are inconclusive but those derived from semi-empirical molecular orbital PM3 calculations support a preference for a syn conformation for 4. The conformation barrier for interconversion between two syn isomers of 4 was estimated to be 36.5 kJ mol⁻¹ on the basis of a dynamic ¹H NMR study. The manganese(II) and zinc(II) complexes of 4 were prepared and the metal to ligand ratios were found to be 1:1 and 2:1, respectively, by elemental analyses. Results from an ¹H NMR analysis of the zinc(II) complex of 4 suggest that only the two nitrogen atoms of the phenanthroline moiety participate in the co-ordination.     

A 310-helix single turn enforced by crosslinking of lysines with 1,1′-ferrocenedicarboxylic acid

Prior work has shown that covalently linking the side chains of amino acids in the i and i+3 and i and i+4 positions in a peptide will enforce a helical conformation. In this work the ability of an organometallic entity to enforce a helical conformation in a peptide was explored. The tetrapeptide Boc-Lys-Ala-Val-Lys-NHCH₃ was prepared, then reacted with 1,1′-ferrocenedicarboxylic acid chloride. Reaction of the lysine side chain amines with the diacid chloride resulted in a metallacyclicpeptide (1) in which the two lysines are crosslinked via the ferrocene. The solution conformation of the metallacyclicpeptide (1) was studied using CD and NMR spectroscopy. The NMR methods employed were Karplus analysis of coupling constants, chemical shift changes of NH protons and ROESY data. The results show that the metallacyclicpeptide (1) adopts a single turn of the 3₁₀-helix conformation.     

A flexible dibenzo-O4S2-macrocycle: twist-and-squeeze type metal binding via synergic action of metal-ligand and metal-π interactions

A 21-membered O₄S₂-donor-macrocycle (L) incorporating a dibenzo-subunit was synthesized. From the reaction of L with AgPF₆, an endo-type 1:1 complex [AgL]PF₆ (1) was obtained. On complexation, the conformation of L changes dramatically due to metal-ligand coordination as well as π-interactions between the metal and the dibenzo-subunit from L. This unique change in configuration showing a twist-and-squeeze type process illustrates how large flexible ligands stabilize complexes through conformational changes.     

Structural characterization of a copper(II) complex containing oxidative cyclization of N-2-(4-picolyl)-N′-(4-methoxyphenyl)thiourea,new ligands of 4-picolylthiourea derivatives and the precursor molecular structure of oxidative cyclization of N-(2-pyridyl)-N′-(4-methoxyphenyl)thiourea

Three new compounds of aryl thiourea derivatives, namely N-2-(4-picolyl)-N′-(4-methoxyphenyl)thiourea (L1), N-2-(6-picolyl)-N′-(4-methoxyphenyl)thiourea (L2) and N-2-(4-picolyl)-N′-(4-nitrophenyl)thiourea (L3), and the new copper(II) complex [Cu(4PicTz4OMePh)(OAC)(EtOH)] (C1), as a result of oxidative cyclization of the ligand (L1), were synthesized. In addition, pure precursor (P1), as the product of the oxidative cyclization of N-(2-pyridyl)-N′-(4-methoxyphenyl)thiourea (L4), was isolated and characterized. Ligands (L1) and (L2) were characterized by ¹H and ¹³C NMR and single crystal X-ray analysis. ¹H NMR spectroscopy showed strong hydrogen bonding interactions between N′H-functionalities and the pyridine nitrogen atoms as well as weak intermolecular hydrogen bonding between the thione sulfur and the NH hydrogen. Structural studies of complex (C1) showed that the copper ion is five-coordinated with a square-pyramidal environment. The oxidative cyclization of ligand (L1) results in an anionic bidentate ligand in complex (C1). Both ligand (L1) and precursor (P1) crystallize as centrosymmetric dimers.     

Synthesis of leucine-enkephalin analogs containing α-amino squaric acid

Novel Leu-enkephalin analogs 10a-c in which the Tyr¹, Gly², or Gly³ residue of Leu-enkephalin 9 was replaced with α-amino squaric acid analog Sq-Tyr 8b or Sq-Gly 8a were synthesized starting from 14 or 18. Conformational analysis of 10a-c together with its model compound 26 and their opioid receptor binding activity were evaluated.