Synthesis of photolabile o-nitroveratryloxycarbonyl (NVOC) protected peptide nucleic acid monomers

The chemical synthesis of peptide nucleic acid (PNA) monomers was accomplished using various combinations of the o-nitroveratryloxycarbonyl (NVOC) group (N-aminoethylglycine backbone) and base labile acyl-type nucleobase protecting groups (anisoyl for adenine and cytosine; isobutyryl for guanine), thus offering a photolithographic solid-phase PNA synthetic strategy compatible with photolithographic oligonucleotide synthesis conditions and allowing the in situ synthesis of PNA microarrays in an essentially neutral medium, by avoiding the use of the commonly used deprotection reagents such as trifluoroacetic acid or piperidine. Convenient methods were also explored to prepare 1-(carboxymethyl)-4-N-(4-methoxybenzoyl)cytosine and 9-(carboxymethyl)-2-N-(isobutyryl)guanine with good yields.     

Syntheses and lipophilicity measurement of N/N-terminus-1,1-dihydroperfluoroalkylated α-amino acids and small peptides

(1,1-Dihydroperfluoroalkyl)phenyliodonium N,N-bis(trifluoromethylsulfonyl)imides (4, n = 0-2) were synthesized and used to transfer the corresponding 1,1-dihydroperfluoroalkyl groups to the α-amino group of (l)tyrosine. The obtained N^α-2,2,2-trifluoroethylated (l)tyrosine (6, n = 0) was further used as the N-terminus in the solid phase peptide synthesis of leucine enkephalin analogue. The lipophilicity of the N^α-1,1-dihydroperfluoroalkylated (l)tyrosines (6, n = 0-2) and N-terminus-2,2,2-trifluoroethylated leucine enkephalin analogue (7), as well as the corresponding parent compounds, was measured.     

Facile synthesis of N-(benzyl, methyl)-lysine as a building block for site-specifically lysine monomethylated peptides

Facile, mild and efficient one-pot preparation of N^α-Fmoc-N^ε-(benzyl, methyl)-lysine, a building block for monomethylated peptide synthesis, was described. This building block was proved to be efficient for the synthesis of site-specifically monomethylated peptide. Benzyl group, which was incorporated by reductive benzylation and removed via catalytic hydrogenolysis, served as an excellent protecting group.     

Backbone-Installed Split Intein-Assisted Ligation for the Chemical Synthesis of Mirror-Image Proteins

Membrane-associated D-proteins are an important class of synthetic molecules needed for D-peptide drug discovery, but their chemical synthesis using canonical ligation methods such as native chemical ligation is often hampered by the poor solubility of their constituent peptide segments. Here, we describe a B ackbone- I nstalled S plit I ntein- A ssisted L igation (BISIAL) method for the synthesis of these proteins, wherein the native L-forms of the N- and C-intein fragments of the unique consensus-fast (Cfa) (i.e. L–Cfa^N and L–Cfa^C) are separately installed onto the two D-peptide segments to be ligated via a removable backbone modification. The ligation proceeds smoothly at micromolar (μM) concentrations under strongly chaotropic conditions (8.0 M urea), and the subsequent removal of the backbone modification groups affords the desired D-proteins without leaving any “ligation scar” on the products. The effectiveness and practicality of the BISIAL method are exemplified by the synthesis of the D-enantiomers of the extracellular domains of T cell immunoglobulin and ITIM domain (TIGIT) and tropomyosin receptor kinase C (TrkC). The BISIAL method further expands the chemical protein synthesis ligation toolkit and provides practical access to challenging D-protein targets.     

Electron ionization-induced fragmentation of N- and O-alkoxymethylated carbostyril and phenanthridinone

Unimolecular fragmentation patterns of N-alkoxymethylated carbostyril and phenanthridinone and their O-alkoxymethyl isomers were studied. The main fragmentation reaction observed for the studied compounds is the elimination of an aldehyde molecule. The main products of this reaction are the appropriate N-methyl derivatives, but ions with other structures are also formed. This reaction is supposed to proceed via 1,3-H shift in the alkoxymethyl group in the case of the N-alkoxymethyl derivatives and by a multi-step mechanism for O-alkoxymethylated compounds. Another important fragmentation common for all studied compounds is the loss of an alkyl radical from N- and O-alkoxymethyl groups, yielding the appropriate stable isomeric cations, which, according to the results of the further fragmentation, undergo fast equilibration reaction via an ion–neutral complex. This process is accompanied by the unusually high kinetic energy release value. Copyright © 2004 John Wiley & Sons, Ltd.     

Synthesis of cyclic peptides via O-N-acyl migration

We describe here a novel and convenient synthesis of head-to-tail cyclic peptide avoiding racemization. Linear depsipeptides including a serine residue as the key element for ester bond formation and acyl transfer were synthesized on 2-chlorotrityl chloride resin. After cleavage from the resin, intramolecular head-to-tail cyclization was performed in solution by C-terminal activation of urethane protected O-acyl serine residue. After removal of the N^α-serine protecting group, the final step consisted in O-N-acyl migration reaction on the ‘switch’ or ‘click’ element to restore native cyclic peptides.     

Application of tri- and tetrasubstituted alkene dipeptide mimetics to conformational studies of cyclic RGD peptides

The first application of a combination of novel ψ[(E)-CXCX]-type alkene dipeptide isosteres to conformation studies of cyclic bioactive peptides was carried out (X=H or Me). For exploration of bioactive conformations of Kessler's cyclic RGD peptides, cyclo(-Arg-Gly-Asp-d-Phe-Val-) 1 and cyclo(-Arg-Gly-Asp-d-Phe-N-MeVal-) 2, d-Phe-ψ[(E)-CXCX]-l-Val-type dipeptide isosteres were utilized having di-, tri- and tetrasubstituted alkenes containing the γ-methylated isosteres that have been reported to be potential type II′ β-turn promoters. All of the (E)-alkene pseudopeptides 3-6 exhibited higher antagonistic potency against α_vβ₃ integrin than 1, although potencies were slightly lower than 2. Detailed structural analysis using ¹H NMR spectroscopy revealed that representative type II′ β/γ backbone arrangements proposed for 1, were not observed in peptides 3-6. Rather on the basis of ¹H NMR data, the conformations of peptides 3-6 were estimated to be more analogous to those of the N-methylated peptide 2.     

Carboxyalkyl peptoid PNAs: synthesis and hybridization properties

N^γ-Carboxyalkyl modified peptide nucleic acids (PNAs), containing the four canonical nucleobases, were prepared via solid-phase oligomerization. The inserted peptoid monomers 1 and 2 were constructed through simple synthetic procedures, utilizing appropriate glycidol and iodoalkyl electrophiles. Thermal denaturation studies, performed with complementary antiparallel DNA strands, demonstrated that the length of the N^γ-side chain strongly influences the modified PNAs hybridization properties. Moreover, multiple negative charges on the oligoamide backbone, when present on γ-nitrogen C₆ side chains proved to be beneficial for the oligomers’ water solubility and DNA hybridization specificity.     

Polyfluorinated arylnitrosamines

N-Methyl-, N-n-butyl-, N-t-butylperfluoroarylamines undergo nitrosation with nitrous acid to give the corresponding N-nitroso derivatives. Perfluoroaryl groups were selected from the benzene, indane, biphenyl, naphthalene and pyridine series. According to ¹H and ¹⁹F NMR spectra, N-nitroso-N-methyl derivatives of polyfluoroarenes consist of E and Z isomers with the former prevailing. The more bulky n-butyl group promotes an increase in the formation of Z isomers. Only Z isomers have been obtained from N-t-butyl derivatives of perfluorinated 4-toluidine and 4-aminopyridine. The structure of the Z isomer of N-nitroso-N-methylperfluoro-4-toluidine is confirmed by X-ray data.     

Synthesis of retro-inverso peptides employing isocyanates of N-Fmoc-amino acids/peptide acids catalyzed by DMAP

The Goldschmidt-Wick type reaction between isocyanates of N^α-Fmoc-amino acids/peptide acids and N^α-Boc-/Z-/Bsmoc-amino acids catalyzed by DMAP leads to the incorporation of a reversed peptide bond. It was found to be a simple, efficient and clean reaction. All the retro-inverso peptides made were obtained as crystalline compounds in 70-92% yields.     

Synthesis and structural characterization of a dichloro zinc complex of N,N′-bis-(2,6-dichloro-benzyl)-(R,R)-1,2-diaminocyclohexane: Application to ring opening polymerization of rac-lactide

A novel dichloro zinc complex (L¹)ZnCl₂, where L¹ is N,N′-bis-(2,6-dichloro-benzyl)-(R,R)-1,2-diaminocyclohexane, has been synthesized and characterized. The dimethyl derivatives, generated in situ from the well characterized dichloro zinc complexes (L¹)ZnCl₂ and (L²)ZnCl₂, where L² is N,N′-bis-(benzyl)-(R,R)-1,2-diaminocyclohexane, were employed as initiators for the ring opening polymerization (ROP) of rac-lactide (rac-LA). The complexes were found to be highly efficient initiators yielding the polylactide (PLA) with a narrow molecular weight distribution. The catalytic activity and heterotactic selectivity of the Zn(II) complexes were affected by the substituents on the phenyl groups of benzyl moieties in (R,R)-1,2-diaminocyclohexane. The dimethyl derivative of (L²)ZnCl₂ produced highly stereocontrolled PLA with P_r = 0.75 at −25 °C.     

The first example of linear peptides containing a N-trifluoroethylated backbone amide linkage and the surprising solution dynamics observed by F NMR

The α-amino group of (l)phenylalanine methyl ester was trifluoroethylated using (2,2,2-trifluoroethyl)phenyliodonium N,N-bis(trifluoromethylsulfonyl)imide. A dipeptide Gly(l)Phe containing a trifluoroethylated peptide bond was synthesized by removing the α-amino proton of N^α-trifluoroethyl (l)phenylalanine methyl ester followed by coupling with N^α-phthaloyl glycine acid fluoride. The dipeptide was further coupled with (l)leucine methyl ester under conventional carboxyl activation conditions to provide two diastereomers of the tripeptide Gly(d,l)Phe(l)Leu. The solution dynamic behavior of the tripeptide was investigated as a function of solvents, by NOESY and variable temperature (VT) ¹⁹F NMR experiments.     

N-(Benzoyloxy)amines: an investigation of their thermal stability, synthesis, and incorporation into novel peptide constructs

A series of N-benzoyloxyamines were pyrolyzed and their decomposition temperatures correlated well with the amine architecture's ability to stabilize a N-centered radical. A variety of amine substrates were treated with a biphasic mixture of benzoyl peroxide (BPO), CH₂Cl₂ and an aqueous carbonate buffer (at pH 10.5). Primary and secondary amines were successfully N-benzoyloxylated in good yield. Tertiary amines and BPO gave low yields of the corresponding N-oxide and complex product mixtures, presumably via radical decomposition. Electron deficient amines (such as fluorinated aliphatic amines, α-aminoacids, α-aminoesters, and α-aminoamides) were not N-benzoyloxylated under these conditions. Instead, N-benzoylation was observed with the fluorinated amines and the reaction was sensitive to temperature and the pH of the aqueous medium. A one-pot-two-step synthesis of N^α-FMOC-l-Leu-N^β-(benzoyloxy)-β-alanine ethyl ester, a peptide containing both an α- and a novel β-amino acid framework, was also developed.     

N,N,N,N-Tetramethyl-1,3-propanediamine as the catalyst of choice for the Baylis-Hillman reaction of cycloalkenone: rate acceleration by stabilizing the zwitterionic intermediate via the ion-dipole interaction

N,N,N^′,N^′-Tetramethyl-1,3-propanediamine (TMPDA) can be used as an efficient catalyst for the Baylis-Hillman reaction of cycloalkenones. The increased reaction rate was thought be derived from the stabilizing effect of the zwitterionic intermediate via the ion-dipole interaction.     

Peptide thioester preparation based on an N-S acyl shift reaction mediated by a thiol ligation auxiliary

Formation of peptide thioesters, based on an N to S acyl shift mediated by an auxiliary, N-4,5-dimethoxy-2-mercaptobenzyl (Dmmb) group, under acidic conditions, is described. The protected peptide was assembled on a hydroxymethylphenylacetamidomethyl resin via an N-Dmmb-amino acid residue according to standard Fmoc solid-phase peptide synthesis following treatment with trifluoroacetic acid. The peptide α-thioester was released from the resin by reaction with 2-mercaptoethanesulfonic acid in the presence of N,N-diisopropylethylamine.     

Syntheses and evaluation of fluorinated benzothiazole anilines as potential tracers for β-amyloid plaques in Alzheimer's disease

[¹¹C]2-(4′-(Methylamino)phenyl)-6-hydroxybenzothiazole ([¹¹C]PIB) is a most potential PET tracer for detecting the β-amyloid plaques in Alzheimer's disease. Here the syntheses of three fluorinated PIB, namely 2-(4′-(methylamino)phenyl)-6-fluoroethoxybenzothiazole (O-FEt-PIB), 2-(4′-(methylamino)phenyl)-6-fluoro-benzothiazole (F-N-Me) and 2-(4′-(dimethylamino)phenyl)-6-fluorobenzo-thiazole (F-N,N-Me), and the radiosynthesis of one corresponding ¹⁸F-labeled PIB compound, [¹⁸F]O-FEt-PIB, as well as their in vitro/in vivo biological characters were reported. The structures of the products were confirmed by IR, ¹H NMR, EI/ESI-MS, elemental analysis and HRMS techniques. The radiolabeled product was characterized by radio-TLC and radio-HPLC and purified by semi-preparative radio-HPLC. The suitable biological characters showed these tracers were potential to be developed as probes for detecting β-amyloid plaques in Alzheimer's disease.     

Thermo- and pH-sensitive comb-type grafted poly(N,N-diethylacrylamide-co-acrylic acid) hydrogels with rapid response behaviors

Poly(N,N-diethylacrylamide) with a terminal hydroxyl end group (PDEA-OH) was synthesized by radical telomerization of N,N-diethylacrylamide (DEA) monomer using 2-hydroxyethanethiol as a chain transfer agent. Macromonomer of thermo-sensitive PDEA was synthesized by condensation reaction of PDEA-OH with acryloyl chloride. The macromonomer was characterized by FTIR and ¹H NMR, and the molecular weight was determined by GPC. Thermo- and pH-sensitive comb-type grafted poly(N,N-diethylacrylamide-co-acrylic acid) (PDEA-co-AA) hydrogels (GHs) were successfully prepared by grafting PDEA chains with freely mobile ends onto the backbone of a cross-linked (PDEA-co-AA) network. The results showed that the deswelling behavior of the hydrogels was dependent on the test temperature. At 45 °C (beneath the VPTT of the hydrogels), both the normal-type hydrogels (NHs) and comb-type grafted P(DEA-co-AA) hydrogels had lower deswelling rates. While at 60 °C (far beyond the VPTT of the hydrogels), the deswelling rates of the GHs were faster than that of the NHs. Furthermore, pulsatile stimuli-responsive studies indicated that the GHs had excellent thermo-reversibility and were superior to the NHs in the magnitude of their swelling ratios to temperature changes. However, the reversibility to pH changes was poor for both the NHs and the GHs.     

DFT study of the reaction sites of N,N′-substituted p-phenylenediamine antioxidants

The geometry of N,N′-diphenyl-p-phenylenediamine (DPPD), N-phenyl-N′-(1′-methylbenzyl)-p-phenylenediamine (SPPD), N-phenyl-N′-(1,3-dimethyl-butyl)-p-phenylenediamine (6PPD), N-phenyl-N′-isopropyl-p-phenylenediamine (IPPD), and N-(1-methyl-1-phenylethyl)-N′-phenyl-p-phenylenediamine (CPPD) as well as of their dehydrogenation products has been optimized at B3LYP/6-31G^∗ level of theory. Our results support the idea of formation of stable ketimine Ph-NC structures (instead of quinonediimine structures) during consecutive dehydrogenation of SPPD, 6PPD, and IPPD antioxidants despite the formation of tertiary carbon-centered radicals in the first dehydrogenation step is energetically preferred for SPPD only.     

Acyclic tertiary diamines and 1,4,7,10-tetraazacyclododecane with fluorine-containing β-diketones: Leading to low melting ionic adducts

N,N,N′,N′-Tetramethylmethanediamine (1a), N,N,N′,N′-tetramethylethanediamine (1b), N,N,N′,N′-tetramethyl-1,3-propanediamine (1c), and N,N,N′,N′-tetramethyl-1,6-hexanediamine (1d) were reacted at 25 °C with 1,1,1,5,5,5-hexafluoro-2,4-pentanedione (2a), 2,2-dimethyl-6,6,7,7,8,8,8-heptafluoro-3,5-octanedione (2b), 2-thenoyltrifluoroacetone (2c), and 4,4,4-trifluoro-1-(2-furyl)-1,3-butanedione (2d) to form the ionic adducts 3-18. 1,4,7,10-Tetraazacyclododecane (1e) reacted at 25 °C with β-diketones (2a-d) and 1,1,1-trifluoro-2,4-pentanedione (2e) to give ionic solids 19-23 in good yields. Some of the products are liquid at 25 °C and are thermally stable over long liquid ranges as determined by thermal gravimetric analyses. Single-crystal X-ray structure determinations show that compounds 9 and 21 crystallize in the monoclinic space groups P2(1)/c and P2(1)/n, respectively. All the new compounds were characterized by ¹H, ¹⁹F and ¹³C NMR, electrospray MS and/or elemental analyses.     

Formation and Dissociation of Phosphorylated Peptide Radical Cations

In this study, we generated phosphoserine- and phosphothreonine-containing peptide radical cations through low-energy collision-induced dissociation (CID) of the ternary metal?Cligand phosphorylated peptide complexes [Cu^II(terpy) _p M]^·2+ and [Co^III(salen) _p M]^·+ [ _p M: phosphorylated angiotensin III derivative; terpy: 2,2':6',2''-terpyridine; salen: N,N '-ethylenebis(salicylideneiminato)]. Subsequent CID of the phosphorylated peptide radical cations ( _p M^·+) revealed fascinating gas-phase radical chemistry, yielding (1) charge-directed b- and y-type product ions, (2) radical-driven product ions through cleavages of peptide backbones and side chains, and (3) different degrees of formation of [M ?C H₃PO₄]^·+ species through phosphate ester bond cleavage. The CID spectra of the _p M^·+ species and their non-phosphorylated analogues featured fragment ions of similar sequence, suggesting that the phosphoryl group did not play a significant role in the fragmentation of the peptide backbone or side chain. The extent of neutral H₃PO₄ loss was influenced by the peptide sequence and the initial sites of the charge and radical. A preliminary density functional theory study, at the B3LYP 6-311++G(d,p) level of theory, of the neutral loss of H₃PO₄ from a prototypical model??N-acetylphosphorylserine methylamide??revealed several factors governing the elimination of neutral phosphoryl groups through charge- and radical-induced mechanisms.