Synthesis of novel analogs of aromatic peptide nucleic acids (APNAs) with modified conformational and electrostatic properties

Aromatic peptide nucleic acid analogs having an N-(2-aminobenzyl)glycine backbone (APNA 1) were previously identified as promising new leads for the design of polyaromatic DNA mimics. Structural modifications of 1, which lock the aromatic backbone into a unique conformation, while maintaining the same space distribution between the nucleobases as in 1, were investigated. The electrostatic potential of the aromatic backbone was also modified in an attempt to improve the solubility of these compounds in aqueous media and to evaluate how the quadrapole of the aromatic backbone may influence the biophysical properties of the APNA oligomers. PNA hexamers containing a single monomer insert of each new APNA monomer were used to explore the hybridization properties of these analogs with poly rA and poly dA. Preliminary results indicated that these modifications do not seriously alter the molecular recognition properties of APNAs towards DNA and RNA.     

Evaluation of two chelators for labelling a PNA monomer with the fac-[Tc(CO)3] moiety

A PNA monomer containing thymine as nucleobase (1) was synthesized, characterized and coupled to the pyrazolyl containing ligand 3,5-Me₂pz(CH₂)₂N((CH₂)₃COOH)(CH₂)₂NHBoc (2) and to a modified cysteine S-(carboxymethyl-pentafluorphenyl)-N-[(trifluor)carbonyl]-l-cysteine methyl ester (3) yielding the bifunctional chelators 6 and 7, respectively. Reactions of 6 and 7 with the Re(I) tricarbonyl starting material [Re(CO)₃(H₂O)₃]Br afforded the complexes fac-[Re(CO)₃(κ³-6)]⁺ (8) and fac-[Re(CO)₃(κ³-7)] (9), respectively. The identity of 8 and 9 has been established based on IR spectroscopy, elemental analysis, ESI-MS spectrometry and HPLC. The multinuclear NMR spectroscopy (¹H, ¹³C, g-COSY, g-HSQC) has also been very informative in the case of complex 8, showing the presence of rotamers in solution. For 9 the NMR spectrum was too complex due to the presence of rotamers and diastereoisomers. The radioactive congeners of complexes 8 and 9, fac-[^99mTc(CO)₃(κ³-6)]⁺ (8a) and fac-[^99mTc(CO)³(κ³-7)] (9a), have been prepared by reacting the precursor fac-[^99mTc(CO)₃(H₂O)₃]⁺ with the corresponding ligands being their identity established by comparing their HPLC chromatograms with the HPLC of the rhenium surrogates.     

A cationic tetrahedral chromophore for amplified DNA detection

The tetrahedral cationic chromophore, tetrakis [4-(9,9-bis(6′-(N,N,N-trimethylammonium)hexyl)-2-fluorenyl)phenyl]methane (1) shows better fluorescence resonance energy transfer (FRET) to the fluorescein (Fl) attached to the 5′-terminus of double-stranded DNA (dsDNA-Fl) as compared to the linear oligomers 2 and 3 and also provides efficient DNA hybridization detection.     

(2S,5R/2R,5S)-Aminoethylpipecolyl aepip-aegPNA chimera: synthesis and duplex/triplex stability

This article reports the design and facile synthesis of novel chiral six-membered PNA analogues (2S,5R/2R,5S)-1-(N-Boc-aminoethyl)-5-(thymin-1-yl)pipecolic acid, aepipPNA IV that upon incorporation into standard aegPNA sequences effected stabilization of complexes with complementary target DNA. Substitution of aegPNA unit by the designed monomer at the C-terminus was more effective than substitution at N-terminus. The stabilizing behaviour improved with degree of substitution and was found to be dependent on their relative positions in the sequence. The six-membered piperidine ring in the design may freeze the rigid chair conformations and the relative stereochemistry of the substituents may in effect direct the complex formation with DNA/RNA by sequence-specific nucleobase recognition. In the present aepipPNA analogues, the l-trans stereochemical disposition of the substituents seems to lead to the favorable pre-organization of the PNA oligomers for complex formation with DNA. The results reported here further expand the repertoire of cyclic PNA analogues.     

A new ferrocene conjugate of a tyrosine PNA monomer: synthesis and electrochemical properties

A new chiral ferrocene-labelled tyrosine PNA monomer 1 has been synthesised in good yield in both racemic and enantiomerically pure forms. It is suitable for insertion in various positions of PNA oligomers, a possibility that has been preliminarily demonstrated by synthesising the dimer 16. Moreover, in view of possible applications to nucleic acid detection, a preliminary voltammetric investigation on the electrochemical activity of monomer 1 and its synthetic precursors has been carried out in DMF. It appears that, despite the bulkiness of the PNA monomer backbone, its insertion on the ferrocene group only moderately lowers the latter’s diffusion coefficients and peak currents, thus affording voltammetric detection limits in the order of 10⁻⁶-10⁻⁷ M.     

Synthesis of a ferrocenyl uracil PNA monomer for insertion into PNA sequences

The deprotection of the tert-butyl group of a ferrocenyl uracil Peptide Nucleic Acid (PNA) monomer, Fmoc-aeg(R)-O^tBu (1) was achieved using a two step synthesis involving hydrolysis in basic conditions to give first the zwitterion of ⁺NH₃-aeg(R)-O⁻ (7). Compound 7 was reacted in situ with N-(9-fluorenylmethoxycarbonyloxy)succinimide to obtain the expected compound Fmoc-aeg(R)-OH (2) (Abbreviations: Aeg = (2-aminoethyl)-glycine; Fmoc = 9-fluorenylmethoxycarbonyl; O^tBu = tert-butyl; R = 5-(N-ferroce-nylmethylbenzamido)uracyl).     

[4+2] Cycloaddition reactions of 4-sulfur-substituted 2-pyridones with electron-deficient dienophiles

[4+2] Cycloaddition reactions of 4-(phenylthio)-1-tosyl-2-pyridone (6a) and 4-(phenylsulfonyl)-1-tosyl-2-pyridone (6b) with electron-deficient dienophiles 7 (N-methylmaleimide, N-phenylmaleimide, and methyl acrylate) gave new isoquinuclidine products 8-10. The N-tosyl group of 6a and 6b was also efficiently converted to N-alkyl derivatives 6c-f, which showed different stereoselectivity toward reactions with dienophiles 7. Several other dienophiles 15 (dimethyl acetylenedicarboxylate, methyl vinyl ketone, ethyl vinyl ether, and methyl methacrylate) were found not to react with 6a or 6b, but led to the formation of tosyl migration products 4-(phenylthio)-O-tosyl-pyridinol (16a) and 4-(phenylsulfonyl)-O-tosyl-2-pyridinol (16b), respectively. The reactivity, regioselectivity, and stereoselectivity of the cycloaddition reactions were also compared with semi-empirical calculations.     

Efficient functional molecule incorporation method to functionalized peptide nucleic acid (PNA): use in synthesis of labeled PNA oligomers

A novel efficient synthetic method for a functionalized PNA (peptide nucleic acid) is described, in which a functional molecule is incorporated in place of a nucleobase. Novel ω-AA-^BocPNA-OH (20-24, AA=amino acid) were designed as PNA precursor monomer units into which functional molecules could be incorporated efficiently. Compounds 20-24 reacted quantitatively with OSu (N-hydroxysuccinimidyl) active ester derivatives and isothiocyanate derivatives of commercial functional molecules to give target functionalized PNA monomer units 25-53. Various types of functionalized PNA monomer units could be efficiently incorporated into multiple predetermined positions in a PNA oligomer by SPPS (solid phase peptide synthesis) in the same way as for the four A(Cbz), G(Cbz), C(Cbz), and T PNA monomer units.     

Molecular recognition of biotin, barbital and tolbutamide with new synthetic receptors

We have measured, by means of NMR titrations, the binding constants for the complexes between hosts N,N′-bis(6-methylpyridin-2-yl)-1,3-benzenedicarboxamide (7) and 4-chloro-N,N′-bis(6-methylpyridin-2-yl)-2,6-pyridinedicarboxamide (8, hydrated) with biotin methyl ester (1), N,N′-dimethylurea (2), 2-imidazolidone (3), N,N′-trimethylenurea (4), barbital (5) and tolbutamide (6) as guests. Molecular Mechanics calculations (Monte Carlo Conformational Search, AMBER and OPLS force fields, MacroModel v.8.1) on the complexes formed between the foregoing guests and hosts 7 and 8, comparatively with 4-oxo-N,N′-bis(6-methylpyridin-2-yl)-1,4-dihydro-2,6-pyridinedicarboxamide (9a) have been carried out in order to determine the correlation between experimental and theoretical results and to understand the behaviour of the designed new hosts. Finally we have performed single point DFT [B3LYP/6-31G(d,p)] calculations on the optimised Molecular Mechanics geometries for the complexes between hosts 7-9 and water.     

Synthesis of l-azaisotryptophan and its analogs: a general access to new 2-substituted azaindoles

l-(N-Cbz)-7-azaisotryptophan, l-(N-Cbz)-1a, a new isostere of tryptophan, was synthesized by reacting Li₂-(N-Boc)-2-amino-3-picoline, Li₂-(N-Boc)-2a, with appropriately protected l-aspartic acid followed by simple functional group manipulation. This synthetic success led us to access a set of analogs of azaisotryptophan (4a–c; 6a–c) as well as a new class of chiral amines (7a–c; 8a–c) for future application in asymmetric synthesis and design of homochiral ligands. Further, we have generalized the method substantiating a variety of new azaindol-2-yl derivatives (10aa–10lc) with functionalized substituents. In a preliminary luminescence characterization, l-(N-Cbz)-1a has exhibited about 30 nm bathochromic shifted fluorescence emission compared to tryptophan and (N-Cbz)-tryptophan.     

Synthesis, characterization and luminescence study of dimethyl(β-ketoiminato)gallium (-indium) complexes: crystal structure of dimethyl[1-phenyl-3-N-(4-methoxyphenylimino)-1-butanonato]gallium

Six dimethylgallium (indium) complexes of type Me₂ML [M = Ga, L = 1-phenyl-3-N-(phenylimino)-1-butanonato (1), 1-phenyl-3-N-(p-methoxyphenylimino)-1-butanonato (2), 1-phenyl-3-N-(o-chloro phenylimino)-1-butanonato (3); M = In, L = 1-phenyl-3-N-(phenyl imino)-1-butanonato (4), 1-phenyl-3-N-(p-methoxyphenylimino)-1-butanonato (5), 1-phenyl-3-N-(o-chlorophenylimino)-1-butanonato (6)] have been synthesized by reaction of trimethylgallium (indium) with appropriate 1-phenyl-3-N-(arylimino)-1-butanones. The complexes obtained have been characterized by elemental analysis, ¹H NMR, IR and mass spectroscopy. Structure of 2 has been determined by X-ray single-crystal analysis, in which Ga atom is four coordinated. Complexes 1-6 emit colors from blue to green (463-491 nm) when irradiated by UV light. The electroluminescent (EL) properties of 1-6 were examined by fabricating EL devices using 1-6 as emitter, respectively. The EL bands are located in the green region (509-522 nm).     

Microwave-promoted synthesis of new optically active poly(ester-imide)s derived from N,N-(pyromellitoyl)-bis-l-leucine diacid chloride and aromatic diols

Pyromellitic dianhydride (benzene-1,2,4,5-tetracarboxylic dianhydride) (1) was reacted with l-leucine (2) in a mixture of acetic acid and pyridine (3:2) and the resulting imide-acid [N,N^′-(pyromellitoyl)-bis-l-leucine diacid] (4) was obtained in quantitative yield. The compound (4) was converted to the N,N^′-(pyromellitoyl)-bis-l-leucine diacid chloride (5) by reaction with thionyl chloride. A new facile and rapid polycondensation reaction of this diacid chloride (5) with several aromatic diols such as phenol phthalein (6a), bisphenol-A (6b), 4,4^′-hydroquinone (6c), 1,8-dihydroxyanthraquinone (6d), 1,5-dihydroxy naphthalene (6e), 4,4-dihydroxy biphenyl (6f), and 2,4-dihydroxyacetophenone (6g) was developed by using a domestic microwave oven in the presence of a small amount of a polar organic medium such as o-cresol. The polymerization reactions proceeded rapidly and are completed within 10 min, producing a series of optically active poly(ester-imide)s (PEIs) with good yield and moderate inherent viscosity of 0.10-0.27 dl/g. All of the above polymers were fully characterized by IR, elemental analyses and specific rotation. Some structural characterization and physical properties of these optically active PEIs are reported.     

New resveratrol oligomers in the stem bark of Vatica pauciflora

Five new resveratrol oligomers; pauciflorols A-C (1-3), isovaticanols B (6) and C (8), and three new oligostilbene glucosides; pauciflorosides A (11), B (13), C (14), were isolated from the stem bark of Vatica pauciflora (Dipterocarpaceae) together with known 17 resveratrol oligomers (4, 5, 7, 9, 10, 12 and 15-25) and bergenin (26). The structures of isolates were established on the basis of detailed spectroscopic analysis. The typical and characteristic spectral properties of some resveratrol oligomers were also discussed.     

Synthesis of a new class of azathia crown macrocycles containing two 1,2,4-triazole or two 1,3,4-thiadiazole rings as subunits

A series of new 1,2/1,3-bis[o-(N-methylidenamino-5-aryl-3-thiol-4H-1,2,4-triazole-4-yl)phenoxy]alkane derivatives 3a-d and bis[o-(N-methylidenamino-2-thiol-1,3,4-thiadiazole-5-yl)phenoxy]alkanes 6a-c were prepared by condensation of 4-amino-5-(aroyl)-4H-1,2,4-triazole-3-thiols 2a-b or 2-amino-5-mercapto-1,3,4-thiadiazole with bis-aldehydes 1a-c. Further reaction of compounds 3a-d and 6a-c with dibromoalkanes afforded the new macrocycles 5a-f and 8a-d. The cyclization does not require high dilution techniques and provides the expected azathia macrocycles in good yields, ranging from 55% to 68%.     

Synthesis, structure, and electrochemical properties of biferrocenes annulated with 1,2-dithiin and 1,2-dithiin 1,1-dioxides

2,2″-Bis(N,N-dimethylaminosulfonyl)-1,1″-biferrocene (6), a precursor of biferrocenes annulated with 1,2-dithiin and 1,2-dithiin 1,1-dioxides, was prepared by a sequence of selective ortho-lithiation and dimerization reaction from N,N-dimethylaminosulfonylferrocene. New biferrocenes annulated with 1,2-dithiin (1) and 1,2-dithiin 1,1-dioxides (2) and (3) were successfully synthesized in satisfactory yields by the reaction of compound 6 with lithium aluminum hydride followed by treatment with chlorotrimethylsilane. The electrochemical properties of the biferrocenes (1)-(3) were furnished by voltammetric studies.     

Syntheses and structures of iron carbonyl complexes derived from N-(5-methyl-2-thienylmethylidene)-2-thiolethylamine and N-(6-methyl-2-pyridylmethylidene)-2-thiolethylamine

The reaction of N-(5-methyl-2-thienylmethylidene)-2-thiolethylamine (1) with Fe₂(CO)₉ in refluxing acetonitrile yielded di-(μ₃-thia)nonacarbonyltriiron (2), μ-[N-(5-methyl-2-thienylmethyl)-η¹:η¹(N);η¹:η¹(S)-2-thiolatoethylamido]hexacarbonyldiiron (3), and N-(5-methyl-2-thienylmethylidene)amine (4). If the reaction was carried out at 45 °C, di-μ-[N-(5-methyl-2-thienylmethylidene)-η¹(N);η¹(S)-2-thiolethylamino]-μ-carbonyl-tetracarbonyldiiron (5) and trace amount of 4 were obtained. Stirring 5 in refluxing acetonitrile led to the thermal decomposition of 5, and ligand 1 was recovered quantitatively. However, in the presence of excess amount of Fe₂(CO)₉ in refluxing acetonitrile, complex 5 was converted into 2-4. On the other hand, the reaction of N-(6-methyl-2-pyridylmethylidene)-2-thiolethylamine (6) with Fe₂(CO)₉ in refluxing acetonitrile produced 2, μ-[N-(6-methyl-2-pyridylmethyl)-η¹ (N_py);η¹:η¹(N); η¹:η¹(S)-2-thiolatoethylamido]pentacarbonyldiiron (7), and μ-[N-(6-methyl-2-pyridylmethylidene)-η²(C,N);η¹:η¹(S)-2- thiolethylamino]hexacarbonyldiiron (8). Reactions of both complex 7 and 8 with NOBF₄ gave μ-[(6-methyl-2-pyridylmethyl)-η¹(N_py);η¹:η¹(N);η¹:η¹(S)-2-thiolatoethylamido](acetonitrile)tricarbonylnitrosyldiiron (9). These reaction products were well characterized spectrally. The molecular structures of complexes 3, 7-9 have been determined by means of X-ray diffraction. Intramolecular 1,5-hydrogen shift from the thiol to the methine carbon was observed in complexes 3, 7, and 9.     

N-Nosyl as a stereoselectivity-improving and easily removable group in the O-glycosylation of d-allal and d-galactal-derived allyl aziridines. Stereospecific synthesis of 4-amino-2,3-unsaturated-O-glycosides

The glycosylation of alcohols, phenol, and partially protected monosaccharides with the diastereoisomeric d-allal and d-galactal-derived N-nosyl aziridines 2α and 2β leads to the corresponding 4-N-(nosylamino)-2,3-unsaturated-α-O- (6α) and β-O-glycosides and disaccharides (6β), respectively, in a stereospecific substrate-dependent O-glycosylation process. The N-(nosylamino) group of 6α and 6β can easily be deprotected to give the corresponding 4-amino-2,3-unsaturated-O-glycosides 7α and 7β, with an increased value to our glycosylation protocol.     

Rhodium complexes with chiral counterions: achiral catalysts in chiral matrices

The neutral complexes [Rh(I)(NBD)((1S)-10-camphorsulfonate)] (2) and [Rh(I)((R)-N-acetylphenylalanate)] (4) reacted with bis-(diphenylphosphino)ethane (dppe) to form the cationic Rh(I)(NBD)(dppe) complexes, 5 and 6, respectively, accompanied by their corresponding chiral counteranions. Analogously, 4 reacted with 4,4^′-dimethylbipyridine to yield complex 7. Complexes 5 and 6 disproportionated in aprotic solvents to form the corresponding bis-diphosphine complexes 8 and 9, respectively. 8 was characterized by an X-ray crystal structure analysis. In order to form achiral Rh(I) complexes bearing chiral countercations new sulfonated monophosphines 13-16 with chiral ammonium cations were synthesized. Tris-triphenylphosphinosulfonic acid (H₃TPPS, 11) was used to protonate chiral amines to yield chiral ammonium phosphines 14-16. Thallium-tris-triphenylphosphinosulfonate (Tl₃TPPS, 12) underwent metathesis with a chiral quartenary ammonium iodide to yield the proton free chiral ammonium phosphine 13. Phosphines 15 and 16 reacted with [Rh(NBD)₂]BF₄ to afford the highly charged chiral zwitterionic complexes [Rh(NBD)(TPPS)₂][(R)-N,N-dimethyl-1-(naphtyl)ethylammonium]₅ (17) and [Rh(NBD)(TPPS)₂][BF₄][(R)-N,N-dimethyl-phenethylammonium]₆ (18), respectively. Complexes 5, 6, and 18 were tested as precatalysts for the hydrogenation of de-hydro-N-acetylphenylalanine (19) and methyl-(Z)-(α)-acetoamidocinnamate (MAC, 20) under homogeneous and heterogeneous (silica-supported and self-supported) conditions. None of the reactions was enantioselective.     

An expedient, regioselective synthesis of 2-alkylamino- and 2-alkylthiothiazolo[5,4-e]indoles

1-Benzenesulfonyl-5-aminoindole 5, prepared from 5-nitroindole 3, was condensed with alkyl isothiocyanates and separately with carbon disulfide and alkyl bromides/iodides to furnish efficiently the corresponding N-alkyl-thioureidoindoles 6a-c and the alkyl N-(indol-5′-yl)dithiocarbamates 9a-e, respectively. Their cyclisation using N-bromosuccinimide (NBS) and 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU), in the cold, followed by indolic N-deprotection, furnished regioselectively the 2-alkylamino- and the 2-alkylthiothiazolo[5,4-e]indoles 8a-c and 11a-e, respectively, in good overall yields.     

Concise and practical route to tri- and tetra-hydroxy seven-membered iminocyclitols as glycosidase inhibitors from d-(+)-glucurono-γ-lactone

An efficient and short total synthesis of tetrahydroxy-1c and trihydroxy-azepane 1d is reported in 72% and 57% overall yields, respectively, from d-(+)-glucurono-γ-lactone. Thus, d-glucuronolactone 2 on acetonide protection, DIBAL-H reduction and one-pot intermolecular reductive amination followed by -NCbz protection afforded 6-(N-benzyl-N-benzyloxycarbonyl) amino-6-deoxy-1,2-O-isopropylidene-α-d-gluco-1,4-furanose 5a. 1,2-Acetonide hydrolysis in 5a and Pd-mediated intramolecular reductive aminocyclization afforded tetrahydroxyazepane 1c. An analogous pathway with 5-deoxy-1,2-O-isopropylidene-α-d-glucurono-6,3-lactone 3b gave trihydroxy-azepane 1d. Glycosidase inhibitory activity of 1c/1d was studied and 1d was found to be potent inhibitor of α-mannosidase and β-galactosidase.