Synthesis and conformational studies of a hybrid β-alanine-morpholine tetramer

A new morpholine-containing foldameric hybrid peptide was synthesized in solution phase, and the conformational preferences were assessed by means of NMR and molecular modeling calculations. All data suggested the existence of two equilibrating conformations involving hydrogen-bonds in the major rotamer. Moreover, calculations on higher model foldamers indicated seven-membered ring hydrogen-bond forming γ-turns as the main driving force in the stabilization of helix-folded conformations. Thus, this study suggests the possibility of using morpholine-3-COOH as a proline surrogate to generate higher α/β hybrid peptides.     

QSAR and conformational analysis of the antiinflammatory agent amfenac and analogues

Summary The new nonsteroidal antiinflammatory drug (NSAID) arylacetic amfenac (2-amino-3-benzoylphenylacetic acid) and 19 substituted derivatives were studied in order to correlate the biological activities with the structure-related parameters.The geometry of amfenac in neutral and anionic form was totally optimized, starting from standard geometries and crystallographic data, using semiempirical AM1 and MNDO quantum-mechanical methods. Conformational analysis shows the existence of a rigid structure for rotations of the acetic acid chain (°) and the central carbonyl group (°) around the bonds with the phenylamine ring, whereas the carboxyl group (°) and the phenyl ring of the benzoyl group (°) can rotate almost freely.Electrostatic potential maps were analyzed and showed that the electrostatic orientation effect seems to make an important contribution to the binding of the active compounds to prostaglandin synthase. An electrostatic orientation model of the binding site is proposed. The frontier orbital charge distribution was also described for each compound. On the other hand, steric, electronic and hydrophobic (log P) parameters were calculated and QSAR analysis showed that the most significant parameter for the antiinflammatory activity was the -electron density of the HOMO orbital in the second aromatic ring. These results suggest a possible electronic charge transfer between the aromatic fragments and the receptor.     

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 and conformational analysis of novel N(OCH3)-linked disaccharide analogues

N(OMe)-linked disaccharide analogues, isosteric to the corresponding natural disaccharides, have been synthesized by chemoselective assembly of unprotected natural monosaccharides with methyl 6-deoxy-6-methoxyamino-alpha-D-glucopyranoside in an aqueous environment. The coupling reactions were found to be chemo- and stereoselective affording beta-(1-->6) disaccharide mimics when using Glc and GlcNAc; in the case of Gal, the beta-anomer was prevalent (beta:alpha=7:1). An iterative method for the synthesis of linear N(OMe) oligosaccharide analogues was demonstrated, based on the use of an unprotected monosaccharide building block in which an oxime functionality at C-6 is converted during the synthesis into the corresponding methoxyamino group. The conformational analysis of these compounds was carried out by using NMR spectroscopy, ab initio, molecular mechanics, and molecular dynamics methods. Optimized geometries and energies of fourteen conformers for each compound have been calculated at the B3LYP/6-31G* level. Predicted conformational equilibria were compared with the results based on NMR experiments and good agreement was found. It appears that N(OMe)-linked disaccharide analogues exhibit a slightly different conformational behavior to their parent natural disaccharides.     

Synthesis and conformational behaviour of ditosyldiaza[2.2]orthometacyclophanes

Summary The N,N-ditosyl-diaza[2.2]orthometacyclophanes5a, b were synthesized from N,N-ditosyl-metaphenylenediamine by reaction with (Z)-1,4-dichlorobutene and 1,2-bis-bromomethylbenzene, respectively. Low temperature NMR studies showed that the compound5b exists as a 1:1 mixture of chair and boat form of the strained (E,Z)-diazanonadiene ring. At room temperature all corresponding resonances are averaged on the NMR time scale (including all four ethylene bridge protons). Going to lower temperatures, in a first step the methylene bridge inversion is frozen (giving twoexo H and twoendo H, G ca. 52kJmol^–1). In a second step the chair and boat form can be observed separately (G ca. 43.5 kJ mol^–1 for the chair/boat flip). The assignments were confirmed by 2D NMR experiments.Dedicated to Prof. Dr. E. L. Eliel on the occasion of his 70th anniversary     

Synthesis and kinetic investigation of the selective acidolysis of para-substituted N-benzyl- or N-phenyl-N-phenylacetyl-α,α-dialkylglycine cyclohexylamides

Several derivatives of N-phenylacetyl-N-benzyl-α,α-dimethylglycine cyclohexylamide and their α,α-dibenzylglycine analogues were synthesised by a Ugi-Passerini reaction. In addition, a few analogues of the former but having an N-phenyl instead of a benzyl group at the nitrogen atom were synthesised. The compounds in each of these three sets differed from each other at position 4 of the N-benzyl (and N-phenyl) group. These adducts were submitted to acidolysis with TFA to obtain the corresponding free acids, the reactions being monitored by HPLC and data collected for kinetic purposes. The kinetic data were submitted to Hammett uni- and biparametric relationships and the results were analysed in terms of structure-reactivity in connection with the sensitivity of the reaction rates to the electronic contributions of the various substituents at position 4 of the aromatic rings. The results allowed comparison with information obtained in previous investigations and rationalise the contribution of the substituent at the nitrogen atom to the lability of the C-terminal amide bond.     

Synthesis and conformational analysis of glycomimetic analogs of thiochitobiose

The synthesis of six analogs of N,N′-diacetylchitobiose is reported, including a novel transglycosylation reaction for the preparation of S-aryl thioglycosides. The conformations of the compounds were studied by a combination of NMR spectroscopy and molecular modeling, using force field calculations. In the case of the S-aryl thioglycosides with exclusively S-glycosidic linkages, dihedral angles of the disaccharidic S-glycosidic bonds, Φ′ and Ψ′ and of the S-arylglycoside bonds, Φ and Ψ, were found to be similar, whereas they were different in mixed glycosides and in a thiazoline derivative. An adequate correlation between the calculated H,H-distances of the local minima and the measured NOE contacts was achieved by applying population-weighted averages over participating conformers based on weighted relative energies.     

Synthesis and conformational analysis of new naphth[1,2-e][1,3]oxazino[3,4-c]quinazoline derivatives

A new highly functionalized aminonaphthol derivative, 1-(amino(2-aminophenyl)methyl)-2-naphthol (4), was synthesized by the reaction of 2-naphthol, 2-nitrobenzaldehyde and tert-butyl carbamate or benzyl carbamate, followed by reduction and/or removal of the protecting group. The aminonaphthol derivative thus obtained was converted in ring-closure reactions with formaldehyde, benzaldehyde and/or phosgene to the corresponding naphth[1,2-e][1,3]oxazino[3,4-c]quinazoline derivatives. The conformational analysis of some derivatives by NMR spectroscopy and accompanying molecular modelling are also reported.     

NMR‐based conformational analysis of perezone and analogues

Complete assignment of the ¹H NMR chemical shift and coupling constant values of perezone (1), O‐methylperezone (2) and 6‐hydroxyperezone (3) was carried out by total‐line‐shape‐fitting calculations using the PERCH iterative spectra analysis software (PERCH Solutions Ltd., Kuopio, Finland). The resulting simulated spectra for the three compounds showed strong similarity to their corresponding experimental spectra. Particularly, all vicinal, allylic and homoallylic coupling constant values for the side chain of the three compounds were very similar, thus revealing that the conformation of these three molecules in solution is indeed almost identical. This fact is in agreement with extended side chain conformations over folded chain conformations because 1, 2 and 3 undergo completely different intramolecular cycloaddition reactions. In addition, results of double pulsed field gradient spin echo NOESY 1D experiments performed on perezone (1) were unable to provide evidence for folded conformers. Copyright © 2013 John Wiley & Sons, Ltd.     

Synthesis and conformational analysis of efrapeptins

The efrapeptin family of peptide antibiotics produced by the fungus Tolypocladium niveum, and the neo‐efrapeptins from the fungus Geotrichum candidumare inhibitors of F₁‐ATPase with promising antitumor, antimalaria, and insecticidal activity. They are rich in C^α‐dialkyl amino acids (Aib, Iva, Acc) and contain one β‐alanine and several pipecolic acid residues. The C‐terminus bears an unusual heterocyclic cationic cap. The efrapeptins C–G and three analogues of efrapeptin C were synthesized using α‐azido carboxylic acids as masked amino acid derivatives. All compounds display inhibitory activity toward F₁‐ATPase. The conformation in solution of the peptides was investigated with electronic CD spectroscopy, FT‐IR spectroscopy, and VCD spectroscopy. All efrapeptins and most efrapeptin analogues were shown to adopt helical conformations in solution. In the case of efrapeptin C, VCD spectra proved that a 3₁₀‐helix prevails. In addition, efrapeptin C was conformationally studied in detail with NMR and molecular modeling. Besides NOE distance restraints, residual dipolar couplings (RDC) observed upon partial alignment with stretched PDMS gels were used for the conformational analysis and confirmed the 3₁₀‐helical conformation.     

Synthesis, characterization, and conformational analysis of new perfunctionalized calix[9]arenes

The synthesis of a series of six new per-substituted p-tert-butylcalix[9]arenes derivatives has been achieved. Functions such as ester, nitrile, or carbonate have been grafted on the phenolic oxygens of calix[9]arene: p-tert-butylcalix[9]arene nona-ethyl acetate, p-tert-butylcalix[9]arene nona-carboxylic acid, p-tert-butylcalix[9]arene nona-cyanopropyloxy, p-tert-butylcalix[9]arene nona-tert-butoxycarbonyle, p-tert-butylcalix[9]arene nona-acetyl, and p-tert-butylcalix[9]arene nona-trifluoroacetyl have been obtained in good yields (from 48% to 78%) and fully characterized. The X-ray structures of p-tert-butylcalix[9]arene nona-tert-butoxycarbonyl and p-tert-butylcalix[9]arene nona-ethyl acetate have been determined. A dynamic NMR study has revealed the high conformational mobility of such structures, even at low temperature.     

Synthesis, conformation and dynamics of 4,4,5,5,6,6,7,7,8,8-decamethyl-1-oxa-spiro[2.5]octane and 1,2,3,3,4,4,5,5,6,6-decamethyl-cyclohexene

The fragmentation of a suitable methylated 1-oxa-spiro[2.5]octane yields permethyl-cyclohexene. The activation parameters for the chair to chair interconversion of the 1-oxa-spiro[2.5]octane and the half-chair to half-chair interconversion of permethyl-cyclohexene were determined via bandshape analyses of exchange-broadened ¹H and ¹³C NMR spectra, respectively.     

Synthesis and conformational analysis of new troponyl aromatic amino acid

Synthetic peptides are in huge demand in expansion of potential peptide mimics, which may have improved or comparable function as natural one. With these concerns, phenyl bearing aromatic amino acids and peptides has extensively explored, because phenyl residue has high probability in forming stable secondary structure, owing to the presence of an extra stabilizing factor as π–π non-covalent interactions. Apart from phenyl bearing benzenoid aromatic amino acids, a few non-benzenoid aromatic derivatives such as tropolone and related compounds are also occurred in nature, but troponyl containing amino acids and peptides are very poorly understood. Tropolonyl derivatives also contain carbonyl functional group, which may play an important role to provide stable conformation in peptide. Herein we report the synthesis, and conformational analysis of rationally designed new unnatural δ-amino acid, troponyl aminoethylglycine (Tr-aeg), which contains troponyl residue as side chain in flexible aminoethylglycine (aeg) amino acid backbone. We also demonstrate the role of troponyl carbonyl of Tr-aeg residue in hydrogen bonding with adjacent amide NH of their hybrid di/tri-peptides with NMR methods and DFT calculations. In future, Tr-aeg amino acid would be a potential building block in development of promisable peptide mimics.     

Assignment of proton NMR resonances and conformational analysis of [Lys8]-vasopressin homologues

The assignment of proton NMR signals and the conformational analysis of N-(Gly)–[Lys⁸]–vasopressin and N-(Gly Gly Gly) [Lys⁸]-vasopressin in dimethyl sulfoxide solution by means of one- and two-dimensional NMR techniques are presented. Dihedral angles obtained from ³J (HN C α-H) vicinal couplings, intramolecular distances estimated from nuclear Overhauser enhancements (NOEs) and two-dimensional experiments in the rotating frame (ROESY), as well as temperature dependences of the amide protons, suggest a more or less rigid ring conformation with an inverse γ-turn for both cyclic peptides.     

Synthesis, structural characterization and conformational aspects of nostoclide analogues

The synthesis and structural analysis of a set of nostoclide analogues with potential herbicide activity is described. The influence of intra- and intermolecular hydrogen bonding, as well as other interactions on the conformation and packing of the compounds is thoroughly described using DFT calculations and single crystal X-ray diffraction analyses. All lactones exhibited the Z configuration as confirmed by NOESY experiments and by single crystal X-ray diffraction measurements.     

Synthesis of perfragilin A, B and some analogues

Synthesis of the cytotoxic isoquinoline quinone perfragilin A, an improved synthesis of perfragilin B and preparation of some analogues of both these compounds are described. Cytotoxicity evaluation of a number of the products is reported. The regioselectivity in Diels-Alder reactions of differently substituted benzoquinones with 2-aza-1,3-bis(t-butyldimethylsilyloxy)-1,3-butadiene is described.     

Model dipeptides incorporating the trans cyclohexane analogues of phenylalanine: further evidence of the relationship between side-chain orientation and β-turn type

In order to study the influence of the side-chain orientation on the peptide backbone conformation we have synthesised the model dipeptides t-BuCO-l-Pro-(1S,2R)-c₆Phe-NHMe and t-BuCO-l-Pro-(1R,2S)-c₆Phe-NHMe, incorporating each enantiomer of the trans cyclohexane analogue of phenylalanine (trans-1-amino-2-phenylcyclohexanecarboxylic acid). The orientation of the aromatic side-chain determines the β-turn type accommodated by these peptides to the point that the (1S,2R)-c₆Phe derivative retains the type I β-turn in the crystalline state, in contrast to the behaviour exhibited by the natural counterpart t-BuCO-l-Pro-l-Phe-NHMe.     

Correlations between conformational isomerism and chromatographic diastereoselectivity of bis amino amide s-triazine derivatives

NMR spectroscopy was used to probe the conformational behavior of diastereomeric s-triazine derivatives containing two chiral amino amide substituents, in order to shed light onto the mechanism of chromatographic diastereoselectivity. Utilizing the amino hydrogen signals in the proton NMR spectrum, the population of the conformations caused by rotation about the bond between the amino nitrogen and aromatic carbon atoms could be observed. The population distribution between the three possible conformations was similar but not identical between the two diastereomers, with similar trends being observed for both bis alanine amide and bis valine amide derivatives. Based on a simple model in which it is assumed that adsorption to the hydrophobic RP-LC stationary phase occurs only for the conformations having both amino amide R-groups on the same side of the triazine ring plane, the different conformation populations between the two diastereomers obtained by NMR was consistent with the observed RP-LC elution order (L-L diastereomer followed by L-D). The predicted diastereoselectivity values from NMR data were compared to RP-LC diastereoselectivity values obtained using both C18 and polymeric columns, with both acetonitrile/water and DMSO/water mobile phases. Values obtained with the polymeric column were in better agreement with calculated values than those obtained with the C18 column, suggesting that the simple adsorption model used to calculate the diastereoselectivity is more relevant towards a simple hydrophobic polymeric surface rather than a more complex C18 stationary phase. This study indicates that proton NMR is a useful tool for studying the diastereoselective mechanism of these derivatives, due to the relatively slow C-N bond rotation caused by the significant sp(2) character of the amino nitrogen atoms.     

Straightforward, racemization-free synthesis of peptides with fairly to very bulky di- and trisubstituted glycines

Several fully protected tri- and pentapeptides containing a central symmetrical α,α-dialkyl glycine residue, with the alkyl group varying from methyl or ethyl to benzyl, were synthesized in good yields by a strategy based on the Ugi-Passerini reaction. Each Ugi-Passerini adduct was selectively cleaved and the product submitted to an assisted N,N′-dicyclohehylcarbodiimide coupling to an amino acid or dipeptide ester, respectively. Tripeptides as the above but containing a 4-methoxybenzyl group at the nitrogen atom of the central residue were also synthesized in fair to good yields by N-[(1H-benzotriazol-1-yl)-(dimethylamino)methylene]-N-methylmethanaminium hexafluorophosphate N-oxide assisted couplings. The results reported here show that our strategy is appropriate for routine synthesis of peptides incorporating these moieties.     

Calix[4]arene bisphosphite ligands bearing two distal 2,2′-biphenyldioxy or 2,2′-binaphthyldioxy moieties: conformational flexibility and allyl-palladium complexes

Achiral and chiral calix[4]arene bisphosphite ligands (2 and 3) bearing two distal 2,2′-biphenyldioxyphosphinoxy and 2,2′-binaphthyldioxyphosphinoxy moieties, respectively, have been synthesized. Each of these ligands exists in two pairs of interconverting conformations in solution. The partial cone conformer (A) of the (bis)biphenyldioxyphosphinoxy ligand 2 has been separated by fractional crystallization and its structure established by X-ray crystallography. The mechanism of interconversion of the pairs of conformers (A/B and C/D) has been probed by two-dimensional NMR spectroscopy. The ¹H and ³¹P NMR evidence strongly supports a similar kind of exchange mechanism for ligand 3. Freezing of the cone conformer from the interconverting C/D pair of conformers of ligand 2 has been achieved by complexation with (allyl)palladium moieties. The methyl-allyl complex (2d) is moderately effective for catalytic regioselective allylic alkylation of crotyl acetate.