Solution structure of the antitumor candidate trunkamide A by 2D NMR and restrained simulated annealing methods

Trunkamide A (1) is a cyclic heptapeptide extracted from the ascidian Lissoclinum sp. and has shown very promising cytotoxic activity. This compound incorporates several of the motifs commonly observed in the Patellin family, including dimethylallyl (Dma) Thr and Ser side chains and a thiazoline heterocycle. Given that little is known about the structures adopted by the cyclopeptides of the Patellin family, and with the aim of establishing structure-activity relationships, we have carried out the conformational analysis of trunkamide A by a combination of 2D NMR experiments and simulated annealing calculations. Our results show that the conformation of 1 is very rigid and is dominated by the volume of the dimethylallyl side chains and two trans-annular hydrogen bonds. We have also studied the conformation of 2, the l-Phe diastereoisomer of 1, the analysis of which provides a possible rationale for its epimerization to 1, a process that is observed in solution. Finally, we show how a thorough NMR characterization can be used, in combination with simulated annealing methods, to confirm the configuration of a stereogenic center in the backbone of a rigid cyclic peptide such as trunkamide A (1).     

A novel protecting/activating strategy for beta-hydroxy acids and its use in convergent peptide synthesis

beta-Hydroxy acids were reacted with hexafluoroacetone and carbodiimides to give carboxy-activated six-membered lactones in good yields. On reaction with amines, the corresponding amides were obtained. We demonstrate the following applications of this protecting/activating strategy: preparation of carboxamides in solution and on solid phase (both normal and reverse mode); recovery and reuse of the excess material in solid-phase synthesis; and convergent solid-phase peptide synthesis (CSPPS) with peptide segments bearing C-terminal Ser or Thr with very low levels of epimerization (<1%, HPLC).     

Efficient synthesis of suitably protected beta-difluoroalanine and gamma-difluorothreonine from L-ascorbic acid

[reaction: see text] Fluorinated amino acids are useful building blocks for the preparation of biologically active peptides and peptidomimetics with increased metabolic stability. We report here the synthesis of two fluorinated amino acids, beta-difluoroalanine and gamma-difluorothreonine, as analogues of Ser and Thr, respectively. These compounds were suitably protected for Fmoc-based solid-phase peptide synthesis. Once incorporated into peptides, they may serve as alternative substrates or inhibitors of lantibiotic synthetases that posttranslationally dehydrate Ser and Thr residues to dehydroalanine and dehydrobutyrine, respectively.     

Solid-phase glycosylation of peptide templates and on-bead MAS-NMR analysis: perspectives for glycopeptide libraries

The efficient solid-phase glycosylation of amino acid side chains (serine (Ser), threonine (Thr), and tyrosine (Tyr)) in peptides was demonstrated with a variety of glycosyl trichloroacetimidate donors in high yields and purities. A novel photolabile linker, with no chiral centre, was introduced to facilitate analysis by both matrix-assisted laser desorption ionisation time of flight (MALDI-TOF) mass spectrometry and nanoprobe magic angle spinning (MAS) NMR spectroscopy. Product analysis by nanoprobe MAS NMR spectroscopy, LC-MS and MALDI-TOF mass spectrometry of the glycosylation reactions indicated that the reactivity order of the hydroxy side-chain functions of amino acids in peptides on the solid-phase was Tyr>Ser>Thr. The nearly quantitative glycosylation yields and the efficient on-bead product analysis by nanoprobe MAS NMR spectroscopy have made a truly solid-phase approach for the synthesis and analysis of glycopeptide libraries possible.     

Solid-phase synthesis of imidazo[1,2-a]pyridine using sodium benzenesulfinate as a traceless linker

[formula: see text] The preparation of the first library of imidazo[1,2-a]pyridine derivatives on a solid support is described. A sulfone linker strategy was applied in the synthesis. Key steps involved in the solid-phase synthetic procedure include (i) alpha-haloketone resin formation by sulfinate-->sulfone alkylation, (ii) imidazo[1,2-a]pyridine ring formation by treatment with 2-aminopyridine, (iii) sulfone anion alkylation, and (iv) traceless product release by oxidation-elimination. A library of 12 imidazo[1,2-a]pyridines was synthesized.     

Solution phase studies towards the synthesis of triarylamine oligomers using a germanium linker on a solid support

In this letter, we describe the iterative solution phase synthesis of a triarylamine trimer as proof of concept towards the synthesis of oligomeric materials by solid-phase synthesis. Our model system utilises the stability of germanium linkers to nucleophilic conditions to develop efficient steps towards oligomer synthesis via (i) selective deprotection of tert-butyl-dimethyl-silyl ether (OTBDMS) functionality, (ii) conversion to reactive trifluoromethanesulfonate (triflate) functionality and (iii) Suzuki cross-coupling reactions.     

Solid-phase synthesis of pyrazolines and isoxazolines with sodium benzenesulfinate as a traceless linker

[reaction: see text] The preparation of pyrazoline and isoxazoline derivatives with traceless solid-phase sulfone linker strategy is described. Key steps involved in the solid-phase synthetic procedure include (i) sulfinate S-alkylation, (ii) sulfone anion alkylation, (iii) gamma-hydroxy sulfone --> gamma-ketosulfone oxidation, and (iv) traceless product release via elimination-cyclization. A library of 12 pyrazolines and isoxazolines was synthesized.     

Synthesis of poly(O-phospho-L-serine) and its structure in aqueous solution

A novel polypeptide, poly(O-phospho-L -Ser), was synthesized through the following three steps: i) preparation of O-diphenylphospho-L -serine N-carboxyanhydride [Ser(PPh₂) NCA]; ii) polymerization of Ser(PPh₂) NCA; iii) removal of phenyl groups from poly[Ser(PPh₂)]. The overall yield in the three- step synthesis was 71%, and the phospho-Ser content in poly(O-phospho-L -Ser) was 98 ± 1%. Circular dichroism spectra suggest that the polypeptide has two different disordered structures in aqueous solution.     

Traceless Sulfone Linker for the Solid-Phase Organic Synthesis of 1-(E)-Styryl-4-substituted-1,2,3-triazoles

A novel, facile, solid-phase, organic synthesis of 1-(E)-styryl-4-substituted-1,2,3-triazoles in good yields and purities via traceless sulfone linker has been developed. Key steps involved in this synthetic procedure include (i) sulfone alkylation of sulfinate resin with (2-azido-1-iodoethyl)benzene, (ii) [3 + 2] cycloaddition with terminal alkynes in the presence of CuI, and (iii) traceless product release by base-mediated elimination process.     

Solid-phase synthesis of lidocaine and procainamide analogues using backbone amide linker (BAL) anchoring

New solid-phase strategies have been developed for the synthesis of lidocaine (1) and procainamide (2) analogues, using backbone amide linker (BAL) anchoring. Both sets were prepared starting from a common resin-bound intermediate, followed by four general steps: (i) attachment of a primary aliphatic or aromatic amine to the solid support via reductive amination (as monitored by a novel test involving reaction of 2,4-dinitrophenylhydrazine with residual aldehyde groups); (ii) acylation of the resultant secondary amine; (iii) displacement of halide with an amine; and (iv) trifluoroacetic acid-mediated release from the support. A manual parallel strategy was followed to provide 60 novel compounds, of which two dozen have not been previously described. In most cases, initial crude purities were >80%, and overall isolated yields were in the 40-88% range.     

Solid-phase synthesis of 3,4-dihydro-1H-pyrimidine-2-ones using sodium benzenesulfinate as a traceless linker

The facile preparation of 3,4-dihydropyrimidine-2-one derivatives with traceless solid-phase sulfone linker strategy is described. Key steps involved in the solid-phase synthetic procedure include (i) sulfinate acidification, (ii) condensation of urea or thiourea with aldehydes and sulfinic acid, and (iii) traceless product release via a one-pot cyclization-dehydration process. A library of 18 compounds was synthesized.     

Solid-phase synthesis of novel isoxazolocyclobutanones and isoxazolinocyclobutenones

[reaction: see text] The preparation of novel isoxazolocyclobutanone and isoxazolinocyclobutenone derivatives via a traceless solid-phase sulfone linker strategy is described. Key steps in the solid-phase protocol reported here include (i) sulfinate right arrow sulfone alkylation, (ii) four-member ring formation by sulfone dianion alkylation, (iii) heterocycle formation by nitrile oxide 1,3-dipolar cycloaddition, and (iv) traceless product release by cyclobutanol right arrow cyclobutanone oxidation with concomitant linker cleavage by sulfinate elimination.     

Fmoc-based solid-phase synthesis of adenylylated peptides using diester-type adenylylated amino acid derivatives

Phosphodiester-type adenylylated (AMPylated) Ser, Thr, and Tyr derivatives were developed for Fmoc solid phase peptide synthesis of AMPylated peptides. One-pot/sequential reaction consisting of condensation of an N-nonprotected adenosine derivative and Fmoc-Ser/Thr/Tyr-OAllyl using allyl-N,N-diisopropylchlorophosphoramidite and subsequent oxidation with m-chloroperbenzoic acid gave phosphotriester-type AMPylated Ser/Thr/Tyr derivatives. After Pd(0)-mediated deprotection of allyl groups, the resulting phosphodiester-type AMPylated Ser/Thr/Tyr derivatives were successfully incorporated into peptides by standard Fmoc solid phase peptide synthesis without significant side reactions including dehydroalanine formation.     

Gas-phase enantioselectivity of chiral amido[4]resorcinarene receptors

Diastereomeric proton-bound [1(L)HA]+ complexes between selected amino acids (A=phenylglycine (Phg), tryptophan (Trp), tyrosine methyl ester (TyrOMe), threonine (Thr), and allothreonine (AThr)) and a chiral amido[4]resorcinarene receptor (1(L)) display a significant enantioselectivity when undergoing loss of the amino acid guest A by way of the enantiomers of 2-aminobutanes (B) in the gas phase. The enantioselectivity of the B-to-A displacement is ascribed to a combination of thermodynamic and kinetic factors related to the structure and the stability of the diastereomeric [1(L)HA]+ complexes and of the reaction transition states. The results of the present and previous studies allow classification of the [1(L)HA]+ complexes in three main categories wherein: i) guest A does not present any additional functionalities besides the amino acid one (alanine (Ala), Phg, and phenylalanine (Phe)); ii) guest A presents an additional alcohol function (serine (Ser), Thr, and AThr); and iii) guest A contains several additional functionalities on its aromatic ring (tyrosine (Tyr), TyrOMe, Trp, and 3,4-dihydroxyphenylalanine (DOPA)). Each category exhibits a specific enantioselectivity depending upon the predominant [1(L)HA]+ structures and the orientation of the 2-aminobutane reactant in the relevant adducts observed. The results may contribute to the understanding of the exceptional selectivity and catalytic properties of enzyme mimics towards unsolvated biomolecules.     

Solution- and solid-phase synthesis of 4-hydroxy-4,5-dihydroisoxazole derivatives from enantiomerically pure N-tosyl-2,3-aziridine alcohols

[reaction: see text] Enantiomerically pure N-tosyl-2,3-aziridine alcohols are directly converted into 4-hydroxy-4,5-dihydroisoxazole 2-oxides through oxidation to the corresponding aldehydes followed by in situ tandem nitroaldol-intramolecular cyclization. This study was concerned with (i) the selection of a suitable aziridine activation, (ii) the preparation of the target 4-hydroxy-4,5-dihydroisoxazole derivatives in solution, and (iii) the elaboration of a solid-phase process using hydroxy Merrifield-supported nitroacetic acid ester.     

Reverse thioether ligation route to multimeric peptide antigens

Multimeric presentation, a rather effective way of enhancing peptide immunogenicity, is best exemplified by MAP (multiple antigenic peptide) dendrimers consisting of a branched Lys core on which several copies of the peptide epitope are displayed. While accessible by solid-phase synthesis, MAPs can also be conveniently made in solution, e.g., by linking the epitope (N-acetylated and with a C-terminal Cys) through a thioether bond onto the α and ε (haloacetyl-activated) positions of the Lys core. We now report the reverse version of this approach, whereby a chloroacetyl-derivatised epitope is tethered to a thiol-functionalised form of a Lys dendron core. This convergent approach can be carried out either in solution or in the solid phase and is advantageous because (i) in situ tris(2-carboxyethyl)phosphine (TCEP)-mediated reduction of disulfide bonds maintains the thiol platform reactive throughout the ligation process; (ii) the low amounts of TCEP used pose minimal risk to chloroacetyl groups in the peptide, resulting in (iii) significantly reduced byproduct formation, hence cleaner products. For the solid phase version of the method, an optimised procedure has been devised to convert the Lys core into a tetrathiol dendron.     

Can collision‐induced negative‐ion fragmentations of [M–H]– anions be used to identify phosphorylation sites in peptides?

A joint experimental and theoretical investigation of the fragmentation behaviour of energised [M-H](-) anions from selected phosphorylated peptides has confirmed some of the most complex rearrangement processes yet to be reported for peptide negative ions. In particular: pSer and pThr (like pTyr) may transfer phosphate groups to C-terminal carboxyl anions and to the carboxyl anion side chains of Asp and Glu, and characteristic nucleophilic/cleavage reactions accompany or follow these rearrangements. pTyr may transfer phosphate to the side chains of Ser and Thr. The reverse reaction, namely transfer of a phosphate group from pSer or pThr to Tyr, is energetically unfavourable in comparison. pSer can transfer phosphate to a non-phosphorylated Ser. The non-rearranged [M-H](-) species yields more abundant product anions than its rearranged counterpart. If a peptide containing any or all of Ser, Thr and Tyr is not completely phosphorylated, negative-ion cleavages can determine the number of phosphated residues, and normally the positions of Ser, Thr and Tyr, but not which specific residues are phosphorylated. This is in accord with comments made earlier by Lehmann and coworkers.     

Development of stable phosphohistidine analogues

Protein phosphorylation is one of the most common and extensively studied posttranslational modifications (PTMs). Compared to the O-phosphorylation of Ser, Thr, and Tyr residues, our understanding of histidine phosphorylation is relatively limited, particularly in higher eukaryotes, due to technical difficulties stemming from the intrinsic instability and isomerism of phosphohistidine (pHis). We report the design and synthesis of stable and nonisomerizable pHis analogues. These pHis analogues were successfully utilized in solid-phase peptide synthesis and semi-synthesis of histone H4. Significantly, the first antibody that specifically recognizes pHis was obtained using the synthetic peptide as the immunogen.     

Solid-phase synthesis of 7-substituted 3H-imidazo[2,1-i]purines

A method for solid-supported synthesis of N,N-disubstituted (3H-imidazo[2,1-i]purin-7-yl)methyl amines has been developed. The key features of this library synthesis are: (i) immobilization of commercially available N6-benzoyl-5'-O-(4,4'-dimethoxytrityl)-2'-deoxyadenosine 3'-(2-cyanoethyl N,N-diisopropylphosphoramidite) by phosphitylation to a hydroxyl-functionalized support, (ii) quantitative conversion of the deprotected adenine base to 3H-imidazo[2,1-i]purine-7-carbaldehyde with bromomalonaldehyde in DMF in the presence of formic acid and 2,6-lutidine, (iii) reductive amination of the formyl group followed by N-alkylation or N-acylation, and (iv) release from the support by acidolytic cleavage of the N-glycosidic bond. Steps (ii) and (iii) have been optimized in some detail by using (adenin-9-yl)acetic acid anchored to a Phe-Wang resin as a model compound.     

Convergent synthesis of the BCDEFGHIJ-ring polyether core of gambieric acids, potent antifungal polycyclic ethers

A convergent synthesis of the nonacyclic BCDEFGHIJ-ring polyether core of gambieric acids, potent antifungal polycyclic ether marine natural products, has been achieved. The present synthesis involved as key features: (i) convergent union of the BCD- and GHIJ-ring fragments through esterification, (ii) construction of the E-ring as a lactone form via reductive acetylation, (iii) stereoselective allylation to establish the C26 stereocenter, and (iv) ring-closing metathesis reaction to form the nine-membered F-ring.