Self-assembly of cyclic homo- and hetero-beta-peptides with cis- furanoid sugar amino acid and beta-hGly as building blocks

The design, synthesis and characterization of a new class of peptide nanotubes, self-assembled from cyclic homo- and hetero-beta-peptides based on cis-furanoid sugar amino acid and beta-hGly residues are described; these results represent the expansion of the conformational pool of cis beta-sugar amino acids in the design of peptide nanotubes.     

Caged O-phosphorothioyl amino acids as building blocks for Fmoc-based solid phase peptide synthesis

The synthesis of 1-(2-nitrophenylethyl) caged O-phosphorothioylserine, -threonine, and -tyrosine derivatives is reported. These amino acid building blocks can be directly incorporated into peptides by Fmoc-based solid phase synthesis as their pentafluorophenyl esters or as symmetric anhydrides. Upon irradiation with UV light, the thiophosphate group, representing a hydrolysis resistant phosphate analog, is revealed.     

New uses of amino acids as chiral building blocks in organic synthesis

[reaction: see text] N,N-Dibenzylamino aldehydes have emerged as a highly useful class of chiral building blocks in synthetic organic chemistry. We envisioned the transformation of the N,N -dibenzylamino aldehydes to the corresponding aldimines followed by diastereoselective methylene transfer with a sulfonium ylide to obtain alpha-amino aziridines in high yields.     

Readily available amino acid building blocks for the synthesis of phosphole-containing peptides

Nucleophilic substitution of a phospholide anion onto protected 3-iodoalanine leads to the formation of an amino acid with an appended phosphole in excellent yield. Manipulation of the protecting groups, leads to building blocks suitable for the synthesis of phosphole-containing polypeptides.     

Synthesis and properties of MIDA boronate containing aromatic amino acids: new peptide building blocks

Herein, we report the synthesis of novel phenylalanine and tyrosine derivatives containing a N-methyliminodiacetic acid boronate group. These compounds can be prepared enantiomerically pure, they are stable to column chromatography and they can be stored in air for two months without degradation occurring. This new class of boronate containing aromatic amino acids has potential applications in both peptide chemistry and natural product synthesis.     

Benzoderivatives of nucleic acid bases as modified DNA building blocks

The tautomeric properties of benzoderivatives of the canonical nucleic acid bases have been studied by using different computational approaches. Attention has been paid to the impact of the benzene group in altering the tautomeric preferences of the canonical bases both in the gas phase and in aqueous solution. To this end, relative solvation free energies of the tautomers determined from Self-Consistent Reaction Field continuum calculations and Monte Carlo-Free Energy Perturbation are combined with gas-phase tautomerization free energies determined from quantum mechanical calculations. The results provide a detailed picture of the tautomeric preferences of the benzoderivatives of nucleic acid bases. This information is used to examine the recognition properties of the preferred tautomers of the benzo-fused derivatives, paying particular attention to the ability to form Watson-Crick hydrogen-bonding and stacking interactions as well as to the hydrophobic nature of the modified bases. The implications of present results on the potential use of benzo-fused bases as potential building blocks in modified DNA duplexes are examined.     

Stepwise solid phase synthesis of uridylylated viral genome-linked peptides using uridylylated amino acid building blocks

The uridylylated amino acid building blocks 2-cyanoethyl-(N^α-9-fluorenylmethoxy-carbonyl-tyrosin-4-yl)-(2′,3′-di-O-acetyluridin-5′-yl) phosphate and 2-chlorophenyl-(N^α-fluorenyl-methoxycarbonyl-serin-3-yl)-(2′,3′-di-O-acetyluridin-5′-yl) phosphate have been used successfully in an on-line SPPS of the VPgpU from the polio, coxsackie and cowpea mosaic virus.     

Synthesis of alkyl 2-(bromomethyl)aziridine-2-carboxylates and alkyl 3-bromoazetidine-3-carboxylates as amino acid building blocks

A short synthesis of alkyl 2-(bromomethyl)aziridine-2-carboxylates and alkyl 3-bromoazetidine-3-carboxylates was developed involving amination, bromination, and base-induced cyclization of alkyl 2-(bromomethyl)acrylates. These new small ring azaheterocyclic α- and β-amino acid derivatives are promising synthons as demonstrated by their transformation to 2-(aminomethyl)aziridine-2-carboxylates and 3-aminoazetidine-3-carboxylates.     

Efficient microwave combinatorial parallel and nonparallel synthesis of N-alkylated glycine methyl esters as peptide building blocks

An easy and convenient microwave-assisted synthesis of N-alkylated glycine methyl esters is described. Parallel and nonparallel combinatorial methods are described and compared. The described reactions are reductive alkylations of several aldehydes and glycine methyl ester in the presence of NaBH3CN. Good yields and short reaction times are the main aspects of these procedures.     

Synthesis of hydrazino-peptide nucleic acid monomers and dimers as new PNA backbone building blocks

We describe the synthesis of new hydrazinoPNA (hydPNA) monomers and new hydPNA-containing dimers. For the hydPNA monomers, the primary terminal amino group of the aminoethylglycine unit of classical aegPNA is replaced by a hydrazine moiety. An appropriate choice of two orthogonal protecting groups on the two hydrazine nitrogen atoms makes it possible to drive their coupling with other monomers selectively on one or the other nitrogen atom, thus obtaining two different types of PNA dimers. These dimers represent new building blocks that can be used to generate novel PNA oligomers.     

Enzyme modification by MPEG with an amino acid or peptide as spacer arms

A method for the modification of enzymes by MPEG carrying an amino acid or peptide as a spacer arm is described and tested with aliphatic or aromatic side chains amino acids. The procedure involves MPEG activation by p-nitrophenylchloroformate for the amino acid or peptide coupling that is in turn activated for the protein binding. The advantage of the method resides in the possibility to introduce proper reporter groups between the polymer and the protein as norleucine for a direct evaluation of the bound polymer chains, tryptophan for structural studies of the polymer-protein adduct, and radioactive amino acid for pharmacokinetic investigations. The method was positively tested with arginase, ribonuclease, and superoxide dismutase as enzymes of therapeutic value.     

Phosphomolybdate clusters as molecular building blocks in the design of one-, two- and three-dimensional organic-inorganic hybrid materials

An attractive approach to the design of inorganic solids exploits the tethering of inorganic clusters through organic spacers to produce hybrid materials with composite properties. We have recently described a modified strategy in which polyoxometalate clusters are linked through organic subunits to give an anionic hybrid substructure which may be further modified through the introduction of secondary metal-ligand complex (SMLC) cations, serving as a third component building block. In this application, the molybdophosphonate cluster {Mo₅O₁₅(O₃PR)₂}⁴⁻ serves as a secondary building unit (SBU) with alkyl (CH₂)_n or aromatic -(C₆H₄)_n- tethers providing one-dimensional structural expansion. A binucleating ligand such as tetrapyridylpyrazine (tpyprz) is used to bridge secondary metal sites into a binuclear {Cu₂(tpyprz)}⁴⁺ SBU which may link phosphomolybdate clusters into two- or three-dimensional structures. The influence of a variety of structural determinants is discussed, including the tether length of the diphosphonate ligand, the coordination preferences of the secondary metal, expansion of the ligand component of the SMLC, and substitution of As for P in the oxide SBU.     

Hexylene- and octylene-bridged polysilsesquioxane hybrid crystals self-assembled by dimeric building blocks with ring structures

We report the synthesis of novel polysilsesquioxane hybrid crystals prepared from two precursors with hexylene- and octylene-bridged groups. Both crystals are composed of bimolecular rings (18- and 22-membered, respectively) formed by one-step condensation of two hydrolyzed monomers. The hydrogen bonds between silanol groups and the weak van der Waal's interactions between alkyl chains link the large rings as building blocks together into self-assembled, three-dimensional molecular crystalline structures. The precise control of the sol-gel process is considered to be the crucial factor in fabricating flexible long alkyl chains into an ordered stacking. These contributions extend the understanding of the sol-gel chemistry of polysilsesquioxanes.     

Enaminones as building blocks in heterocyclic synthesis: New syntheses of nicotinic acid and thienopyridine derivatives

Reacting 1,3‐diphenyl‐propan‐2‐one with equimolecular amount of dimethylformamide dimethylacetal afforded the enaminone 4. This when reacted with another equimolecular amount of dimethylformamide dimethylacetal afforded the dienaminone 5. Compound 4 condenses with cyanothioacetamide and with cyanoacetamide to yield 2‐thioxo‐ and 2‐oxo‐pyridine‐3‐carbonitrile derivatives 6a,b respectively. Compound 6a reacted with α‐chloroacetone 8 to yield the thieno[2,3‐b]pyridine derivative 10 that cyclized further into 4,7,8‐trisubstituted pyrido[2′,3′:2,3] thieno[4,5‐d]pyrimidine 12. Compound 4 also afforded 2,5,6‐trisubstituted nicotinic acid ethyl ester 13 by reaction with ethyl acetoacetate in acetic acid in the presence of ammonium acetate. The dienaminone 5 reacted with acetic acid, ammonium acetate/acetic acid, phenylhydrazine and 5‐amino‐3‐methylpyrazole yielding 3,5‐diphenyl‐pyran‐4‐one 15a , 3,5‐diphenyl‐1H‐pyridin‐4‐one 15b and 1,3,5‐trisubstituted pyridin‐4‐ones 16a‐b.     

Tilted amides in amino acid and peptide derivatives

Background: Amide bonds in peptides and proteins typically adopt planar cis or trans conformations. Conversions between cis and trans amide conformations are necessary for protein folding and for many other processes, but are difficult to achieve since they involve disruption of the planarity of the bond. As a first step to understanding cis-trans isomerization, we set out to synthesize and characterize peptides that mimic the tilted or twisted amide structures that are postulated to form the intermediate states in this process.Results: We have synthesized a model amino acid and four dipeptide derivatives containing a methyl-substituted aziridine residue. Single crystals of phenacyl (2R, 3R)-benzyloxycarbonyl-3-methyl-2-aziridinecarboxylate and phenacyl (2R, 3R)-acetyl-glycyl-3-methyl-2-aziridine-carboxylate were obtained. Using X-ray diffraction analysis, we determined that the amide nitrogens of the aziridine rings have tetrahedral sp³-like geometry with tilt angles in the range of 37–38°. The ¹³C-NMR spectra indicate that the amide carbonyl is dramatically shifted downfield as a consequence of the tilt.Conclusions: In peptides containing a substituted aziridine ring, the orbitals of the amide nitrogen are constrained into a tilted configuration. These peptides may mimic the transition state between cis and trans amide conformations. This technique thus provides a novel strategy for the study of isomerization and other biorecognition processes.     

Diproline templates as folding nuclei in designed peptides. Conformational analysis of synthetic peptide helices containing amino terminal Pro-Pro segments

The effect of N-terminal diproline segments in nucleating helical folding in designed peptides has been studied in two model sequences Piv-Pro-Pro-Aib-Leu-Aib-Phe-OMe (1) and Boc-Aib-Pro-Pro-Aib-Val-Ala-Phe-OMe (2). The structure of 1 in crystals, determined by X-ray diffraction, reveals a helical (alphaR) conformation for the segment residues 2 to 5, stabilized by one 4-->1 hydrogen bond and two 5-->1 interactions. The N-terminus residue, Pro(1) adopts a polyproline II (P(II)) conformation. NMR studies in three different solvent systems support a conformation similar to that observed in crystals. In the apolar solvent CDCl3, NOE data favor the population of both completely helical and partially unfolded structures. In the former, the Pro-Pro segment adopts an alphaR-alphaR conformation, whereas in the latter, a P(II)-alphaR structure is established. The conformational equilibrium shifts in favor of the P(II)-alphaR structure in solvents like methanol and DMSO. A significant population of the Pro(1)-Pro(2) cis conformer is also observed. The NMR results are consistent with the population of at least three conformational states about Pro-Pro segment: trans alphaR-alphaR, trans P(II)-alphaR and cis P(II)-alphaR. Of these, the two trans conformers are in rapid dynamic exchange on the NMR time scale, whereas the interconversion between cis and trans form is slow. Similar results are obtained with peptide 2. Analysis of 462 diproline segments in protein crystal structures reveals 25 examples of the alphaR-alphaR conformation followed by a helix. Modeling and energy minimization studies suggest that both P(II)-alphaR and alphaR-alphaR conformations have very similar energies in the model hexapeptide 1.