Zoltan Timar

Fmoc/Acyl protecting groups in the synthesis of polyamide (peptide) nucleic acid monomers

The chemical synthesis of polyamide (peptide) nucleic acid (PNA) monomers 22–25 has been accomplished using Fmoc [N-(2-aminoethyl)glycine backbone], anisoyl (adenine), 4-tert-butylbenzoyl (cytosine) and isobutyryl/diphenylcarbamoyl (guanine) protecting-group combinations, thus allowing oligomer synthesis on both peptide and oligonucleotide synthesizers. An alternative method for the preparation of (N 6-anisoyladenin-9-yl)acetic acid 7 is described using partial hydrolysis of a dianisoylated derivative. Different methods were studied for guanine alkylation including (a) Mitsunobu reaction; (b) low-temperature, sodium hydride- and (c) N,N-diisopropylethylamine-mediated alkylation reactions to give preferentially N 9-substituted derivatives. Empirical rules are proposed for differentiating N 9/N 7-substituted guanines based on their 13C NMR chemical-shift differences.

Ab initio studies on the H-bonding of hypoxanthine and DNA bases

Novel and interesting points are underlined by ab initio (QM) calculations of H-bonding of all the six nucleobase dimers of hypoxanthine and DNA bases, namely Hypanti⋯Asyn, Hypanti⋯Aanti, Hypsyn⋯Ganti, Hypanti⋯Gsyn, Hypanti⋯Tanti, Hypanti⋯Canti. HF, DFT (Becke) and B3LYP (hybrid-DFT) methods were applied with and without polarisation functions. The H-bonding preference of hypoxanthine to natural DNA bases is Gsyn>Canti>Aanti>Asyn>Tanti≈Ganti. Becke and B3LYP give buckle and propeller arrangements for Hoogsteen dimers, but the use of an auxillary basis set overestimates the angles. Hartree–Fock optimised structures are almost planar and this method does not find the local minima of Hoogsteen pairs. Among the methods giving reliable geometries the Becke calculation needs the least computational resources.

Synthesis and analysis of peptide nucleic acid oligomers using Fmoc/acyl-protected monomers

The optimization of PNA oligomer synthesis has been accomplished employing Fmoc/acyl-protected monomers on TentaGel™ and Wang resins. Among the tested activating agents (CMP, BET, HATU) the latter was of choice in solid phase syntheses. “Leakage” of TentaGel™ resin greatly hampers the solution and MS analyses. Synthesis and acyl group deprotection steps have been separately examined using Wang resin. Optimal conditions also worked well on the CPG support. HPLC and MS analyses of the PNA oligomers were carried out under various conditions.

An electrospray mass spectrometric method for accurate mass determination of highly acid-sensitive phosphoramidites

An accurate mass determination method utilizing electrospray ionization mass spectrometry is described for analysis of several different types of phosphoramidites that are extremely acid-sensitive compounds. An earlier method, which applied a LiCl/acetonitrile system, was extended for this special application by using polymeric standards including poly(ethylene glycol) (PEG), poly(ethylene glycol) dimethyl ether (PDE) and poly(propylene glycol) (PPG). Concentrations of standards, samples and LiCl were optimized and potential impurities that affect the analyses were also investigated.

Aspartic acid scaffold in bradykinin B1 antagonists

Several novel bradykinin B1 receptor (B1R) antagonists were synthesized utilizing a new aspartic acid scaffold. This core is derived from the highly potent dihydroquinoxalinone scaffold published recently by researchers at Merck (Ha et al. Biochem. Biophys. Res. Commun. 2005, 331, 159–166). Despite the considerably limited chemical space of B1 antagonists, the synthesized compounds still showed significant biological activity. None of the four most potent compounds showed significant activity on the bradykinin B2 receptor (B2R), consequently they can be considered as valuable starting points for designing more potent and selective B1 antagonists. Furthermore, the synthesis of these aspartic acid derivatives is much simpler than that of the original Merck compounds suggesting efficient parallel synthesis approaches during their optimization. Docking known and novel B1 antagonists into the refined B1R homology model including the second extracellular loop (EC2) underlined the importance of this loop in ligand binding. Comparative binding mode analysis revealed that our novel compounds bind similar to the dihydroquinoxalinone template. Our results indicate that the rigid core of the dihydroquinoxalinone containing B1 antagonists is not crucial for maintaining B1 activity. Copyright

Accurate mass analysis of phosphoramidites by electrospray mass spectrometry.

A method of accurate mass determination of phosphoramidites is described. The commonly used methanol/water/acid system was replaced by LiCl-containing acetonitrile and the concentrations of LiCl, poly(ethylene glycol), and phosphoramidite samples were optimized.

Synthesis of Peptide Nucleic Acid Monomers

Abstract The chemical synthesis of peptide nucleic acid (PNA) monomers is described using Fmoc (backbone), anisoyl (cytosine, adenine), 4-tert-butylbenzoyl (cytosine) and isobutyryl/diphenylcarbamoyl (guanine) protecting group combinations. For the guanine monomer the alkylation was realized both in a Mitsunobu [DIAD, triphenylphosphine or (4-dimethylaminophenyl)diphenylphosphine, tert-butyl glycolate] and in a low-temperature, sodium-hydride mediated alkylation (tert-butyl bromoacetate) to give the N9 -substituted derivative.