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Trifluoroacetic acid (TFA) is a common reagent in both solid-phase and solution peptide synthesis. It is used for the deprotection and/or cleavage of the synthesized peptide from the resin. The use of TFA under these standardized conditions is thought to be sufficiently mild, thereby preventing degradation of the desired product. However, peptides of the general structure R1-(N-alkyl X1)-X2-R2 are hydrolyzed by standard TFA solid-phase peptide synthesis (SPPS) cleavage/deprotection conditions providing fragments R1-(N-alkyl X1)-OH and H-X2-R2. The fragmentation is observed during a TFA cleavage both from the resin and in solution. The hydrolysis is proposed to proceed via an oxazolone-like intermediate in which equilibration of the chiral center of the N-alkylated residue occurs. This mechanism is supported by H/D exchange as observed MS and NMR in conjunction with HPLC.

The structure of At3g04780.1-des15, an Arabidopsis thaliana ortholog of the C-terminal domain of human thioredoxin-like protein, was determined by NMR spectroscopy. The structure is dominated by a beta-barrel sandwich. A two-stranded anti-parallel beta-sheet, which seals off one end of the beta-barrel, is flanked by two flexible loops rich in acidic amino acids. Although this fold often provides a ligand binding site, the structure did not reveal an appreciable cavity inside the beta-barrel. The three-dimensional structure of At3g04780.1-des15 provides an entry point for understanding its functional role and those of its mammalian homologs.

Syntheses of optically active ether-linked β-lactams and aza-proline analogues via 4-bromo-2-hydroxybutanoic acid esters derived from (S)- or (R)-malic acid are described. From these intermediates peptide secondary structure mimetics can be synthesized.

The preparation of sterically hindered secondary amino esters from the reaction of N-protected α-amino aldehydes and 3-, or 2-oxo esters with α-amino esters by reductive amination is described. The resulting amino esters were converted to the β-lactam or acylated to form N-acyl secondary amides.

Monte Carlo calculations show a classical γ-turn in a family of metabolites known as the malformins. This led to the synthesis of epimeric seven-membered ring γ-turn mimetics starting from leucine. NMR temperature coefficient studies were also performed.

Combinatorial chemistry, in its ability to generate vast arrays of non-peptide and non-oligonucleotide libraries, has had a major impact on the drug discovery effort. The design and generation of a combinatorial library, coupled with the ever important and effective feedback from high-throughput screening and data management, are critical to any drug discovery process. This review will focus on some aspects of computational chemistry, solid-phase organic chemistry and downstream analysis. The emphasis will be on computational aspects of library design and the use of cyclic scaffolds in the context of a focused library for optimization in drug discovery.

Zinc fingers of the transcription factor IIIA (TFIIIA) type, in which zinc is co-ordinated by two cysteine and two histidine ligands (Cys2/His2), contain a length of helix packed against a β-hairpin. These zinc fingers comprise the wider range of structurally homologous proteins for which 1H chemical shifts are available. A number of key resonances have chemical shifts that are highly sensitive to tertiary structure and are conserved between these peptides. The high conservation of these fingerprint chemical shifts is correlated with the common global fold of Cys2/His2 zinc fingers. These chemical shifts are largely independent of primary structure and should facilitate NMR assignments for future zinc finger proteins, as well as provide a diagnostic signature for the characteristic Cys2/His2 zinc finger fold.

A synthetic peptide corresponding to zinc finger 31 of the Xenopus protein Xfin adopts a folded conformation in the presence of zinc. The same peptide in the absence of zinc is not folded in a stable tertiary conformation, as determined by NMR. Binding experiments have shown that the peptide binds non-specifically to DNA only in the presence of zinc. Moreover, competitive DNA binding experiments indicate interaction with 3.9 +/- 0.4 base pairs.