A new flourene-derived anchor for solid-phase synthesis of protected peptides

Synthesis and NMR structure of p41icf, a potent inhibitor of human cathepsin L

The total synthesis and structural characterization of the MHCII-associated p41 invariant chain fragment (P41icf) is described. P41icf plays a crucial role in the maturation of MHC class II molecules and antigen processing, acting as a highly selective cathepsin L inhibitor. P41icf synthesis was achieved using a combined solid-phase/solution approach. The entire molecule (65 residues, 7246 Da unprotected) was assembled in solution from fully protected peptides in the size range of 10 residues. After deprotection, oxidative folding in carefully adjusted experimental conditions led to the completely folded and functional P41icf with a disulfide pairing identical to that of native P41icf. CD, NMR, and surface plasmon resonance (SPR) were used for the structural and functional characterization of synthetic P41icf. CD thermal denaturation showed clear cooperative behavior. Tight cathepsin L binding was demonstrated by SPR. (1)H NMR spectroscopy at 800 MHz of unlabeled P41icf was used to solve the three-dimensional structure of the molecule. P41icf behaves as a well-folded protein domain with a topology very close to the crystallographic cathepsin L-bound form.

A new method for the preparation of unprotected peptides on biocompatible resins with application in combinatorial chemistry

[formula: see text] A synthetic strategy for the preparation of side chain free peptides on biocompatible solid supports is described. Final peptide detachment is afforded in mild basic conditions with no presence of scavengers or other additives, thus allowing single peptide-resin beads to be cleaved in mass spectrometry sample plates for direct sequencing using MALDI-TOF post-source decay. This methodology offers clear advantages for the development of one-bead--one-compound combinatorial libraries in addition to parallel and regular synthesis of peptides.

Synthesis and binding properties of oligonucleotides carrying nuclear localization sequences

The synthesis of oligonucleotides carrying nuclear localization peptide sequences is described using two strategies: first, oligonucleotides carrying a thiol group at the 5' end were reacted with maleimido peptides; second, peptide and oligonucleotide were prepared stepwise on the same support, yielding oligonucleotide-3'-peptide conjugates. This second approach was thoroughly studied. Using amino acids and small peptides as model compounds, some side reactions were analyzed, detected, and minimized. Oligonucleotides complementary to Ha-ras gene and carrying nuclear localization peptides at the 3' and 5' ends were prepared. Melting temperature studies showed that duplexes containing nuclear localization peptides were more stable than duplexes with unmodified oligonucleotides. Moreover, oligonucleotide-peptide conjugates maintain a good mismatch discrimination when they bind to their target RNA.

Preparation of head-to-tail cyclic peptides via side-chain attachment: implications for library synthesis

Cyclic peptide mixtures represent a promising approach for drug lead discovery. Diversity can be expanded via changes in ring size, amide bond replacements, D- and L-natural and unnatural amino acids, and by the incorporation of beta-turn mimics and related conformational constraints. We expand the scope of our side-chain attachment/resin-bound cyclization strategy first developed using aspartic acid, asparagine, and elated acid-based attachments. In this report, we describe the preparation and use of Boc-Lys-OFm, Boc-Orn-OFm, and Boc-Dab-OFm. The synthetic strategies were verified by the independent synthesis of two small RGD-based cyclic mixtures, cyclo(Pro-Xxx-Lys-Arg-Gly-Asp), where Xxx = Ala, Ser, Leu, Tyr, using Boc-Asp-OFm, and then Boc-Lys-OFm for the initial resin-bound side-chain linkage. A new orthogonal synthetic approach to cyclic peptides, based on the use of the paranitrobenzyl (ONB) ester for alpha-carboxyl protection (selectively cleaved via SnCl2 reduction), was developed. It led to the successful synthesis of individual cyclic pentapeptides using serine (Boc-Ser-ONB), and tyrosine (Fmoc-Tyr-ONB) as the side chain-linked residues.

Synthesis and enzymatic stability of phosphodiester-linked peptide-oligonucleotide hybrids

Nucleopeptides Ac-Tyr(p3' dACGT)-Ala-Phe-Gly-NH2, Ac-Thr(p3'dACGT)-Ala-Phe-Gly-OH, Ac-Ser(p3'dACGT)-Ala-Phe-Gly-OH, and Phac-Hse(p3'dACGT)-Ala-Phe-Gly-OH, in which the 3'-end of a tetradeoxyribonucleotide is linked by a phosphodiester bond to a hydroxylated amino acid, were synthesized using a stepwise solid-phase methodology to study the influence of the linking amino acid on their stability to 3'-exonucleases. HPLC analysis of the reaction crudes after treatment of each nucleopeptide with snake venom phosphodiesterase showed that the lability of the amino acid-nucleoside linkage increases in the order Thr < Ser < Hse < Tyr.

New carbamate supports for the preparation of 3'-amino-modified oligonucleotides

A novel approach for the preparation of oligonucleotides carrying amino groups at the 3'-end is described. Several CPG supports having aminoalkyl groups and 3'-amino-2',3'-dideoxynucleosides linked through base-labile carbamate linkages such as 2-(2-nitrophenyl)ethoxycarbonyl and fluorenylmethoxycarbonyl were prepared using two different strategies. These supports are compatible to the standard solid phase phosphite-triester methodology and yield oligonucleotides containing amino groups at the 3'-end. Several properties of the 3'-amino oligonucleotides, such as nuclease resistance, hybridization, and preparation of oligonucleotide conjugates are discussed.