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Tamis Darbre

Publications and source records attributed to Tamis Darbre.

14 recordsLinked to original sources
PubMed2006

Artificial aldolases from peptide dendrimer combinatorial libraries.

Peptide dendrimers were investigated as synthetic models for aldolase enzymes. Combinatorial libraries were prepared with aldolase active residues such as lysine and proline placed at the dendrimer core or near the surface. On-bead selection for aldolase activity was carried out using the dye-labelled 1,3-diketone 1a, suitable for covalent trapping of enamine-reactive side-chains, and the fluorogenic enolization probe 6. Aldolase dendrimers catalyzed the aldol reaction of acetone, dihydroxyacetone and cyclohexanone with nitrobenzaldehyde. Much like enzymes, the dendrimers exhibited strong aldolase activity in aqueous medium, but were also active in organic solvent. Dendrimer-catalyzed aldol reactions reached complete conversion in 3 h at 25 degrees C with 1 mol% catalyst and gave aldol products with up to 65% ee. A positive dendritic effect in catalysis was observed with both lysine and proline based aldolase dendrimer catalysts.

Amino Acids↗
PubMed2006

Synthesis and activity of histidine-containing catalytic peptide dendrimers.

Peptide dendrimers built by iteration of the diamino acid dendron Dap-His-Ser (His = histidine, Ser = Serine, Dap = diamino propionic acid) display a strong positive dendritic effect for the catalytic hydrolysis of 8-acyloxypyrene 1,3,6-trisulfonates, which proceeds with enzyme-like kinetics in aqueous medium (Delort, E.; Darbre, T.; Reymond, J.-L. J. Am. Chem. Soc. 2004, 126, 15642-3). Thirty-two mutants of the original third generation dendrimer A3 ((Ac-His-Ser)8(Dap-His-Ser)4(Dap-His-Ser)2Dap-His-Ser-NH2) were prepared by manual synthesis or by automated synthesis with use of a Chemspeed PSW1100 peptide synthesizer. Dendrimer catalysis was specific for 8-acyloxypyrene 1,3,6-trisulfonates, and there was no activity with other types of esters. While dendrimers with hydrophobic residues at the core and histidine residues at the surface only showed weak activity, exchanging serine residues in dendrimer A3 against alanine (A3A), beta-alanine (A3B), or threonine (A3C) improved catalytic efficiency. Substrate binding was correlated with the total number of histidines per dendrimer, with an average of three histidines per substrate binding site. The catalytic rate constant kcat depended on the placement of histidines within the dendrimers and the nature of the other amino acid residues. The fastest catalyst was the threonine mutant A3C ((Ac-His-Thr)8(Dap-His-Thr)4(Dap-His-Thr)2Dap-His-Thr-NH2), with kcat = 1.3 min(-1), kcat/k(uncat) = 90'000, KM = 160 microM for 8-bytyryloxypyrene 1,3,6-trisulfonate, corresponding to a rate acceleration of 18'000 per catalytic site and a 5-fold improvement over the original sequence A3.

Binding Sites↗
PubMed2006

Dual mechanism of zinc-proline catalyzed aldol reactions in water.

The aldol reaction of acetone with aldehydes in aqueous medium under catalysis by zinc-proline (Zn(L-Pro)2) and secondary amines such as proline, (2S,4R)-4-hydroxyproline (Hyp) and (S)-(+)-1-(2-pyrrolidinomethyl)pyrrolidine (PMP) is shown to proceed by an enamine mechanism, as evidenced by reductive trapping of the iminium intermediate, while the aldol reaction of dihydroxyacetone (DHA) under catalysis by zinc-proline and by general bases such as N-methylmorpholine (NMM) is shown to occur under rate-limiting deprotonation of the alpha-carbon and formation of an enolate intermediate.

Journal Article↗
PubMed2006

Combinatorial synthesis, selection, and properties of esterase peptide dendrimers.

A 65,536-member combinatorial library of peptide dendrimers was prepared by split-and-mix synthesis and screened on solid support for esterolytic activity in aqueous buffer using 8-butyryloxypyrene-1,3,6-trisulfonate (2) as a fluorogenic substrate. Active sequences were identified by analysis of fluorescent beads. The corresponding dendrimers were resynthesized by solid-phase synthesis, cleaved from the resin, and purified by preparative reverse-phase HPLC. The dendrimers showed the expected catalytic activity in aqueous buffer. Catalysis was studied against a pannel of fluorogenic 8-acyloxypyrene-1,3,6-trisulfonate substrates. The catalytic peptide dendrimers display enzyme-like kinetics in aqueous buffer with substrate binding in the range K(M) approximately 0.1 mM, catalytic rate constants k(cat) approximately 0.1 min(-1), and specific rate accelerations over background up to k(cat)/k(uncat) = 10,000.

Arylsulfonates↗
PubMed2006

Peptide dendrimers as artificial enzymes, receptors, and drug-delivery agents.

The dendritic architecture applied to peptides provides a practical entry into globular macromolecules resembling proteins. A modular design was chosen using a divergent synthesis on solid support alternating proteinogenic alpha-amino acids with branching diamino acids, producing peptide dendrimers with a molecular weight of 3-5 kDa. Initial studies focused on models for hydrolases and produced esterase peptide dendrimers featuring histidine as the key catalytic residue. Variations of amino acid composition and the branching diamino acid led to enantioselective catalysts. Rate accelerations of k(cat)/k(uncat) = 90,000 were obtained when the design was changed to monomeric peptide dendrimers alternating two amino acids with the branching unit. A combinatorial approach was developed allowing for the preparation of large libraries (>60,000 members), which were screened for B12 binding and catalytic activity. The peptide dendrimers were also investigated for drug delivery. Glycopeptide dendrimers conjugated to colchicine selectively inhibited the proliferation of targeted cells, whereas colchicine alone displayed high toxicity.

Combinatorial Chemistry Techniques↗
PubMed2005

Inhibition of mitosis by glycopeptide dendrimer conjugates of colchicine.

Glycopeptide dendrimers have been prepared bearing four or eight identical glycoside moieties at their surface (beta-glucose, alpha-galactose, alpha-N-acetyl-galactose, or lactose), natural amino acids within the branches (Ser, Thr, His, Asp, Glu, Leu, Val, Phe), 2,3-diaminopropionic acid as the branching unit, and a cysteine residue at the core. These dendrimers have been used as drug-delivery devices for colchicine. Colchicine was attached to the dendrimers at the cysteine thiol group through a disulfide or thioether linkage. The biological activities of the glycopeptide dendrimer conjugates were evaluated in HeLa tumor cells and non-transformed mouse embryonic fibroblasts (MEFs). The concentrations of glycopeptide dendrimer drug conjugates required to achieve inhibition of cell proliferation by interference with the tubulin system were found to be higher (IC50 > 1 microM) compared to the required colchicine concentration. On the other hand, the glycopeptide dendrimer conjugates inhibited the proliferation of HeLa cells 20-100 times more effectively than the proliferation of MEFs. In comparison, non-glycosylated dendrimers and colchicine itself showed a selectivity of 10-fold or less for HeLa cells.

Animals↗
PubMed2004

A strong positive dendritic effect in a peptide dendrimer-catalyzed ester hydrolysis reaction.

The contribution of the dendritic structure in catalysis of ester hydrolysis was investigated with a systematic peptide dendrimer series of increasing generation number (G1-G4) containing a catalytic consensus sequence His-Ser in all branches. A strong positive dendritic effect was observed with up to 100-fold increased histidine reactivity between G1 and G4. Kinetic studies and isothermal calorimetric titration experiments showed that the strong positive dendritic effect resulted from cooperativity between binding and catalysis.

Calorimetry↗
PubMed2004

Selective catalysis with peptide dendrimers.

Peptide dendrimers incorporating 3,5-diaminobenzoic acid 1 as a branching unit (B) were prepared by solid-phase synthesis of ((Ac-A(3))(2)B-A(2))(2)B-Cys-A(1)-NH(2) followed by disulfide bridge formation. Twenty-one homo- and heterodimeric dendrimers were obtained by permutations of aspartate, histidine, and serine at positions A(1), A(2), and A(3). Two dendrimers catalyzed the hydrolysis of 7-hydroxy-N-methyl-quinolinium esters (2-5), and two other dendrimers catalyzed the hydrolysis of 8-hydroxy-pyrene-1,3,6-trisulfonate esters (10-12). Enzyme-like kinetics was observed in aqueous buffer pH 6.0 with multiple turnover, substrate binding (K(M) = 0.1-0.5 mM), rate acceleration (k(cat)/k(uncat) > 10(3)), and chiral discrimination (E = 2.8 for 2-phenylpropionate ester 5). The role of individual amino acids in catalysis was investigated by amino acid exchanges, highlighting the key role of histidine as a catalytic residue, and the importance of electrostatic and hydrophobic interactions in modulating substrate binding. These experiments demonstrate for the first time selective catalysis in peptide dendrimers.

Amino Acids↗
PubMed2003

Zn-proline catalyzed direct aldol reaction in aqueous media.

Zn complexes of proline, lysine and arginine are efficient catalysts for the aldol addition of p-nitrobenzaldehyde and acetone in aqueous medium, giving quantitative yields and enantiomeric excesses up to 56% with 5 mol% of the catalysts at room temperature.

Acetone↗
PubMed2003

Zinc mediated methyl transfer from trimethyl phosphate to chelating and non-chelating alkyl thiols. Model for Zn-dependent methyltransferases.

The methyl transfer from trimethyl phosphate to alkyl thiols was investigated in the presence of zinc ions and in the absence of strong base. The chelating thiol N-(2-mercaptoethyl)picolylamine (MEPAH) was methylated by trimethyl phosphate, in MeOH, in the presence of Zn salts whereas the reaction did not take place in the absence of Zn(2+). The pre-formed complex (MEPA)(2)Zn was methylated faster than the MEPAH in the presence of zinc ions The methyl transfer also took place in chloroform with similar yields at room temperature. When non-chelating hexanethiol was the methyl acceptor, a slower reaction took place in the presence of pyridine which was independent of Zn(2+). Kinetic studies of the methyl transfer from trimethyl phosphate to (MEPA)(2)Zn gave a second-order rate constant of 5.0 x 10(-5) M(-1) s(-1) as measured by 1H NMR spectroscopy in MeOH. The results obtained suggest that the methyl transfer to MEPA-Zn involves a zinc-bound thiolate.

Chelating Agents↗