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Biomedical subjects

D Seebach

Publications and source records attributed to D Seebach.

At least 19 recordsLinked to original sources
PubMed2001

Peptide folding induces high and selective affinity of a linear and small beta-peptide to the human somatostatin receptor 4.

beta-Peptides with side chains in the 2- and 3-positions on neighboring residues (of (S) configuration) are known to fold and form a turn (similar to an alpha-peptidic beta-turn). Thus, we have synthesized an appropriately substituted beta-tetrapeptide derivative to mimic the hormone somatostatin in its binding to the human receptors hsst(1-5), which is known to rest upon a turn containing the amino acid residues Thr, Lys, Trp, and Phe. The N-acetyl-peptide amide Ac-beta(3)-HThr-beta(2)-HLys-beta(3)-HTrp-beta(3)-HPhe-NH(2) (1) indeed shows all characteristics of the targeted turn-mimic: Lys CH(2) groups are in the shielding cone of the Trp indole ring (by NMR analysis, Figure 2) and there is high and specific nanomolar affinity for hsst(4) receptor (Table 1). In contrast, the isomer 2 bearing the Lys side chain in 3-, rather than in the 2-position, has a 1000-fold smaller affinity to hsst(4). The syntheses of the required Fmoc-protected beta-amino acids (8-11, 17) are described (Schemes 1-3). Coupling of the beta-amino acids was achieved by the manual solid-phase technique, on Rink resin.

Cell Line↗
PubMed2001

Preparation of dendritic and non-dendritic styryl-substituted Salens for cross-linking suspension copolymerization with styrene and multiple use of the corresponding Mn and Cr complexes in enantioselective epoxidations and hetero-Diels-Alder reactions.

Following work with TADDOLs and BINOLs, we have now prepared Salen derivatives (2, 3, 14, 15, 18, 19, 20, 21) carrying two to eight styryl groups for cross-linking copolymerization with styrene. The Salen cores are either derived from (R,R)-diphenyl ethylene diamine (3, 15, 19, 21) or from (R,R)-cyclohexane diamine (2, 14, 18, 20). The styryl groups are attached to the salicylic aldehyde moieties, using Suzuki (cf. 1) or Sonogashira cross-coupling (cf. 11), and/or phenolic etherification (cf. 5, 7) with dendritic styryl-substituted Fréchet-type benzylic branch bromides. Subsequent condensation with the diamines provides the chiral Salens. Corresponding Salens lacking the peripheral vinyl groups (cf. 12, 13, 16, 17) were also prepared for comparison of catalytic activities in homogeneous solution with those in polystyrene. Cross-linking radical suspension copolymerization of styrene and the styryl Salens, following a procedure by Itsuno and Fréchet, gave beads (ca. 400 microm diameter) which were loaded with Mn or Cr (ca. 0.2 mmol of complex per g of polymer), with more than 95% of the Salen incorporated being actually accessible for complexation (by elemental analysis). The polymer-bound Mn and Cr complexes were used as catalysts for epoxidations of six phenyl-substituted olefins (m-CPBA/NMO; products 22a-f), and for dihydropyranone formation from the Danishefsky diene and aldehydes (PhCHO, C5H11CHO, C6H11CHO, products 23a-c). There are several remarkable features of the novel immobilized Salens: i) The dendritic branches do not slow down the catalytic activity of the complexes in solution; ii) the reactions with Salen catalysts incorporated in polystyrene give products of essentially the same enantiopurity as those observed in homogeneous solution with the dendritically substituted or with the original Jacobsen - Katsuki complexes; iii) some Mn-loaded beads have been stored for a year, without loss of activity; iv) especially the biphenyl- and the acetylene-linked Salen polymers (p-2, -3, -20, -21, Figure 2, 3) give Mn complexes of excellent performance: after ten uses (without re-charging with Mn!) there is no loss of enantioselectivity or degree of conversion under the standard conditions.

Journal Article↗
PubMed2001

Lithiated 4-isopropyl-3-(methylthiomethyl)-5,5-diphenyloxazolidin-2-one: a chiral formyl anion equivalent for enantioselective preparations of 1,2-diols, 2-amino alcohols, 2-hydroxy esters, and 4-hydroxy-2-alkenoates.

The heterocyclic compound specified in the title (and readily prepared from commercial precursors) has a sterically protected C==O group, so that direct lithiation by BuLi at the exocyclic CH(2) group is possible (3 --> Li-3). The lithiated N,S-acetal derivative (Li-3) adds diastereoselectively to aldehydes (Table 2), unsymmetrical ketones (Table 3), chalcone (1,4-addition, Scheme 2), and N-phosphinoyl- and N-sulfonylimines (Table 4). Protection of the newly formed OH groups (Scheme 3) and/or MeS/OH displacement by Hg(O(2)CCF(3))(2) in aqueous THF/acetonitrile converts the N,S-acetals into hemiaminals (--> 20) which, in turn, are readily cleaved to aldehydes, with recovery of the chiral auxiliary (1, Scheme 4). The aldehydes (especially those lacking alpha-carbonyl hydrogens) may be isolated, or they are trapped in situ by reduction to (selectively protected) diols or amino alcohols, by addition of Grignard or Li reagents, which provides diols with two stereogenic centers, by oxidation to give 2-hydroxy esters, or by olefination to provide 4-hydroxy-2-alkenoates (Scheme 5). The scope and limitations of the new, overall enantioselective transformation are determined, and the readily recovered chiral auxiliary used is compared with oxazolidinones of other substitution patterns (Scheme 7). The configuration of a number of products has been assigned by single-crystal X-ray diffraction (cf. Figure 5). These structures and similarities of NMR data led to configurational assignment of the other products (see formulas in the schemes and tables) by analogy. A simple mechanistic model for the stereochemical course of the addition of Li-3 to aldehydes and ketones is presented (Figure 6).

Journal Article↗
PubMed2001

The beta-peptide hairpin in solution: conformational study of a beta-hexapeptide in methanol by NMR spectroscopy and MD simulation.

The structural and thermodynamic properties of a 6-residue beta-peptide that was designed to form a hairpin conformation have been studied by NMR spectroscopy and MD simulation in methanol solution. The predicted hairpin would be characterized by a 10-membered hydrogen-bonded turn involving residues 3 and 4, and two extended antiparallel strands. The interproton distances and backbone torsional dihedral angles derived from the NMR experiments at room temperature are in general terms compatible with the hairpin conformation. Two trajectories of system configurations from 100-ns molecular-dynamics simulations of the peptide in solution at 298 and 340 K have been analyzed. In both simulations reversible folding to the hairpin conformation is observed. Interestingly, there is a significant conformational overlap between the unfolded state of the peptide at each of the temperatures. As already observed in previous studies of peptide folding, the unfolded state is composed of a (relatively) small number of predominant conformers and in this case lacks any type of secondary-structure element. The trajectories provide an excellent ground for the interpretation of the NMR-derived data in terms of ensemble averages and distributions as opposed to single-conformation interpretations. From this perspective, a relative population of the hairpin conformation of 20% to 30% would suffice to explain the NMR-derived data. Surprisingly, however, the ensemble of structures from the simulation at 340 K reproduces more accurately the NMR-derived data than the ensemble from the simulation at 298 K, a question that needs further investigation.

Magnetic Resonance Spectroscopy↗
PubMed2000

Immobilization of BINOL by cross-linking copolymerization of styryl derivatives with styrene, and applications in enantioselective Ti and Al Lewis acid mediated additions of Et2Zn and Me3SiCN to aldehydes and of diphenyl nitrone to enol ethers

The chiral ligand 1,1'-bi-2-naphthol (BINOL) has been succesfully immobilized on polystyrene. Several dendritic and non-dendritic BINOL derivatives (3, and 13-17), bearing at least two polymerizable styryl groups, were prepared and fully characterized. Suspension copolymerization of the MOM- or TIPS-protected cross-linking BINOL ligands (MOM = methyloxymethyl, TIPS = triisopropylsilyl) with styrene, cleavage of the protecting-groups, and loading with a Lewis-acid afforded catalytically active polystyrene-supported BINOLates. The polymer-bound BINOLs p-3, and p-13-p-16 were tested in the Ti-BINOLate-mediated addition of Et2Zn to PhCHO. The enantioselectivities (up to 93%) and conversions obtained with the polymer-bound catalysts were in most cases identical (within experimental error) to those obtained with the unsubstituted 1,1'-bi-2-naphthol and with the non-polymerized BINOL cross-linkers under homogeneous conditions. Special focus was put on the reusability of the supported catalyst: the polymer-beads were used in up to 20 consecutive catalytic runs, with the best polymers showing no or only minor loss of selectivity. BINOL-polymers p-17, obtained by copolymerization of a 3,3'-distyryl-substituted BINOL 17a with styrene, were used in the BINOL. AlMe-mediated cycloaddition of diphenyl nitrone with alkyl vinyl ethers. In all cases the exo/endo selectivity (> or =92:8) and the enantioselectivities with which the exo-cycloadducts were formed (> or =95%) correspond to those observed in the homogeneous reactions. A dendritically cross-linked BINOL-polymer was also employed in the Ti-BINOLate-mediated cyanosilylation of pivalaldehyde. The enantiopurity of the cyanohydrine obtained in the first run was as high as in the homogeneous reaction (72%); surprisingly the catalytic performance of the supported catalyst increased steadily during the first catalytic cycles to reach 83%. Thus, cross-linking BINOLs can be succesfully incorporated into a polystyrene matrix (without racemization!) to give polymer-bound BINOL ligands that give excellent performance over many catalytic cycles with catalytic activities comparable with those of soluble analogues.

Journal Article↗
PubMed2000

A valine-derived lithiated 3-methylthiomethyl-1,3-oxazolidin-2-one for enantioselective nucleophilic hydroxymethylation, formylation, and alkoxycarbonylation of aldehydes

The 3-methylthiomethyl-4-isopropyl-5,5-diphenyl-1,3-oxazolidin-2-one (I, prepared in three steps from Boc-valine ester) is lithiated and added to aldehydes, with protecting in situ trapping of the primary adducts, to give the N,S-acetal derivatives II of 2-hydroxy aldehydes in high yields and diastereoselectivities. Cleavage (with ready recovery of the oxazolidinone auxiliary) is possible, to afford, for instance, enantiopure 1,2-diols, selectively protected (OBn, OMOM, OTBS) in the 2-position.

Journal Article↗
PubMed2000

X-Ray, Molecular Diffusion, and NOESY NMR Studies of Chiral, Tetranuclear Cu(I) Catalysts Based on Monodentate Thiol Analogues of TADDOL.

The new, stable, chiral thiol-TADDOL Cu(I) catalysts 1 (X=OH, OMe, NMe(2)) reveal an unexpected monodentate complexation mode, both in solution and in the solid state. For the first time, the aggregation state of organocopper complexes has been determined by NMR diffusion measurements. NOESY NMR data on model isocyanide Cu complexes reveal a different conformation of the TADDOL moiety as a function of the second potential donor group. TADDOL=alpha,alpha,alpha',alpha'-tetraaryl-2,2-dimethyl-1,3-dioxolane-4,5-dimethanol.

Journal Article↗
PubMed2000

Synthetic substrates and inhibitors of beta-poly(L-malate)-hydrolase (polymalatase).

Polymalatase from Physarum polycephalum calalysed the hydrolysis of beta-poly[L-malate] and of the synthetic compounds beta-di(L-malate), beta-tetra(L-malate), beta-tetra(L-malate) beta-propylester, and L-malate beta-methylester. Cyclic beta-tri(L-malate), cyclic beta-tetra(L-malate), and D-malate beta-methylester were not cleaved, but were competitive inhibitors. The O-terminal acetate of beta-tetra(L-malate) was neither a substrate nor an inhibitor. L-Malate was liberated; the Km, Ki and Vmax values were measured. The appearance of comparable amounts of beta-tri(L-malate), and beta-di(L-malate) during the cleavage of beta-tetra(L-malate) indicated a distributive mechanism for small substrates. The accumulation of a series of oligomers, peaking with the 11-mer and 12-mer in the absence of higher intermediates, indicated that the depolymerization of beta-poly(L-malate) was processive. The results indicate that beta-poly(L-malate) is anchored at its OH-terminus by the highly specific binding of the penultimate malyl residue. The malyl moieties beyond 12 residues downstream from the OH-terminus extend into a diffuse second, electrostatic binding site. The catalytic site joins the first binding site, accounting for the cleavage of the polymer into malate residues. It is proposed that the enzyme does not dissociate from beta-poly(L-malate) during hydrolysis, when both sites are filled with the polymer. When only the first binding site is filled, the reaction partitions at each oligomer between hydrolysis and dissociation.

Animals↗
PubMed1999

Nonapeptide analogues containing (R)-3-hydroxybutanoate and beta-homoalanine oligomers: synthesis and binding affinity to a class I major histocompatibility complex protein.

Crystal structures of antigenic peptides bound to class I MHC proteins suggest that chemical modifications of the central part of the bound peptide should not alter binding affinity to the MHC restriction protein but could perturb the T-cell response to the parent epitope. In our effort in designing nonpeptidic high-affinity ligands for class I MHC proteins, oligomers of (R)-3-hydroxybutanoate and(or) beta-homoalanine have been substituted for the central part of a HLA-B27-restricted T-cell epitope of viral origin. The affinity of six modified peptides to the B2705 allele was determined by an in vitro stabilization assay. Four out of the six designed analogues presented an affinity similar to that of the parent peptide. Two compounds, sharing the same stereochemistry (R,R,S,S) at the four stereogenic centers of the nonpeptidic spacer, bound to B2705 with a 5-6-fold decreased affinity. Although the chiral spacers do not strongly interact with the protein active site, there are configurations which are not accepted by the MHC binding groove, probably because of improper orientation of some lateral substituents in the bound state and different conformational behavior in the free state. However we demonstrate that beta-amino acids can be incorporated in the sequence of viral T-cell epitopes without impairing MHC binding. The presented structure-activity relationships open the door to the rational design of peptide-based vaccines and of nonnatural T-cell receptor antagonists aimed at blocking peptide-specific T-cell responses in MHC-associated autoimmune diseases.

3-Hydroxybutyric Acid↗
PubMed1998

Reversible peptide folding in solution by molecular dynamics simulation.

Long-standing questions on how peptides fold are addressed by the simulation at different temperatures of the reversible folding of a peptide in solution in atomic detail. Molecular dynamics simulations correctly predict the structure that is thermodynamically stable at 298 K, irrespective of the initial peptide conformation. The rate of folding and the free energy of folding at different temperatures are estimated. Although the conformational space potentially accessible to the peptide is extremely large, very few conformers (10(1) to 10(2)) are significantly populated at 20 K above the melting temperature. This implies that the search problem in peptide (or even protein) folding is surmountable using dynamics simulations.

Computer Simulation↗
PubMed1998

Substituting nonpeptidic spacers for the T cell receptor-binding part of class I major histocompatibility complex-binding peptides.

X-ray diffraction studies as well as structure-activity relationships indicate that the central part of class I major histocompatibility complex (MHC)-binding nonapeptides represents the main interaction site for a T cell receptor. In order to rationally manipulate T cell epitopes, three nonpeptidic spacers have been designed from the x-ray structure of a MHC-peptide complex and substituted for the T cell receptor-binding part of several antigenic peptides. The binding of the modified epitopes to the human leukocyte antigen-B*2705 protein was studied by an in vitro stabilization assay, and the thermal stability of all complexes was examined by circular dichroism spectroscopy. Depending on their chemical nature and length, the introduced spacers may be classified into two categories. Monofunctional spacers (11-amino undecanoate, (R)-3-hydroxybutyrate trimer) simply link two anchoring peptide positions (P3 and P9) but loosely contact the MHC binding groove and thus decrease more or less the affinity of the altered epitopes to human leukocyte antigen-B*2705. A bifunctional spacer ((R)-3-hydroxybutyrate tetramer) not only bridges the two distant anchoring amino acids but also strongly interacts with the binding cleft and leads to a 5-fold increase in binding to the MHC protein. To our knowledge, this is the first report of a nonpeptidic modification of T-cell receptor binding residues that significantly enhances the binding of altered peptide ligands to their host MHC protein. The presented modified ligands constitute interesting tools for perturbing the T cell response to the parent antigenic peptide.

Computer-Aided Design↗
PubMed1997

Proof for a nonproteinaceous calcium-selective channel in Escherichia coli by total synthesis from (R)-3-hydroxybutanoic acid and inorganic polyphosphate.

Traditionally, the structure and properties of natural products have been determined by total synthesis and comparison with authentic samples. We have now applied this procedure to the first nonproteinaceous ion channel, isolated from bacterial plasma membranes, and consisting of a complex of poly(3-hydroxybutyrate) and calcium polyphosphate. To this end, we have now synthesized the 128-mer of hydroxybutanoic acid and prepared a complex with inorganic calcium polyphosphate (average 65-mer), which was incorporated into a planar lipid bilayer of synthetic phospholipids. We herewith present data that demonstrate unambiguously that the completely synthetic complex forms channels that are indistinguishable in their voltage-dependent conductance, in their selectivity for divalent cations, and in their blocking behavior (by La3+) from channels isolated from Escherichia coli. The implications of our finding for prebiotic chemistry, biochemistry, and biology are discussed.

Calcium Channels↗
PubMed1995

Alpha-methyl-proline restores normal levels of bone collagen Type I synthesis in ovariectomized rats.

Collagen type I is the major protein of bone matrix and significantly reduced in osteoporosis. We tested the effect of alpha - methyl - proline on collagen synthesis in the model of the ovariectomized rat. Collagen synthesis was studied at the transcriptional level using Northern and dot blotting and at the protein level using hydroxyproline determination and a specific dye binding collagen assay. Alpha - methyl- proline treatment significantly increased collagen synthesis as compared to untreated ovariectomized and estradiol treated ovariectomized rats and restored collagen synthesis to levels of sham operated rats. Proline analogues were described to stimulate procollagen synthesis at the transcriptional level, however, if incorporated, lead to negative collagen production due to rapid intracellular degradation of the deficient collagen. Our synthesized analogue is not being incorporated, thus not interfering with collagen conformation and can therefore induce collagen production.

Animals↗
PubMed1995

Biodegradation of cyclic and substituted linear oligomers of poly(3-hydroxybutyrate).

Cyclic oligo(3-hydroxybutyrate), oligo(3-HB), was synthesized and purified, resulting in oligolides that contained three to seven (R)-3-hydroxybutyrate units (triolides up to heptolides). In addition, linear 3-HB octamers obtained as either tert-butyl or methyl esters were substituted with different end groups at the hydroxy end. The hydroxy terminus was replaced by either a benzyloxy, trifluoroacetoxy, crotonyloxy (S)-3-hydroxybutyryloxy, or fluorenylmethylcarbonyloxy (FMOC) group. P(3-HB) hairpin loops occurred on the surface of certain regions of the polymer, especially of lamellar crystallites. Cyclic 3-HB oligomers provide a model system for these loops. It is assumed that they provide attachment points for the depolymerizing enzymes. All of the (R)-oligolides tested were degraded except the (R)-triolide. Triolides were not degraded, suggesting that enzymatic attack was prevented presumably by steric hindrance on the rigid ring system. Unsubstituted linear octamers were degraded. Biodegradation was prevented when the hydroxy terminus was protected by the FMOC group, but was not dependent on a free hydroxy terminal group; all other protecting groups did not prevent degradation. Substitution of the carboxy end of a methyl or tert-butyl ester group did not influence biodegradation.

Biodegradation, Environmental↗
PubMed1994

Isolation and 1H-NMR spectroscopic identification of poly(3-hydroxybutanoate) from prokaryotic and eukaryotic organisms. Determination of the absolute configuration (R) of the monomeric unit 3-hydroxybutanoic acid from Escherichia coli and spinach.

Trace amounts of poly[(R)-3-hydroxybutanoate] were isolated from competent Escherichia coli, spinach, bovine serum albumin, beef heart mitochondria, and aortal tissues, all sources in which it is not accumulated as storage material. Its identity was in all cases proved by 1H-NMR spectroscopy. In some runs, the poly[(R)-3-hydroxybutanoate] isolated from competent E. coli also contained some 3-hydroxyvalerate, an observation confirmed by 1H-NMR spectroscopy and gas chromatography. The absolute configuration of the polymers isolated from E. coli and spinach was shown to be (all-R) by gas chromatography on chiral columns.

Animals↗