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At least 1,117 records · Page 62Linked to original sources
PubMed2000

Synthesis, conformational analysis, and biological activity of C-thioribonucleosides related to tiazofurin.

The syntheses of furanthiofurin [5beta-D-(4'-thioribofuranosyl)furan-3-carboxamide, 1] and thiophenthiofurin [5beta-D-(4'-thioribofuranosyl)thiophene-3-carboxamide, 2], two C-thioribonucleoside analogues of tiazofurin, are described. Direct trifluoroacetic acid-catalyzed C-glycosylation of ethyl furan-3-carboxylate with 1-O-acetyl-2,3,5-tri-O-benzyl-4-thio-D-ribofuranose gave 2- and 5-glycosylated regioisomers, as a mixture of alpha and beta anomers. Ethyl 5-(2,3,5-tri-O-benzyl)-beta-D-(4'-thioribofuranosyl)furan-3-carboxylate (6beta) was debenzylated and then converted into the corresponding amide (furanthiofurin) by reaction with ammonium hydroxide. A similar C-glycosylation of ethyl thiophene-3-carboxylate with 1,2,3,5-tetra-O-acetyl-4-thio-D-ribofuranose catalyzed by stannic chloride afforded an anomeric mixture of 2- and 5-glycosylated regioisomers. Deacetylation of ethyl 5-(2,3,5-tri-O-acetyl)-beta-D-(4'-thioribofuranosyl)thiophene-3-carboxylate (13beta) with methanolic ammonia and treatment of the ethyl ester with ammonium hydroxide gave thiophenthiofurin. The glycosylation site and anomeric configuration were established by (1)H NMR spectroscopy. Thiophenthiofurin was found to be cytotoxic in vitro toward human myelogenous leukemia K562, albeit 39-fold less than thiophenfurin, while furanthiofurin proved to be inactive. K562 cells incubated with thiophenthiofurin resulted in inhibition of inosine 5'-monophosphate dehydrogenase (IMPDH) and an increase in IMP pools with a concurrent decrease in GTP levels. From computational studies it was deduced that, among the C-nucleoside analogues of tiazofurin, activity requires an electrophilic sulfur adjacent to the C-glycosidic bond and an energetically favorable conformer around chi = 0 degrees. Among these, the more constrained (least flexible) compounds (tiazofurin and thiophenfurin) are more active than the less constrained thiophenthiofurin. Those compounds which contain a nucleophilic oxygen in place of the thiazole or thiophene (oxazofurin, furanfurin, and furanthiofurin) show the least activity.

Antineoplastic Agents↗
PubMed1998

Conformational analysis of the interdomain linker of the central homology region of chloroplast initiation factor IF3 supports a structural model of two compact domains connected by a flexible tether.

A peptide corresponding to the interdomain linker of chloroplast IF3 has been synthesized and its structure studied by NMR and CD as a function of temperature and pH. At low temperature and neutral pH the apparent helical content is 25%. pH and ionic strength dependent CD studies demonstrate that sidechain-sidechain interactions stabilize the structure observed at low temperature. The helicity decreases with temperature and above 25 degrees C the peptide is less than 15% helical. These results indicate that the peptide has little intrinsic tendency to form helical structure at physiologically relevant temperatures and strongly suggests that the linker region is flexible in intact chloroplast IF3.

Amino Acid Sequence↗
PubMedDate not supplied

Conformational analysis of synthetic peptides encompassing the factor XI and prekallikrein overlapping binding domains of high molecular weight kininogen.

High molecular weight kininogen, a plasma glycoprotein, circulates as a noncovalent complex with either prekallikrein or factor XI, two other plasma glycoproteins. The binding domain for factor XI within kininogen, Pro556-Met613 (58 residues), wholly contains the binding domain for prekallikrein, Ser565-Lys595 (31 residues), but Trp569-Lys595 (27 residues) retains some ability to bind prekallikrein. Complex formation between these proteins is mediated by recognition between complementary domains. The 58-residue factor XI peptide domain has now been prepared following a strategy of condensation of long-chain peptide fragments prepared using orthogonal chemistry protocols. The 58-, 31-, and 27-residue peptides assume very different structures in aqueous solution as revealed by differential scanning calorimetry, intrinsic fluorescence emission, and circular dichroism spectroscopies. Thus, the 31-residue peptide shows a broad endothermic transition in differential scanning calorimetry (DSC), but the 58-mer undergoes a well-defined, two-state transition (Tm 43 degrees C; transition enthalpy approximately 30 kcal/mol). The 58- and 27-residue peptides continuously lose structure with increasing temperature, but the 31-mer retains significant structure even at temperatures approaching 90 degrees C. Lys595 plays a critical role in maintaining structure through electrostatic contacts, probably with Asp572 in the N-terminal segment of the 31-residue sequence. Isothermal ligand titration calorimetry was used to directly assess the ability of the 31-, 27-, and 58-residue peptides to bind prekallikrein. The 31-residue peptide binds prekallikrein with 25-fold higher affinity (Kd = 1.0 x 10(-6) M) than the 58-residue peptide and with 5.4-fold higher affinity than the 27-residue peptide. Hence, the essential features of the 31-residue peptide domain required for binding prekallikrein are absent in the 58-residue peptide, which is optimized for binding factor XI. The results suggest that a conformational change may occur within kininogen that causes expression of one domain structure in preference to the other.

Amino Acid Sequence↗
PubMed2005

Conformational analysis and rotational barriers of alkyl- and phenyl-substituted urea derivatives.

Potential energy surfaces (PES) for rotation about the N-C(sp(3)) or N-C(aryl) bond and energies of stationary points on PES for rotation about the C(sp(2))-N bond are reported for methylurea, ethylurea, isopropylurea, tert-butylurea, and phenylurea, using the B3LYP/DZVP2 and MP2/aug-cc-pVDZ methods. The analysis of alkylureas reveals cis and (less stable) trans isomers that adopt anti geometries, whereas syn geometries do not correspond to stationary points. In contrast, the analysis of phenylurea reveals that the lowest energy form at the MP2 level is a trans isomer in a syn geometry. The fully optimized geometries are in good agreement with crystal structure data, and PESs are consistent with the experimental dihedral angle distribution. Rotation about the C(sp(2))-N bond in alkylureas and phenylurea is slightly more hindered (8.6-9.4 kcal/mol) than the analogous motion in the unsubstituted molecule (8.2 kcal/mol). At the MP2 level of theory, the maximum barriers to rotation for the methyl, ethyl, isopropyl, tert-butyl, and phenyl groups are predicted to be 0.9, 6.2, 6.0, 4.6, and 2.4 kcal/mol, respectively. The results are used to benchmark the performance of the MMFF94 force field. Systematic discrepancies between MMFF94 and MP2 results were improved by modification of several torsional parameters.

Alkylation↗
PubMed2001

Synthesis and conformational analysis of the insulin-like 4 gene product.

Insulin-like 4 (INSL-4) is a protein expressed in the early placenta. Its primary structure is insulin-like with reference to the distribution of cysteine residues and the single chain pro-form. Insulin-like 4 was generated by solid-phase peptide synthesis of the two chains followed by the sequential synthesis of the three disulfide bonds. Two disulfide isomers were produced, one with an insulin-like disulfide bonding pattern and the other with a reversed chain orientation. The CD spectra of the two disulfide isomers were indistinguishable without any features produced by periodic structures. In addition, the hydrodynamic properties of the two isomers were identical which implied a very open structure of the disulfide-bonded two-chain molecules. It appears that insulin-likeness cannot be defined solely on the basis of the primary structure of cDNA.

Amino Acid Sequence↗
PubMed1995

Conformational analysis of heparin epoxide in aqueous solution. An NMR relaxation study.

1H and 13C NMR relaxation measurements at various magnetic fields have been used to characterize the nature of overall and internal motions in heparin epoxide in aqueous solution. A two-dimensional homonuclear NOESY experiment showed a considerable number of cross-relaxing protons in the molecule. The inter-proton distances calculated from NOE data were compared with those obtained by molecular mechanics calculations. Several discrepancies between the experimental and the theoretical inter-proton distances as well as the variations in 13C spin-lattice relaxation times, measured at two magnetic fields, indicated that the polysaccharide tumbles anisotropically in solution. The rates of overall and internal motions as well as the order parameters have been calculated using a model-free spectral density function. The numerical values indicate that the correlation times which characterize overall molecular motion are outside the extreme narrowing limit (tau parallel = 8 x 10(-10) s and tau perpendicular = 4.2 x 10(-8) s) and that internal motion correlation time is on a picosecond timescale.

Carbohydrate Conformation↗
PubMed2003

Sterically congested tripodal phosphites: conformational analysis, solid-state polymorphism, metal complexation, and application to the asymmetric hydrosilation of ketones.

The synthesis as well as isolation and crystallographic analysis of two solid-state polymorphs of the tripodal ligand tri[2,2',2' '-tris[(2,4,8,10-tetrakis(1,1-dimethylethyl)dibenzo[d,f][1,3,2]dioxaphosphepin-6-yl)oxy]ethyl]amine (3) is described. Form I crystallized from ethyl acetate in the space group P2(1)/n with the unit-cell parameters a = 20.070(10) A, b = 17.477(2) A, c = 27.620(3) A, and beta = 93.050(10) degrees, V = 9674.5(14) A(3), and Z = 4. Form II crystallized from a mixture of acetone and toluene in the space group P1 with the unit-cell parameters a = 12.493(1) A, b = 19.701(2) A, c = 21.027(2) A, alpha = 116.23(1) degrees, beta = 100.15(1) degrees, and gamma = 91.07(1) degrees, V = 4542 A(3), and Z = 2. Differences in the relative absolute stereochemistry of the stereoaxes in the seven-membered dibenzo[d,f][1,3,2]dioxaphosphepin ring are discussed. The synthesis and X-ray characterization of enantiomerically pure (S,S,S)-tri[2,2',2' '-tris[(2,4,8,10-tetrakis(1,1-dimethylethyl)dibenzo[d,f][1,3,2]dioxaphosphepin-6-yl)oxy]propyl]amine [(S,S,S)-7] are reported. Two crystallographically independent molecules exist in the unit cell that cannot be superimposed with each other by either a translation or a symmetry operation. The two solid-state conformers in the unit cell differed predominately by the absolute stereochemistry of the stereoaxes in the seven-membered dibenzo[d,f][1,3,2]dioxaphosphepin ring. The Rh(I)-catalyzed hydrosilation of acetophenone with the chiral ligands (R,R,S)-7 and (S,S,S)-7 showed significant differences in chiral induction. Chiral cooperativity between the stereoaxes and stereocenters in (S,S,S)-7 is observed. The mechanism of the communication between the stereocenters and stereoaxes leading to chiral cooperativity in the stereoselective transition state is suggested to be primarily steric in nature.

Journal Article↗
PubMed1979

Conformational analysis of serum apolipoprotein AII in lipoprotein complexes with bifunctional crosslinking reagents.

Apolipoprotein AII isolated from human serum high density lipoproteins was recombined with phosphatidylcholine to yield homogeneous particles of 80-120 A diameter. The radioactive bifunctional crosslinkers dimethyl [1,1'-14C]suberimidate and dimethyl 4,4'-dithiobis([1-14C]butyrimidate) were reacted with these particles. The kinetics of the reactions and the localisation of the crosslinked lysines of the polypeptide chains were determined. Thermolysin hydrolysis followed by two-dimensional separation of the peptides and isolation of the mono- and bifunctionally modified peptides allowed the assignment of the crosslinked peptides of the apoprotein AII seqeunce. The crosslinking pattern indicates a close-neighbour relationship (13-15 A) of the peptide chains between amino acid residues 3, 23, 46 and 55 of the symmetrical halves of the apo AII molecule. A reconstruction of the secondary structure of Apo AII in the lipoprotein complex on the basis of theoretical calculations is given and correlated with the chemical data.

Amino Acid Sequence↗
PubMed2003

Synthesis, biological activity, and conformational analysis of CD-ring modified trans-decalin 1 alpha,25-dihydroxyvitamin D analogs.

A novel series of analogs of 1,25-dihydroxyvitamin D3, the hormonally active metabolite of vitamin D3, characterised by the presence of a trans-fused decalin CD-ring system, possesses surprising biological activities in combination with specific structural modifications in the flexible parts of the molecule, when compared with the natural hydrindane derivatives. (1) A large difference in biological activity is observed between the 20-epimeric trans-decalin analogs that follows a pattern opposite to what is usually observed for the natural ring size. (2) Several trans-decalin analogs that are modified in the seco-B-ring region, including previtamin derivatives, possess a pronounced vitamin D-like activity, whereas the corresponding hydrindane derivatives are inactive. The molecular origin of this behavior is still under study.

Animals↗
PubMed1998

Structure-activity relationship and conformational analysis of monoglycosylceramides on the syngeneic mixed leukocyte reaction.

We examined effects of alpha-, beta-galactosylceramides (CalCers) and alpha-, beta-glucosylceramides (GlcCers) on the syngeneic mixed leukocyte reaction (MLR) using spleen cells (responder cells) and dendritic cells (DC, stimulator cells). The DC pretreated with these alpha-monoglycosylceramides markedly stimulated the proliferation of spleen cells, in contrast to the little stimulatory effects produced by the DC pretreated with the corresponding beta-anomers. In addition, when we compared the effects of alpha-GalCer derivatives on the syngeneic MLR, it appeared that the 2"- and 3-hydroxyl groups in alpha-GalCers play a critical role in their stimulation of the MLR response. Based on these results, we performed a computer-aided molecular modeling study, and found that the orientations of the 2"-, 4"- and 3-hydroxyl groups common to alpha-GalCer and alpha-GlcCer are not accessible to those of inactive monoglycosyleeramides such as beta-GalCer. These results suggest that there might be a receptor-like site for alpha-monoglycosylceramides on the cells which are involved in the MLR response.

Animals↗
PubMed1984

[3,3'-bi-1,3-thiazolidine]-4,4'-dione system. I. Synthesis, conformational analysis and pharmacological activities of 2,2'-diaryl derivatives.

The two configurational isomers, d1, and meso, of some 2,2'-diaryl-[3,3'-bi-1,3-thiazolidine]-4,4'-dione derivatives have been obtained and characterized. The 1H-N.M.R. spectra of both stereoisomers in DMSO-d6 solution are temperature-dependent and their dynamic behaviour has been related to the hindered rotation of the N--N bond. Evidence for an orthogonal disposition of the two heterocyclic rings, in the ground state, is presented. These new bicyclic compounds possess interesting antiinflammatory, analgesic and antipyretic activities as well as low acute toxicity and ulcerogenicity. The antiinflammatory effect, which in some compounds is higher than that of indomethacin and phenylbutazone, appears to be a function of the relative disposition of the substituents at position 2 and 2': generally the meso isomers are more active than the d1 ones. The lipophilicity of the tested compounds was determined by reversed-phase thin-layer chromatography.

Analgesics↗
PubMed1992

Accessibility of aminoglycosides, isolated and in interaction with phosphatidylinositol, to water. A conformational analysis using the concept of molecular hydrophobicity potential.

The mode of interaction between aminoglycosides and negatively charged phospholipids plays a critical role in the inhibition of lysosomal phospholipases induced by these antibiotics and therefore in their nephrotoxicity. Previous works suggested that accessibility of the drug interacting with phospholipids to water could be crucial in this respect. We have used the concept of molecular hydrophobicity potential described by Brasseur [J Med Chem 266: 16120-16127, 1991] to visualize the hydrophobic and hydrophilic envelopes around aminoglycosides assembled with phosphatidylinositol molecules, and to obtain a three-dimensional representation of the complex formed. Using a series of different aminoglycosides, we showed that molecules with a lower inhibitory potential (gentamicin B, amikacin and isepamicin) are surrounded by both hydrophobic and hydrophilic envelopes whereas aminoglycosides which are more inhibitory are enveloped primarily by either hydrophilic (kanamycin A or B) or hydrophobic (gentamicin C1a) envelopes. This approach, which is here for the first time applied to the study of drug-lipid complexes, could help in the better understanding of the molecular mechanism of lysosomal phospholipase inhibition induced by aminoglycosides.

Aminoglycosides↗
PubMed1992

Flavones. 3. Synthesis, biological activities, and conformational analysis of isoflavone derivatives and related compounds.

A series of 2-alkylisoflavone derivatives 1 was prepared with the intent to study the importance of the phenyl group (at the 3-position) of the isoflavone in imparting antihypertensive activity and the substitution effects at the 2-position of isoflavone. With the exception of the 2-isopropyl analog, the antihypertensive activity of these compounds appears to have a slow onset and long duration. None of the analogs appears better than the corresponding flavone (3) and 3-phenylflavone (2) analogs. An unsuccessful attempt to correlate the relationship between antihypertensive activity and the calculated torsional angle of C2-C3-C1'-C2' is discussed. Antiinflammatory activities of these compounds along with 7-(oxypropylamine)flavones were also evaluated and found to be not very potent. The antiinflammatory activity appears to be sensitive to steric effects of the alkyl group on the nitrogen and of substituents at the 2-position of the isoflavones, while the hydroxyl group of the propanolamine side chain is not essential.

Animals↗
PubMed2006

Enhancement of bound-state residual dipolar couplings: conformational analysis of lactose bound to Galectin-3.

Residual dipolar couplings (RDCs) have proven to be a valuable NMR tool that can provide long-range constraints for molecular structure determination. The constraints are orientational in nature and are, thus, highly complementary to conventional distance constraints from NOE data. This complementarity would seem to extend to the study of the geometry of ligands bound to proteins. However, unlike transferred NOEs, where collection, even with a large excess of free ligand, results in measurements dominated by bound contributions, RDCs of exchanging ligands can be dominated by free-state contributions. Here we present a strategy for enhancement of RDCs from bound states that is based on specifically enhancing the alignment of the protein to which a ligand will bind. The protein is modified by addition of a hydrophobic alkyl tail that anchors it to the bicelles that are a part of the ordering medium needed for RDC measurement. As an illustration, we have added a propyl chain to the C terminus of the carbohydrate recognition domain of the protein, Galectin-3, and report enhanced RDCs that prove consistent with known bound-ligand geometries for this protein.

Alkylation↗
PubMed1996

Conformational analysis of a toxic peptide from Trimeresurus wagleri which blocks the nicotinic acetylcholine receptor.

The 22-residue toxic peptide (WTX1) from the venom of the Southeast Asian snake Trimeresurus wagleri has multiple sites of action, but its lethal effect has been attributed to blocking the postsynaptic acetylcholine receptor at the neuromuscular junction. The 3-dimensional structure of WTX1 was studied using 2-dimensional nuclear magnetic resonance spectroscopy, circular dichroism, and computer simulations. In aqueous solution, WTX1 was shown to have extended and flexible "tails" defined by a short, rigid disulfide-bonded loop. The flexible regions can undergo structural rearrangement when moved from an aqueous to a less polar environment and may contribute to its effectiveness at different receptor sites. By substituting Gly or Phe for His at position 10, significant effects on the disulfide bond formation and, thereby, the activity of the peptide were observed. These results suggest that even subtle differences in single residues can have profound effects on the dynamics of folding, disulfide bond formation, and activity of this toxic peptide.

Amino Acid Sequence↗
PubMed1998

Molecular specificity of a medium chain acyl-CoA synthetase for substrates and inhibitors: conformational analysis.

Amino acid conjugation is an important route of detoxification of xenobiotic and endogenous carboxylic acids. The specificity of the purified medium chain acyl-CoA synthetase catalyzing the first reaction of amino acid conjugation was investigated further for substrates and inhibitors. Molecular modeling techniques were applied to derive the molecular characteristics of substrates and inhibitors for the medium chain acyl-CoA synthetase. The purified enzyme accepted not only straight medium chain fatty acids but also aromatic acids. Of the arylacetic acids, activity was obtained with naphthylacetic acids, whereas introduction of a methyl group at the alpha-position caused loss of activity. High activity was also observed with cyclohexanoic acid. Diflunisal, 2-hydroxydodecanoic acid, and nalidixic acid inhibited the medium chain acyl-CoA synthetase activity for hexanoic acid, with Ki values of 0.8, 4.4, and 12.3 microM, respectively. The inhibitory carboxylic acids were competitive with respect to hexanoic acid. The hydroxyl or ketone (oxo) groups at the beta-position of carboxylic acids were an important determinant for inhibitory activity. All substrates and inhibitors contained a flat hydrophobic region coplanar to the carboxylate group. In addition, the substrates had negative values for charge on the carbon in the beta-position of carboxylic acids.

Acetates↗
PubMed1976

Conformational analysis of the glycosaminoglycans. II. Bond-angle studies, torsional potential, and steric map for the beta-D-(1leads to 3) linkage.

The geometry of the glycosidic valence-bond angle for both the beta-D-(1linked to4) and beta-D-(1linked to 3) linkages has been investigated by using CNDO and PCILO molecularorbital techniques on model compounds. In each case, the glycosidic valence-bond angle of minimum energy was about 111 degrees, corresponding to the value observed in ether analogs. A secondary energy-minimum was found near 116 degrees, which is the value experimentally observed for saccharides. It was concluded that long-range intra-and/or inter-molecular interactions are responsible for overall preference for the 116 degrees value of the valence-bond angle. The force constants predicted from the shapes of the 116 degrees bond-angle minima gave poor agreement with the experimental values found for ethers and employed in normal coordinate analyses of saccharides. The results did suggest that the beta-D-(1linked to3) bond angle should be 115.6 degrees, which is smaller than the corresponding beta-D-(1linked to4) bond angle. An intrinsic torsional potential-function and general steric map were also determined for the torsion-angle rotations of the beta-D-(1linked to3) linkage.

Binding Sites↗
PubMed2005

Synthesis, conformational analysis, and biological activity of new analogues of thiazole-4-carboxamide adenine dinucleotide (TAD) as IMP dehydrogenase inhibitors.

Thiazole-4-carboxamide adenine dinucleotide (TAD) analogues T-2'-MeAD (1) and T-3'-MeAD (2) containing, respectively, a methyl group at the ribose 2'-C-, and 3'-C-position of the adenosine moiety, were prepared as potential selective human inosine monophosphate dehydrogenase (IMPDH) type II inhibitors. The synthesis of heterodinucleotides was carried out by CDI-catalyzed coupling reaction of unprotected 2'-C-methyl- or 3'-C-methyl-adenosine 5'-monophosphate with 2',3'-O-isopropylidene-tiazofurin 5'-monophosphate, and then deisopropylidenation. Biological evaluation of dinucleotides 1 and 2 as inhibitors of recombinant human IMPDH type I and type II resulted in a good activity. Inhibition of both isoenzymes by T-2'-MeAD and T-3'-MeAD was noncompetitive with respect to NAD substrate. Binding of T-3'-MeAD was comparable to that of parent compound TAD, while T-2'-MeAD proved to be a weaker inhibitor. However, no significant difference was found in inhibition of the IMPDH isoenzymes. T-2'-MeAD and T-3'-MeAD were found to inhibit the growth of K562 cells (IC(50) 30.7 and 65.0muM, respectively).

Adenine Nucleotides↗