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PubMed1989

Correlation between the effects of polyamine analogues on DNA conformation and cell growth.

Effects of a number of synthetic analogues of the natural polyamines on the B-Z transition of poly(dG-me5dC) and on the aggregation of calf thymus DNA in solution were studied using circular dichroic and UV spectroscopy. The efficiency of induction of the B-Z transition decreased with a decrease in the length of the central alkyl chain of the analogues, and the ability of analogues to aggregate DNA was markedly reduced for compounds ethylated at the terminal amines. Both structural variations appear to have important effects on the biological functions of polyamines. Most analogues studied depleted intracellular levels of natural polyamines, but only those that did not readily induce the B-Z transition and/or aggregate DNA were good inhibitors of cell growth. All but one of the analogues studied were able to rescue cells--at least in part--from the growth-inhibitory effects of alpha-difluoromethylornithine. The single analogue that was unable to effect rescue also failed to induce both the B-Z transition and the aggregation of DNA.

Animals↗
PubMed2000

Investigation of the proposed interdomain ribose zipper in hairpin ribozyme cleavage using 2'-modified nucleosides.

The hairpin ribozyme achieves catalytic cleavage through interaction of essential nucleotides located in two distinct helical domains that include internal loops. Initial docking of the two domains is ion dependent and appears to be followed by a structural rearrangement that allows the ribozyme to achieve a catalytically active state that can undergo cleavage. The proposed structural rearrangement may also be ion dependent and is now of increased importance due to recent evidence that docking is not rate limiting and that metal ions are unlikely to be involved in the chemical cleavage step. An initial structural model of the docked hairpin ribozyme included a proposal for a ribose zipper motif that involves two pairs of hydroxyl groups at A(10) and G(11) in domain A pairing with C(25) and A(24) in domain B, respectively. We have used a chemical functional group substitution technique to study whether this proposed ribose zipper is likely to be present in the active, conformationally rearranged ribozyme that is fit for cleavage. We have chemically synthesized a series of individually modified hairpin ribozymes containing 2'-analogues of nucleosides, that include 2'-deoxy and 2'-deoxy-2'-fluoro at each of the four nucleoside positions, 2'-amino-2'-deoxy, 2'-deoxy-2'-thio, and 2'-arabino at position C(25), and 2'-oxyamino at position A(10), as well as some double substitutions, and we studied their cleavage rates under both single- and multiple-turnover conditions. We conclude that at least some of the hydrogen-bonding interactions in the ribose zipper motif, either as originally proposed or in a recently suggested structural variation, are unlikely to be present in the active rearranged form of the ribozyme that undergoes cleavage. Instead, we provide strong evidence for a very precise conformational positioning for the residue C(25) in the active hairpin. A precise conformational requirement would be expected for C(25) if it rearranges to form a base-triple with A(9) and the essential residue neighboring the cleavage site G(+1), as recently proposed by another laboratory. Our results provide further support for conformational rearrangement as an important step in hairpin ribozyme cleavage.

Base Sequence↗
PubMed2005

Fancy bioisosteres: synthesis, SAR, and pharmacological investigations of novel nonaromatic dopamine D3 receptor ligands.

Structural variations of the lead compound FAUC 88 led to dopaminergic enynes with an extended pi-system when Pd-catalyzed cross coupling reactions were employed for the key reaction steps. The dienyne 9b displayed substantial affinity for the dopamine receptor subtype D3 and remarkable selectivity over D4. Compared to FAUC 88, the novel fancy bioisostere 9b displayed reduced ligand efficacy. DFT-based conformational analysis of the test compound 9b, including the calculation of diagnostic magnetic shielding properties and their comparison with experimentally derived NMR data, indicated a clear energetic preference for the s-trans geometry of the diene substructure.

Animals↗
PubMed1988

Evaluation of the side arm of (naphthylvinyl)pyridinium inhibitors of choline acetyltransferase.

A number of quaternary salts of trans-4-(beta-1-naphthylvinyl)pyridine (NVP) were synthesized and evaluated as inhibitors of the enzymes choline acetyltransferase (ChAT) and acetylcholinesterase (AChE). Structural variations in the side arm attached to the pyridine nitrogen atom demonstrate that an inductive effect is small but significant for activity. Inhibition of ChAT by alkylated derivatives decreases when electron-withdrawing groups are placed in the side chain. Substitution of a methyl group on the pyridine ring only slightly affects activities toward ChAT and AChE. When the pyridinium moiety is replaced by an imidazolium ring, no ChAT inhibition was observed. The imidazolium compound, however, was a weak inhibitor of AChE. For design of affinity columns for purification of ChAT, the data also supports the use of long chain alkylated amide derivatives of NVP.

Animals↗
PubMed2002

Chromatographic determination of plant saponins.

The methods used for saponin determination in plant materials are presented. It is emphasised that the biological and spectrophotomeric methods still being used for saponin determination provide, to some extent, valuable results on saponin concentrations in plant material. However, since they are sensitive to the structural variation of individual saponins they should be standardized with saponin mixtures isolated from the plant species in which the concentration is measured. However, one plant species may contain some saponins which can be determined with a biological test and others which cannot. That is why biological and colorimetric determinations do not provide accurate data and have to be recognized as approximate. Thin-layer chromatography on normal and reversed-phases (TLC, HPTLC, 2D-TLC) provides excellent qualitative information and in combination with on-line coupling of a computer with dual-wavelength flying-spot scanner and two-dimensional analytical software can be used for routine determination of saponins in plant material. The densitometry of saponins has been very sensitive, however, to plate quality, spraying technique and the heating time and therefore appropriate saponin standards have to be run in parallel with the sample. Gas-liquid chromatography has limited application for determination since saponins are quite big molecules and are not volatile compounds. Thus, there are only few applications of GC for determination of intact saponins. The method has been used for determination of TMS, acetyl or methyl derivatives of an aglycones released during saponin hydrolysis. However, structurally different saponins show different rates of hydrolysis and precise optimisation of hydrolysis conditions is essential. Besides, during hydrolysis a number of artefacts can be formed which can influence the final results. High performance liquid chromatography on reversed-phase columns remains the best technique for saponin determination and is the most-widely used method for this group of compounds. However, the lack of chromophores allowing detection in UV, limits the choice of gradient and detection method. The pre-column derivatisation with benzoyl chloride, coumarin or 4-bromophenacyl bromide has been used successfully in some cases allowing UV detection of separation. Standardisation and identification of the peaks in HPLC chromatograms has been based on comparison of the retention times with those observed for authentic standards. But new hyphenated techniques, combining HPLC with mass spectrometry and nuclear magnetic resonance are developing rapidly and allow on-line identification of separated saponins. Capillary electrophoresis has been applied for saponin determination only in a limited number of cases and this method is still being developed.

Chromatography, Gas↗
PubMed1992

Structural changes that accompany the reduced catalytic efficiency of two semisynthetic ribonuclease analogs.

The structures of two catalytically defective semi-synthetic RNases obtained by replacing aspartic acid 121 with asparagine or alanine have been determined and refined at a resolution of 2.0 A (R = 0.186 and 0.172, respectively). When these structures are compared with the refined 1.8-A structure (R = 0.204) of the fully active aspartic acid-containing enzyme (Martin, P.D., Doscher, M.S., and Edwards, B. F. P. (1987) J. Biol. Chem. 262, 15930-15938), numerous and widespread changes, much greater in number and magnitude than the small structural variations noted previously between the semisynthetic complex and RNase A, are found to have occurred. These changes include the movement of the loop containing residues 65-72 away from the active site, a more or less generalized relocation of crystallographically bound water molecules, and a number of rearrangements in the hydrogen bonding network at the active site. Most changes are far removed from the immediate site of the modifications and are distributed essentially throughout the molecule. The details of many of these changes are unique to each analog. In the asparagine analog, a destabilization in the positioning of active site residue His-119 also appears to have occurred.

Alanine↗
PubMed1981

A calorimetric study of the thermotropic behaviour of 1,2-dipentadecylmethylidene phospholipids.

Differential scanning calorimetry was used to study the thermotropic behaviour of 1,2-dipentadecylmethylidene phospholipids with various head groups. The structural variation in the glycerol backbone region leads to a strong restriction of conformational freedom for the first two methylene segments of the chains, so that dipentadecylmethylidene phospholipids show lower transition temperatures, lower enthalpies and lower cooperativity of the transition from the gel to the liquid crystalline phase. The extreme chemical stability of these lipids in the alkaline pH region enables investigations of phosphatidylethanolamine and phosphatidic acid dispersions at high pH values. Both phospholipids show a decrease in the transition temperature and in the transition enthalpy as they become singly and doubly charged, respectively. A complex behaviour of the transition enthalpy of doubly charged 1,2-dipentadecylmethylidene phosphatidic acid was observed when the NaCl concentration of the dispersion was increased.

Calorimetry, Differential Scanning↗
PubMed1966

Transformation of monocytes in tissue culture into macrophages, epithelioid cells, and multinucleated giant cells. An electron microscope study.

The sequential transformation of chicken monocytes into macrophages, epithelioid cells, and multinucleated giant cells in vitro was studied by electron microscopy after fixation and embedment in situ. The following changes occur. In the nucleus, margination of chromatin, evident in monocytes, decreases in later forms. Nucleoli become more complex and nuclear pores increase in number. In cytoplasm, a progressive increase in volume of the ectoplasm and endoplasm occurs in culture. Lysosomes increase in number and size prior to phagocytosis. During phagocytosis (most active from 1 to 3 days of culture) lysosome depletion occurs. Lysosomes are present in greatest number and show maximal structural variation in the epithelioid and young giant cells. Aging giant cells lose lysosomes. All stages possess variably large quantities of rough-surfaced endoplasmic reticulum and free ribosomes. The Golgi apparatus, small in monocytes, increases in size and complexity. Massive accumulations of lysosomes within the Golgi apparatus of macrophages and epithelioid cells suggest that lysosomes originate there. In giant cells, multiple Golgi regions occur, often ringing the nuclei. Monocytes and macrophages have few mitochondria. Mitochondria of epithelioid cells are larger, more numerous, and may have discontinuous outer membranes. Mitochondria are most numerous in giant cells where they increase with age and become polymorphous. Cytoplasmic filaments are approximately 50 to 60 A in diameter and of indeterminate length. They occur both singly and in bundles which touch cytoplasmic vesicles and mitochondria. Few filaments occur in monocytes and macrophages. A large increase in the number of filaments occurs in epithelioid cells, where filaments (90 to 100 A) surround the cytocentrum as a distinctive annular bundle often branching into the cytoplasm. The greatest concentration of filaments occurs in aged giant cells. Pseudopodia are always present. They are short and filiform in monocytes and giant cells, and broad, with abundant micropinocytotic vesicles, in macrophages and epithelioid cells. At every stage, the cell membrane contains dense cuplike structures. These may represent the membranous residue of lysosomes which have discharged to the outside, analogous to merocrine secretion. Contiguous epithelioid cells display elaborate cytoplasmic interdigitation. In places, the plasma membranes break down and epithelioid cells fuse to form giant cells.

Cell Differentiation↗
PubMed2000

Synthesis, molecular modeling, and pharmacological testing of bis-quinolinium cyclophanes: potent, non-peptidic blockers of the apamin-sensitive Ca(2+)-activated K(+) channel.

The synthesis and pharmacological testing of two series of novel bis-quinolinium cyclophanes as blockers of the apamin-sensitive Ca(2+)-activated K(+) (SK(Ca)) channel are presented. In these cyclophanes the two 4-aminoquinolinium groups are joined at the ring N atoms (linker L) and at the exocyclic N atoms (linker A). In those cases where A and L contain two or more aromatic rings each, the activity of the compound is not critically dependent upon the nature of the linkers. When A and L each have only one benzene ring, the blocking potency changes dramatically with simple structural variations in the linkers. One of these smaller cyclophanes having A = benzene-1,4-diylbis(methylene) and L = benzene-1, 3-diylbis(methylene) (3j, 6,10-diaza-1,5(1,4)-diquinolina-3(1,3),8(1, 4)-dibenzenacyclodecaphanedium tritrifluoroacetate, UCL 1684) has an IC(50) of 3 nM and is the most potent non-peptidic SK(Ca) channel blocker described to date. Conformational analysis on the smaller cyclophanes using molecular modeling techniques suggests that the differences in the blocking potencies of the compounds may be attributable to their different conformational preferences.

Alkanes↗
PubMed2005

Inhibition of monoamine oxidase-A activity in rat brain by synthetic hydrazines: structure-activity relationship (SAR).

A series of hydrazine derivatives was synthesized in order to evaluate their monoamine oxidase A (MAO-A) inhibitory effects. MAO-A inhibitory activity of 4-tosyl benzoic acid carbohydrazide was quite potent, similarly to that of the corresponding 4-benzyloxy-benzoic acid carbohydrazide and its N-cyanoethylated derivative. Structural variations of these compounds, such as the replacement of the 4-substitutent, of the aromatic ring on which the carbohydrazide moiety is grafted, as well as cyclization of the hydrazide moiety in five- or six-membered rings caused either significant decline or complete loss of MAO inhibitory properties. The most active compound (4-tosyl benzoic acid carbohydrazide) was also subjected to the forced swim test, an animal model of depression, eliciting a marked reduction in immobility time in rats, without affecting the locomotor activity, implying that it possesses anti-depressant properties due to inhibition of MAO type-A.

Animals↗
PubMed1995

Effects of bis(benzyl)polyamine analogs on Leishmania donovani promastigotes.

A number of bis(benzyl)polyamine analogs were found to be potent inhibitors of Leishmania donovani growth in vitro (IC50 = 4.3-25 microM). Structural variations appear to have important effects on the biological functions of these analogs. Subinhibitory concentration of all of the analogs with the exception of MDL 27994 could rescue the cells from DL-alpha-difluoromethylornithine toxicity. The analogs inhibited macromolecular synthesis as evaluated by [3H]thymidine, [14C]uracil, and [35S]methionine incorporation. They inhibited the activity of the two enzymes, ornithine decarboxylase (ODC) and S-adenosylmethionine decarboxylase (AdoMetDC), involved in the biosynthesis of polyamines. These analogs depleted intracellular levels of natural polyamines. We conclude, therefore, that the major mechanism by which these analogs act may be by disruption of macromolecular biosynthesis and cell death. Repression of polyamines by these analogs may be yet another factor involved in slowing the growth of the parasite.

Adenosylmethionine Decarboxylase↗
PubMedDate not supplied

Binary quantitative structure-activity relationship (QSAR) analysis of estrogen receptor ligands.

The use of high throughput screening (HTS) to identify lead compounds has greatly challenged conventional quantitative structure-activity relationship (QSAR) techniques that typically correlate structural variations in similar compounds with continuous changes in biological activity. A new QSAR-like methodology that can correlate less quantitative assay data (i.e., "active" versus "inactive"), as initially generated by HTS, has been introduced. In the present study, we have, for the first time, applied this approach to a drug discovery problem; that is, the study of the estrogen receptor ligands. The binding affinities of 463 estrogen analogues were transformed into a binary data format, and a predictive binary QSAR model was derived using 410 estrogen analogues as a training set. The model was applied to predict the activity of 53 estrogen analogues not included in the training set. An overall accuracy of 94% was obtained.

Cluster Analysis↗
PubMed2002

A theoretical study of model lipid monolayers.

Studies of pure phospholipid monolayers or various well defined lipid mixtures have greatly contributed to the current knowledge of the relationship between monolayer composition and its properties and to understand how their physicochemical properties, e.g. refraction, polarization, are controlled by structural variations at the molecular level. Therefore, an attempt was made to investigate model lipid molecules adsorbed on the air/water interface. Semi-empirical (AM1) quantum chemical calculations were performed for several clusters and were compared with experimental data. The optimized acidic molecules show a marked tendency to group forming domains. An increase in the number of surfactant molecules in the cluster leads to a decrease in the effective headgroup area. On the other hand, the area grows with the increase of the degree of ionization. Both relations are in accordance with the experimental trends and the electrostatic theory. The employed theoretical approach proves to be applicable to the study of monolayers, thus providing a reliable description at molecular level of the traditionally phenomenological investigations in the field.

Cell Membrane↗
PubMed2000

Synthesis and amphiphilic properties of glycosyl-1,4-benzodiazepin-2,5-diones.

Glycosyl-1,4-benzodiazepin-2,5-diones were prepared by coupling polyhydroxylated groups at N-1 of the corresponding benzodiazepine. The groups include 1-deoxy-D,L-xylit-1-yl, 6-deoxy-D-glucopyranos-6-yl, and 6-deoxy-3-OR-D-glucopyranos-6-yl (R = n-CnH(2n +1); n = 8, 12, and 16). The structural variations of the sugar group allowed comparison of such amphiphilic data as water solubility (Sw), critical micelle concentration (CMC), and corresponding surface tension (gamma) values. At 25 degrees C, unsubstituted benzodiazepines have Sw values from 0.9 to 4.2 10(-3) mol L(-1), whereas xylit-1-yl and 6-deoxy-D-glucopyranos-6-yl derivatives are, respectively, 7.4-25 and 58-204 times more soluble. Also, compounds with R = n-C8H17 are more soluble than corresponding benzodiazepines (1.4-5.8 times) and give micelles with CMC from 2.7 to 5.6 10(-3) mol L(-1) and corresponding gamma from 29 to 37 mN m(-1). In contrast, compounds with R = n-C12H25 and n-C16H33 are not soluble enough to reach the critical micelle concentration.

Benzodiazepinones↗
PubMed1993

Quantitative structure-activity relationships of antibacterial agents, 7-heterocyclic amine substituted 1-cyclopropyl-6,8-difluoro-4-oxoquinoline-3-carboxylic acids.

Quantitative structure-activity relationships (QSAR) of various 7-(3-substituted-azetidin-1-yl)-1-cyclopropyl-6,8-difluoro-1,4-dih ydro-4- oxoquinoline-3-carboxylic acids, 14-25, were studied to clarify the structural requirements for 3-substituted azetidines to potentiate antibacterial activity. A good parabolic relationship seemed to exist between the relative mean antibacterial activity indices against five representative gram-negative bacteria, GNM, and the calculated hydrophobic parameters, CLOG P, of these molecules. The CLOG P value of the most potent derivative was predicted to be around 2.3. On the other hand, against five representative gram-positive bacteria, the relative mean antibacterial activity indices, GPM, remained high and rather constant regardless of structural variation in the azetidine moiety. In order to confirm these findings, the QSAR analysis was extended with success to the quinolonecarboxylic acids, 26-34, which bear various substituted pyrrolidine, piperazine and piperidine derivatives instead of azetidines. The findings showed that the introduction of any amide substituent group to these heterocyclic amine moieties would lead to marked decrease in GNM, whereas incorporation of some amino substituent groups at a position two or three carbons remote from the N-1 position resulted in great enhancement of GNM. As azetidine quinolones exhibited somewhat low in vivo antibacterial activities, possibly reflecting their lesser bioavailability, we finally selected 3-amino-4-methoxypyrrolidine as one of the most promising C-7 substituent groups based on our QSAR analysis.

Anti-Bacterial Agents↗
PubMed2004

Molecular docking of the scorpion toxin Tc1 to the structural model of the voltage-gated potassium channel Kv1.1 from human Homo sapiens.

In this study, structural model of the pore loop region of the voltage-gated potassium channel Kv1.1 from human Homo sapiens was constructed based on the crystallographic structure of KcsA by structural homology. The pore loop region of Kv1.1 exhibits similar folds as that of KcsA. The structural feature of the selectivity filter of Kv1.1 is nearly identical to that of KcsA, whereas most of the structural variations occur in the turret as well as in the inner and outer helices. Molecular docking experiments of the scorpion toxin Tc1 from Tityus cambridgei to the outer vestibule of KcsA as well as Kv1.1 were subsequently performed with various initial Tc1 orientations. Tc1 was found to form the most stable complexes with these two K+ channels when the side chain of Lys14 occupies the pore of the selectivity filter through electrostatic interaction. Tc1 binds preferentially towards Kv1.1 than KcsA due to stronger hydrophobic and electrostatic interactions formed between the toxin and the selectivity filter and outer vestibule of Kv1.1. Furthermore, surface complementarity of the outer vestibules of the channels to the Tc1 spatial conformations also plays an important role in stabilizing both the Tc1/KcsA and Tc1/Kv1.1 complexes.

Amino Acid Sequence↗
PubMed2006

Elucidation of the enantioselective recognition mechanism of a penicillin G acylase-based chiral stationary phase towards a series of 2-aryloxy-2-arylacetic acids.

A series of structurally related 2-aryloxy-2-arylacetic acids (1-3, 5-16) together with a thioisostere derivative (4) have been synthesized and characterized by GC-MS and 1H NMR. The designed compounds were analyzed on a Penicillin G Acylase chiral stationary phase (PGA-CSP) and the influence of the structure variations on retention and enantioselectivity was investigated. The chromatographic study includes the direct separation of the enantiomers of the synthesized compounds and the determination of the elution order of selected racemic mixtures. 10 out of 16 racemates were separated; high chromatographic enantioseparation factors (alpha > 2) were achieved for some compounds. For the enantiomers of four compounds whose absolute configuration was known (1, 3, 12, 16), the elution order was R:S with the exception of 2-(4-chloro-phenoxy)phenylacetic acid (1), for which the elution order was reversed. Preliminary molecular modeling studies suggest that both polar and charge-transfer interactions as well as steric effects play an important role in determining the retention factors and the enantioselectivities observed.

Acetic Acid↗
PubMed1984

Structure-activity studies on amphetamine analogs using drug discrimination methodology.

Animals (rats) trained to discriminate 1.0 mg/kg of S(+)-amphetamine sulfate from saline, using a standard operant training procedure, were administered doses of various amphetamine analogs in tests of stimulus generalization in order to study structure-activity relationships (SAR). The types of structural variation of the amphetamine molecule that were investigated included (a) benz-fusion of the aromatic nucleus, (b) alpha-demethylation of the alkyl side chain, (c) conversion of the benzylic methylene to a carbonyl group, and (d) conformational restriction of the side chain. Benz-fusion and alpha-demethylation appear to have a detrimental effect on activity in that none of these analogs produced amphetamine-appropriate responding. However, the carbonylated analog, i.e., cathinone, was found to be equipotent with amphetamine. Furthermore, as with amphetamine, the S-isomer of cathinone was found to be more active than its enantiomer. With respect to the conformationally-restricted analogs, the most potent compound was 2-aminotetralin which was about half as active as racemic amphetamine.

Alkaloids↗