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At least 811 records · Page 45Linked to original sources
PubMed2002

Identification of novel small molecules that bind to two different sites on the surface of tetanus toxin C fragment.

A combination of computational methods, electrospray ionization mass spectroscopy (ESI-MS), and NMR spectroscopy has been used to identify novel small molecules that bind to two adjacent sites on the surface of the C fragment of tetanus toxin (TetC). One of these sites, Site-1, binds gangliosides present on the surface of motor neurons, while Site-2 is a highly conserved deep cleft in the structures of the tetanus (TeNT) and botulinum (BoNT) neurotoxins. ESI-MS was used to experimentally determine which of the top 11 computationally predicted Site-2 candidates bind to TetC. Each of the six molecules that tested positive was further screened, individually and as mixtures, for binding to TetC in aqueous solutions by NMR. A trNOESY competition assay was developed that used doxorubicin as a marker for Site-1 to provide insight into whether the predicted Site-2 ligands bound to a different site. Of the six predicted Site-2 ligands tested, only four were observed to bind. Naphthofluorescein-di-beta-galactopyranoside was insoluble under conditions compatible with TetC. Sarcosine-Arg-Gly-Asp-Ser-Pro did not appear to bind, but its binding affinity may have been outside the range detectable by the trNOESY experiment. Of the remaining four, three [3-(N-maleimidopropionyl)biocytin, lavendustin A, and Try-Glu-Try] bind in the same site, presumably the predicted Site-2. The fourth ligand, Ser-Gln-Asn-Tyr-Pro-Ile-Val, binds in a third site that differs from Site-1 or predicted Site-2. The results provide a rational, cost- and time-effective strategy for the selection of an optimal set of Site-1 binders and predicted Site-2 binders for use in synthesizing novel bidendate antidotes or detection reagents for clostridial neurotoxins, such as TeNT and BoNT.

Antidotes↗
PubMed2000

pH-metric solubility. 2: correlation between the acid-base titration and the saturation shake-flask solubility-pH methods.

PURPOSE: The objective of this study was to compare the results of a normal saturation shake-flask method to a new potentiometric acid-base titration method for determining the intrinsic solubility and the solubility-pH profiles of ionizable molecules, and to report the solubility constants determined by the latter technique. METHODS: The solubility-pH profiles of twelve generic drugs (atenolol, diclofenac.Na, famotidine, flurbiprofen, furosemide, hydrochlorothiazide, ibuprofen, ketoprofen, labetolol.HCl, naproxen, phenytoin, and propranolol.HCl), with solubilities spanning over six orders of magnitude, were determined both by the new pH-metric method and by a traditional approach (24 hr shaking of saturated solutions, followed by filtration, then HPLC assaying with UV detection). RESULTS: The 212 separate saturation shake-flask solubility measurements and those derived from 65 potentiometric titrations agreed well. The analysis produced the correlation equation: log(1/S)titration = -0.063(+/- 0.032) + 1.025(+/- 0.011) log(1/S)shake-flask, s = 0.20, r2 = 0.978. The potentiometrically-derived intrinsic solubilities of the drugs were: atenolol 13.5 mg/mL, diclofenac.Na 0.82 microg/mL, famotidine 1.1 mg/ mL, flurbiprofen 10.6 microg/mL, furosemide 5.9 microg/mL, hydrochlorothiazide 0.70 mg/mL, ibuprofen 49 microg/mL, ketoprofen 118 microg/mL, labetolol.HCl 128 microg/mL, naproxen 14 microg/mL, phenytoin 19 microg/mL, and propranolol.HCl 70 microg/mL. CONCLUSIONS: The new potentiometric method was shown to be reliable for determining the solubility-pH profiles of uncharged ionizable drug substances. Its speed compared to conventional equilibrium measurements, its sound theoretical basis, its ability to generate the full solubility-pH profile from a single titration, and its dynamic range (currently estimated to be seven orders of magnitude) make the new pH-metric method an attractive addition to traditional approaches used by preformulation and development scientists. It may be useful even to discovery scientists in critical decision situations (such as calibrating computational prediction methods).

Hydrogen-Ion Concentration↗
PubMed1997

Sequences of terminal non-coding regions from four dengue-2 viruses isolated from patients exhibiting different disease severities.

We have determined the 5' and 3' non-coding regions (NCR) of four dengue-2 viruses isolated from dengue patients with different clinical severities in Nakhon Phanom, Northeastern Thailand in 1993. The results were compared to prototype dengue-2 strains and were found to have highest homology with the New Guinea C strain. The sequence of the 5' NCR was completely conserved among all 4 isolates and were identical to the sequence of the New Guinea C strain. Homology of the 3' NCR sequence of the four isolates with the prototype strain ranged from 97.3 to 97.8%. Isolate ThNH-p11/93 from a mild dengue fever case showed the highest divergence from the prototype strain and the rest of the isolates from severe hemorrhagic cases, (1.11%). This includes a change in triad 297-299 nucleotides from the 3' terminus. Computer predicted secondary structures showed that isolate ThNHp-11/93 had significant structural differences from the other three isolates at this region.

Base Sequence↗
PubMed1997

Sequencing of a 5.5-kb DNA fragment and identification of a gene coding for a subunit of the helicase/primase complex of avian laryngotracheitis virus (ILTV).

The nucleotide sequence of a 5,520-bp EcoRI restriction fragment of avian infectious laryngotracheitis (ILTV) DNA was reported and submitted to GeneBank with an accession number of AF001078. Computer prediction revealed one large potential open reading frame (ORF) with sequence similar to one subunit of the DNA helicase-primase complex of alpha-herpesviruses. The DNA helicase/primase complex of HSV-1 consists of three sub-units with molecular weights of 12,000, 97,000 and 70,000, encoded by genes UL52, UL5 and UL8, respectively. This enzyme complex is essential for herpesvirus DNA replication. The UL52 and UL5-equivalent genes of ILTV have been reported previously (Fuchs, W. and Mettenleiter, T.C.; J Gen Virol, 1996, 77: 2221-2229; Johnson, M.A. et. al., Arch Virol, 1995, 14: 623-634). Amino acid sequence comparison and homology search revealed that this ORF shares sequence similarity of the UL8-equivalent gene of alpha-herpesviruses, that is, the ORF 52 of vericura-zoster virus (VZV), the ORF 54 of equine herpesvirus type-1 (EHV-1), as well as the equivalent gene of bovine herpesvirus type 1 (BHV-1) and canine herpesvirus (Vlcek, C. et al., Virology, 1995, 210: 100-108; Remond, M. et al., J Gen Virol, 1996, 77: 37-48).

Animals↗
PubMed2001

Attenuated lapinized chinese strain of classical swine fever virus: complete nucleotide sequence and character of 3'-noncoding region.

The complete nucleotide sequence including precise 5'- and 3'-terminal non-coding regions (NCRs) of the attenuated lapinized Chinese strain (HCLV) of Classical Swine Fever Virus (CSFV) was determined from overlapping cDNA clones constructed by separated RT-PCR and rapid amplification of cDNA ends (RACE) methods. The genomic RNA of the HCLV strain consists of 12.310 nucleotides (nts) including 374 nts and 242nts in the 5'- and 3'-NCRs, respectively. It contains one large open reading frame (ORF) encoding a polyprotein of 3,898 amino acids with a calculated molecular weight of 437.6 kDa. There is one notable insertion of 12 continuous nts, CTTTTTTCTTTT in the 3'-NCR of HCLV genomic cDNA when compared with its parental virulent Shimen strain. Sequence alignment of partial 3'-NCR reveals two groups of CSFV vaccine strains carrying similar T-rich insertions at different positions in this region. Computer-predicted secondary structures suggest that T-rich insertion greatly change the structures and thus decrease the promoter functions of 3'-NCRs during the replications of these two groups of CSFV vaccine strains.

3' Untranslated Regions↗
PubMed2001

Transition between two forms of heterochromatin at plant subtelomeres.

The manner of packing of the terminal DNA loci into nucleosomes and higher order structures may strongly influence their functional interactions. Besides the structural flexibility of telomeric DNA sequences, conserved features of their chromatin including short nucleosome phasing (157 bp) and nucleosome sliding have been described previously. To gain a complementary knowledge of subtelomeres, we have analysed the chromatin structure of two subtelomeric tandem repeats from the plant Silene latifolia: X43.1 and 15Ssp. X43.1 shows two distinct nucleosome periodicities--157 and 188 bp. Preferred positions of its two nucleosomes have been mapped at both low and high resolution and the experimental results correspond to computer-predicted positions. 15Ssp is a newly-discovered sequence showing a telomere-associated position by PCR and a subtelomeric location by pulsed-field gel electrophoresis and fluorescence in situ hybridisation. Its 159 bp sequence unit shows a tandem arrangement and the presence of micrococcal nuclease-hypersensitive sites when either naked DNA or chromatin is digested. Use of a chemical nuclease results in a regular nucleosome ladder of 157 bp periodicity. Moreover, 15Ssp mononucleosomes show instability and absence of specific positioning, features typical for telomeric chromatin.

Base Sequence↗
PubMedDate not supplied

Towards a new age of virtual ADME/TOX and multidimensional drug discovery.

With the continual pressure to ensure follow-up molecules to billion dollar blockbuster drugs, there is a hurdle in profitability and growth for pharmaceutical companies in the next decades. With each success and failure we increasingly appreciate that a key to the success of synthesized molecules through the research and development process is the possession of drug-like properties. These properties include an adequate bioactivity as well as adequate solubility, an ability to cross critical membranes (intestinal and sometimes blood-brain barrier), reasonable metabolic stability and of course safety in humans. Dependent on the therapeutic area being investigated it might also be desirable to avoid certain enzymes or transporters to circumvent potential drug-drug interactions. It may also be important to limit the induction of these same proteins that can result in further toxicities. We have clearly moved the assessment of in vitro absorption, distribution, metabolism, excretion and toxicity (ADME/TOX) parameters much earlier in the discovery organization than a decade ago with the inclusion of higher throughput systems. We are also now faced with huge amounts of ADME/TOX data for each molecule that need interpretation and also provide a valuable resource for generating predictive computational models for future drug discovery. The present review aims to show what tools exist today for visualizing and modeling ADME/TOX data, what tools need to be developed, and how both the present and future tools are valuable for virtual filtering using ADME/TOX and bioactivity properties in parallel as a viable addition to present practices.

Biological Availability↗
PubMed2002

Towards a new age of virtual ADME/TOX and multidimensional drug discovery.

With the continual pressure to ensure follow-up molecules to billion dollar blockbuster drugs, there is a hurdle in profitability and growth for pharmaceutical companies in the next decades. With each success and failure we increasingly appreciate that a key to the success of synthesized molecules through the research and development process is the possession of drug-like properties. These properties include an adequate bioactivity as well as adequate solubility, an ability to cross critical membranes (intestinal and sometimes blood-brain barrier), reasonable metabolic stability and of course safety in humans. Dependent on the therapeutic area being investigated it might also be desirable to avoid certain enzymes or transporters to circumvent potential drug-drug interactions. It may also be important to limit the induction of these same proteins that can result in further toxicities. We have clearly moved the assessment of in vitro absorption, distribution, metabolism, excretion and toxicity (ADME/TOX) parameters much earlier in the discovery organization than a decade ago with the inclusion of higher throughput systems. We are also now faced with huge amounts of ADME/TOX data for each molecule that need interpretation and also provide a valuable resource for generating predictive computational models for future drug discovery. The present review aims to show what tools exist today for visualizing and modeling ADME/TOX data, what tools need to be developed, and how both the present and future tools are valuable for virtual filtering using ADME/TOX and bioactivity properties in parallel as a viable addition to present practices.

Biological Availability↗
PubMed2004

BAX Inhibitor-1, an ancient cell death suppressor in animals and plants with prokaryotic relatives.

BAX Inhibitor-1 (BI-1) was originally described as testis enhanced gene transcript in mammals. Functional screening in yeast for human proteins that can inhibit the cell death provoking function of BAX, a proapoptotic Bcl-2 family member, led to functional characterisation and renaming of BI-1. The identification of functional homologues of BI-1 in plants and yeast widened the understanding of BI-1 function as an ancient suppressor of programmed cell death. BI-1 is one of the few cell death suppressors conserved in animals and plants. Computer predictions and experimental data together suggest that BI-1 is a membrane spanning protein with 6 to 7 transmembrane domains and a cytoplasmic C-terminus sticking in the endoplasmatic reticulum and nuclear envelope. Proteins similar to BI-1 are present in other eukaryotes, bacteria, and even viruses encode BI-1 like proteins. BI-1 is involved in development, response to biotic and abiotic stress and probably represents an indispensable cell protectant. BI-1 appears to suppress cell death induced by mitochondrial dysfunction, reactive oxygen species or elevated cytosolic Ca(2+) levels. This review focuses on the present understanding about BI-1 and suggests potential directions for further analyses of this increasingly noticed protein.

Amino Acid Sequence↗
PubMed2001

Lipocalin allergens.

Most animal-derived major allergens causing respiratory sensitization belong to the family of proteins called lipocalins. Their sequential identity varies but the three-dimensional structure is conserved. They are present in body fluids and secretions. Several lipocalins are able to bind and transport small hydrophobic ligands like retinol. The immunological characteristics of lipocalin allergens are poorly known. Cow dust-derived allergen, Bos d2, which is a potent inducer of IgE production, was observed to induce the weak proliferative responses of peripheral blood mononuclear cells of asthmatic patients upon stimulation in vitro. The responses were Th2-deviated and directed to a few epitopes in Bos d2. One of the epitopes, situated adjacent to a structurally conserved region of lipocalins, was recognized by the T cells of all patients. Computer predictions suggested that human endogenous lipocalins may contain epitopes in the corresponding region. We have proposed that the allergenicity of lipocalins may be associated with the adaptation of the immune system to the presence of endogenous lipocalins.

Allergens↗
PubMed2002

Characterization of the solution conformations of leuprolide acetate.

Leuprolide acetate (pGlu-His-Trp-Ser-Tyr-d-Leu-Leu-Arg-Pro-NHEt), a potent LHRH agonist in wide clinical use, was characterized conformationally by NMR and circular dichroism. It displayed quite different preferred conformations under different solution conditions: two low population beta-turns in water, a nascent helix in TFE/water at low pH, and a high population beta-turn in TFE/water at slightly acidic pH. The pH-related conformational change in TFE/water is attributed to the pK(a) of the acetate counterion, not to ionizable groups on the peptide. None of these conformations are in exact agreement with previous computational predictions.

Amino Acid Sequence↗
PubMed1981

Structure of mouse metallothionein-I gene and its mRNA.

Metallothioneins are small cysteine-rich proteins that bind heavy metals such as zinc, cadmium, copper and mercury. Recent interest in these proteins has focused on the part they play in zinc metabolism and heavy metal detoxification. Our interest in metallothionein genes stems largely from the observations that these proteins are inducible by both heavy metals and glucocorticoid hormones. To explore the regulation of these genes, we have isolated cDNA and genomic clones corresponding to mouse metallothionein-I (MT-I), and have used them to show that both inducers act at the transcriptional level in vivo and in a wide variety of cell lines. We have also shown that the MT-I gene is amplified during selection for cadmium resistance. To investigate the mechanisms of gene regulation, knowledge of the primary DNA sequence is necessary. Here we present the entire sequence of mouse MT-I gene along with approximately 300 bases of 5' flanking region that presumably includes promoter and regulatory sites. The 5' mRNA sequence, defined by S1 nuclease mapping, was combined with sequences of the coding and 3' untranslated regions obtained previously to allow a computer prediction of the most stable secondary structure of MT-I mRNA.

Animals↗
PubMed1976

Comparative field cage tests of the population suppressing efficiency of three genetic control systems for Aedes Aegypti.

Cycling populations of Aedes aegypti were set up in cages and managed in such a way that the populations had a maximum of threefold recovery potential in response to control measures. Into three such populations daily releases were made of males which had been chemosterilised, or were double translocation heterozygotes (T1T3) or T1T3 with sex ration distortion (DT1T3). Eradication of the populations was achieved with all cases, but the rate of suppression was markedly slower with T1T3 than the other two systems, with which the rates were similar. T1T3 and DT1T3 releases introduced considerable inherited genetic loads into the target populations. The results were in general agreement with computer predictions.

Aedes↗
PubMed1991

Human IgE-binding synthetic peptides of bovine beta-lactoglobulin and alpha-lactalbumin. In vitro cross-reactivity of the allergens.

The allergenicity of cow's milk whey proteins, purified by high performance liquid chromatography (HPLC), was examined by the radio-allergosorbent test (RAST) against the sera of children immediately hypersensitive to milk. beta-lactoglobulin and alpha-lactalbumin bound specific IgE in the sera of 63% and 75% of these patients respectively. These allergens were tested for cross reactivity with each other by RAST inhibition. Both inhibited the binding of IgE, in the sera of allergic patients, to the other protein. Two possible determinant peptides, one from beta-lactoglobulin and one from alpha-lactalbumin, were selected by computer prediction of antigenic sites and synthesized by the fluorenylmethoxycarbonyl (FMOC)-polyamide method. The peptides were adsorbed to nitrocellulose discs and used in further RAST studies with sera from the allergic children. Both peptides bound specific IgE in the RAST assay.

Allergens↗
PubMed2005

A bacterial one-hybrid system for determining the DNA-binding specificity of transcription factors.

The DNA-binding specificities of transcription factors can be used to computationally predict cis-regulatory modules (CRMs) that regulate gene expression. However, the absence of specificity data for the majority of transcription factors limits the widespread implementation of this approach. We have developed a bacterial one-hybrid system that provides a simple and rapid method to determine the DNA-binding specificity of a transcription factor. Using this technology, we successfully determined the DNA-binding specificity of seven previously characterized transcription factors and one novel transcription factor, the Drosophila melanogaster factor Odd-skipped. Regulatory targets of Odd-skipped were successfully predicted using this information, demonstrating that the data produced by the bacterial one-hybrid system are relevant to in vivo function.

Animals↗
PubMed2006

Natural selection on human microRNA binding sites inferred from SNP data.

A fundamental problem in biology is understanding how natural selection has shaped the evolution of gene regulation. Here we use SNP genotype data and techniques from population genetics to study an entire layer of short, cis-regulatory sites in the human genome. MicroRNAs (miRNAs) are a class of small noncoding RNAs that post-transcriptionally repress mRNA through cis-regulatory sites in 3' UTRs. We show that negative selection in humans is stronger on computationally predicted conserved miRNA binding sites than on other conserved sequence motifs in 3' UTRs, thus providing independent support for the target prediction model and explicitly demonstrating the contribution of miRNAs to darwinian fitness. Our techniques extend to nonconserved miRNA binding sites, and we estimate that 30%-50% of these are functional when the mRNA and miRNA are endogenously coexpressed. As we show that polymorphisms in predicted miRNA binding sites are likely to be deleterious, they are candidates for causal variants of human disease. We believe that our approach can be extended to studying other classes of cis-regulatory sites.

3' Untranslated Regions↗
PubMed2002

Inhibition of angiogenesis in vitro by alphav integrin-directed antisense oligonucleotides.

The integrin alpha v beta 3 plays a central role in angiogenesis. In this study, we used antisense oligodeoxyribonucleotides (ONs) directed against the alpha v subunit of alpha v beta 3 to inhibit integrin expression. Ten ON sequences, which were selected by systematic alignment of computer-predicted secondary structures of alpha v mRNA, were transfected into human umbilical vein endothelial cells (HUVECs). Following stimulation by PMA, five antisense ONs significantly inhibited alpha v mRNA and protein expression in activated HUVEC at a concentration of 0.05 mciroM with complete prevention of PMA-induced alpha v up-regulation by the most potent antisense ON. Inhibition of alpha v expression was associated with significant inhibition of migration of HUVEC by 28% and had no effect on proliferation and apoptosis. Moreover, transfection of antisense ON inhibited the formation of tube-like structures of HUVEC in Matrigel by 44%. In a cell culture model of angiogenesis consisting of a co-culture of endothelial cells with fibroblasts, transfection of antisense ONs resulted in an inhibition of tube formation of 61%. In conclusion, alpha v antisense ONs are potent inhibitors of angiogenesis in vitro. They might, therefore, be a therapeutic alternative to antagonists, which directly bind to alpha v integrins, and might be useful for the treatment of malignant tumors and hematological malignancies.

Apoptosis↗
PubMed1997

Microsatellite deletions in the c-myb transcriptional attenuator region associated with over-expression in colon tumour cell lines.

In the hemopoietic system c-myb expression is required for proliferation of immature cells and its down-regulation is required for differentiation. In colonic mucosa c-myb expression occurs at levels comparable to immature hemopoietic cells. Inhibition of c-myb expression in colon cell lines, using anti-sense oligonucleotides, indicates that c-myb expression is required for proliferation. However, the mechanism of c-myb regulation during colon cell differentiation has not been explored. Using the LIM1215 and CaCo-2 colon carcinoma cell lines induced to differentiate with sodium butyrate, we demonstrate that c-myb mRNA is down-regulated as an early event in differentiation by a mechanism involving transcriptional attenuation in intron 1. By analogy with procaryotic and eucaryotic genes, transcriptional attenuation probably occurs in a region containing nineteen consecutive thymidine residues. Computer prediction of the secondary structure of the nascent mRNA chain encoded by this region suggests a strong potential for stem-loop formation. Sequence analysis of several colon tumour cell lines reveals mutations in this region that may disrupt transcriptional attenuation and result in the increased c-myb expression observed in colon tumours and tumour cell lines.

Base Sequence↗