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PubMed2000

Potential drugs and nondrugs: prediction and identification of important structural features

Using decision trees, a model to discriminate between potential drugs and nondrugs has been developed. Compounds from the Available Chemical Directory and the World Drug Index databases were used as training set; the molecular structures were represented using extended atom types. The error rate on an independent validation data set is 17.4%. The number of false negatives can be reduced by penalizing the misclassification of drugs so that 92 out of 100 potential drugs are correctly recognized. At the same time, 34 out of 100 nondrugs are classified as potential drugs. The predictions of the model can be used to guide the purchase or selection of compounds for biological screening or the design of combinatorial libraries. The visualization of the generated models in the form of colored trees allowed us to identify a few, surprisingly simple features that explain the most significant differences between drugs and nondrugs in the training set: Just by testing the presence of hydroxyl, tertiary or secondary amino, carboxyl, phenol, or enol groups, already three quarters of all drugs could be correctly recognized. The nondrugs, on the other hand, are characterized by their aromatic nature with a low content of functional groups besides halogens. The general applicability of the model is shown by the predictions made for several Organon databases.

Journal Article↗

PubMed1998

Anti-Hu immunolabeling as an index of neuronal differentiation in human brain tumors: a study of 112 central neuroepithelial neoplasms.

Anti-Hu is a polyclonal immunoglobulin G associated with a syndrome of paraneoplastic sensory neuropathy/encephalomyelitis that principally afflicts patients with small cell lung carcinoma. Anti-Hu antibodies, which identify a family of RNA-binding proteins that are normally neuron restricted and that appear to be integral to neuronal differentiation and maintenance, selectively label the nuclei (and, less strongly, the cytoplasm) of neurons throughout the human neuraxis. Small cell carcinomas of the lung and many neuroblastomas are also labeled. We screened 112 tumors of central neuroepithelial lineage for immunohistochemical evidence of Hu expression with anti-Hu immunoglobulin G that was purified from patient sera and with a recombinant Fab fragment (Fab GLN 495) selected from a patient-derived combinatorial antibody phage display library using a recombinant Hu protein (HuD). Both antibodies uniformly labeled, in addition to native neurons, the nuclei of central neurocytomas (6 of 6) and the neuronal components of "classic" (12 of 12) and desmoplastic infantile (2 of 2) gangliogliomas. Of 33 embryonal tumors, 29 were anti-Hu reactive, including 87% of medulloblastomas (26 of 30). Glial neoplasms (n = 59) were anti-Hu negative save for one "oligodendroglioma" (of 17 oligodendroglial/oligoastrocytic tumors) that may have been an extraventricular neurocytoma. Anti-Hu immunoglobulin G/Fab GLN 495 identifies neoplasms of differentiated neuronal type and embryonal tumors with neuronogenic potential.

Antibodies, Neoplasm↗

PubMed2005

BCUT descriptors to predicting affinity toward A3 adenosine receptors.

The BCUT descriptors have been applied to the study of the A(3) adenosine receptor agonist effect of 32 adenosine analogues. A model, able to describe more than 80% of the variance in the experimental activity was developed with the use of the above-mentioned approach. Four different approaches (topological, Galvez topological charges indexes, Randić molecular profiles, and geometrical descriptors) failed to give satisfactory models for this property with the same number of variables in the equation. Although statistically significant models were derived containing descriptors other than BCUT, the best fitted model was still found with these descriptors.

Adenosine↗

PubMed2001

The effect of casting solvent quality on the structure of polymeric Langmuir-Blodgett films.

The effect of casting solvent quality (good vs. [symbol: see text] solvent) on the structure of Langmuir-Blodgett films of a flexible-chain polymer [poly(dimethylsiloxane)] was examined on the basis of differences in the shape of Langmuir-Blodgett isotherms for two solvents, two temperatures, four polymer molecular weights, and three compression rates. The magnitude of a new index that describes the shape characteristics of the isotherm beyond the point of monolayer formation is found to be capable of separating all 48 isotherms studied into two groups, exclusively on the basis of the quality of the casting solvent. Experimental observations are supplemented by qualitative polymer physics interpretations regarding the structure of the films upon casting and compression.

Butanones↗

PubMed2005

Leukemias following retroviral transfer of multidrug resistance 1 (MDR1) are driven by combinatorial insertional mutagenesis.

Previous studies have demonstrated leukemic complications in mice after high-copy retroviral gene transfer of the multidrug resistance 1 (MDR1) cDNA, encoding a membrane-located efflux pump expressed in hematopoietic stem cells. In contrast, no such complications or MDR1-associated alterations of hematopoiesis were observed in numerous other studies exploring MDR1 gene transfer into cell lines, mice, dogs, nonhuman primates, and human subjects. Here, we show that leukemias associated with retroviral expression of MDR1 depend on high vector dose, and involve the selection of clones with combinatorial insertional mutagenesis of proto-oncogenes or other signaling genes. Compared with insertion patterns in normal long-term repopulating hematopoietic cells, such hits were overrepresented in leukemic clones, pointing to a causal role. A similar constellation of insertion sites was also observed in a leukemia arising after high-copy retroviral gene transfer of a fluorescent protein. Spectral karyotyping demonstrated additional chromosomal translocations in a subset of cases, indicative of secondary genetic instability. We also show that insertional mutants can be amplified in vitro prior to transplantation. On the basis of these findings, we suggest the use of preclinical dose-escalation studies to define a therapeutic index for retroviral transgene delivery.

ATP Binding Cassette Transporter, Subfamily B, Mem↗

PubMed2005

Euler vector for search and retrieval of gray-tone images.

A new combinatorial characterization of a gray-tone image called Euler Vector is proposed. The Euler number of a binary image is a well-known topological feature, which remains invariant under translation, rotation, scaling, and rubber-sheet transformation of the image. The Euler vector comprises a 4-tuple, where each element is an integer representing the Euler number of the partial binary image formed by the gray-code representation of the four most significant bit planes of the gray-tone image. Computation of Euler vector requires only integer and Boolean operations. The Euler vector is experimentally observed to be robust against noise and compression. For efficient image indexing, storage and retrieval from an image database using this vector, a bucket searching technique based on a simple modification of Kd-tree, is employed successfully. The Euler vector can also be used to perform an efficient four-dimensional range query. The set of retrieved images are finally ranked on the basis of Mahalanobis distance measure. Experiments are performed on the COIL database and results are reported. The retrieval success can be improved significantly by augmentiong the Euler vector by a few additional simple shape features. Since Euler vector can be computed very fast, the proposed technique is likely to find many applications to content-based image retrieval.

Algorithms↗

PubMed2000

The library of p-nitrophenyl esters of oligopeptides as a model to study the anticancer drug-peptide conjugates activated during tumor angiogenesis.

An indexed library of oligopeptide p-nitrophenyl esters immobilized via methoxy-1,3,5-triazine scaffold on the cellulose support, was synthesized by the step by step procedure and by segment coupling, involving 2-chloro-4,6-dimethoxy-1,3,5-triazine as a condensing reagent. The substrate specificity towards homogenate supernatant of mouse lung cancer LL2 cells has been studied.

Animals↗

PubMed2003

Imaging surface plasmon resonance system for screening affinity ligands.

A surface plasmon resonance (SPR) system for screening ligands for application in affinity chromatography is described. A combinatorial library of 13 ligands was synthesised, characterised and immobilised to agarose beads and gold SPR devices. Binding and elution behaviour and a range of K(AX) values (10(3) to 10(5) M(-1)) were measured against two target proteins, an insulin analogue (MI3) and a recombinant clotting factor (rFVIIa), in order to create a relational database between the traditional chromatographic format and the new SPR screening system. The SPR transducer surface was fabricated with affinity ligands in a two-dimensional, spatially addressable format, which was durable (>100 cycles) and stable over 6 months. The imaging SPR system comprised a direct optical, CCD-based, instrument capable of imaging the change in refractive index created by biochemical interactions and allowed affinity ligands to be evaluated 15-fold faster with 130-fold less target protein than conventional chromatographic methods. The binding and elution data from both the SPR and chromatographic systems for both target proteins were comparable, with the K(AX) value generating a nearly linear correlation (R(2)=0.875) and a slope bias of approximately 2.5+/-0.25-fold higher for the SPR system. The imaging SPR system has proven capable of screening and evaluating affinity ligands for potential use in the recovery of biopharmaceutical proteins.

Affinity Labels↗

PubMed2000

The library of p-nitrophenyl esters of oligopeptides as a model to study the anticancer drug-peptide conjugates activated during tumor angiogenesis.

Animals↗

PubMed1997

Screening solution-phase combinatorial libraries using pulsed ultrafiltration/electrospray mass spectrometry.

A method is described whereby a family of homologues is synthesized in a one-pot reaction, without isolation or purification, and the reaction mixture is screened using a competitive binding assay based on pulsed ultrafiltration/electrospray mass spectrometry (PUF/ESMS) to tentatively identify those derivatives having the highest affinity for a target receptor. As a model system to test this approach, a synthetic scheme designed to prepare a series of analogues of the adenosine deaminase inhibitor erythro-9-(2-hydroxy-3-nonyl)adenine (EHNA), as diastereomeric mixtures, was carried out. Pulsed ultrafiltration screening of the crude reaction mixture against controls without protein detected protonated molecules corresponding to EHNA-type derivatives and three of its linear, alkyl homologues but did not show protonated molecules for an isobutyl or benzylic EHNA derivative, suggesting the latter was inactive. To verify this conclusion, we prepared E/THNA, the linear homologues, and the benzylic derivative (each as a diastereomeric mixture) and bioassayed them for them adenosine deaminase inhibition index ([I]/[S]0.5). The bioassay results for the individually synthesized analogues were in good agreement with that predicted by the observed relative ion enhancement in the PUF experiments. Thus, the PUF protocol might be used as a general method to quickly provide direction to the chemist in search of drug candidates.

Adenine↗

PubMedDate not supplied

Ruminations regarding the design of small mixtures for biological testing.

Synthesis and screening of compound mixtures offer avenues to increase throughput and reduce cycle time in the discovery of new drugs and agrochemicals. Equations are derived which show that the efficiency of synthesis and screening of mixtures is a function of the screening hit rate and the number of compounds in each mixture when simple one-step deconvolution by retesting the individual compounds in each active mixture is employed. Values of hit rate and number of compounds in each mixture which afford various levels of increased efficiency are delineated. Two-step deconvolution, in which the active mixtures from the first round of testing are subdivided into mixtures with fewer compounds for a second round of mixture screening prior to final testing of individual compounds, is shown to be more efficient than simple one-step deconvolution under most conditions. For optimum efficiency, the number of compounds in each mixture in the second round testing should be the square root of the number of compounds in each mixture in the first round. At high hit rates the efficiency of the double scan or indexed approach to deconvolution is shown to be higher than that of simple deconvolution. This discussion is oriented mainly toward mixtures of 4-20 compounds and screens which give hit rates in the 1-10% range. The equations describing efficiency are applied in the context of a 49-member amide library produced as mixtures of seven compounds. This library includes the commercial herbicide pronamide and was screened for herbicidal and insecticidal utility.

Combinatorial Chemistry Techniques↗

PubMed2006

The vascular targeting property of paclitaxel is enhanced by SU6668, a receptor tyrosine kinase inhibitor, causing apoptosis of endothelial cells and inhibition of angiogenesis.

PURPOSE: Different antiangiogenic approaches have been proposed in cancer treatment where therapeutic efficacy has been shown with the addition of cytotoxic agents. Here, we used SU6668, a small-molecule receptor tyrosine kinase inhibitor, to investigate the combinatorial effect with paclitaxel on the cellular populations of the developing vasculature. EXPERIMENTAL DESIGN: The effect of this combination was evaluated in vitro in a 72-hour proliferation assay on human umbilical vein endothelial cells (HUVEC) and human microvascular endothelial cells derived from lungs, endothelial cells, aortic smooth muscle cells, and human ovarian carcinoma cells sensitive (1A9) and resistant (1A9-PTX22) to paclitaxel. Combination data were assessed by isobologram analysis. Cell survival was determined by terminal deoxyribonucleotide transferase-mediated nick-end labeling and Annexin V staining. The activity of the combination in vivo was evaluated in fibroblast growth factor-2-induced angiogenesis in Matrigel plugs s.c. implanted in mice. The 1A9-PTX22, paclitaxel-resistant xenograft model was used to evaluate tumor response. RESULTS: Combination index values and isobologram analysis showed synergy in inhibition of proliferation of HUVEC, human microvascular endothelial cells derived from lungs, and aortic smooth muscle cells. The combination induced greater apoptosis in HUVEC than the single agents. The addition of paclitaxel to the treatment with SU6668 significantly decreased the hemoglobin content and the number of CD31-positive vessels in Matrigel plugs in vivo. The combination of the drugs was more active than either single agent against 1A9-PTX22 xenografts; the tumor growth delay was accompanied by a significant reduction of vascular density. CONCLUSIONS: These findings show that the activity of angiogenesis inhibitors on vascular cells could be potentiated when administered in combination with chemotherapeutic agents that themselves have vascular targeting properties.

Animals↗

PubMed2006

Identification of compounds with anti-West Nile Virus activity.

The lack of antiviral compounds targeting flaviviruses represents a significant problem in the development of strategies for treating West Nile Virus (WNV), Dengue, and Yellow Fever infections. Using WNV high-throughput screening techniques developed in our laboratories, we report the identification of several small molecule anti-WNV compounds belonging to four different structural classes including pyrazolines, xanthanes, acridines, and quinolines. The initial set of "hits" was further refined using cell viability-cytotoxicity assays to two 1,3,5-triaryl pyrazoline compounds: 1-(4-chlorophenylacetyl)-5-(4-nitrophenyl)-3-(thiophen-2-yl)-4,5-dihydro-1H-pyrazole and 1-benzoyl-5-(4-chlorophenyl)-3-(thiophen-2-yl)-4,5-dihydro-1H-pyrazole. On the basis of their activity and favorable therapeutic indexes, these compounds were identified as viable leads and subjected to additional evaluation using an authentic viral titer reduction assay employing an epidemic strain of WNV. The compounds were further evaluated in a transient replicon reporting system to gain insight into the mechanism of action by identifying the step at which inhibition takes place during viral replication. The results indicate the pyrazolines inhibit RNA synthesis, pointing to viral RNA polymerase, RNA helicase, or other viral replication enzymes as potential targets. Progress was also made in understanding the structural requirements for activity by synthesizing a focused chemical library of substituted pyrazolines. Preliminary SAR data are presented that show the aryl-rings are required for activity against WNV. More importantly, the results indicate WNV activity is tolerant to aryl-substitutions paving the way for the design and development of much larger combinatorial libraries with varied physicochemical properties.

Acridines↗

PubMed2004

Bioie: retargetable information extraction and ontological annotation of biological interactions from the literature.

The need for extracting general biological interactions of arbitrary types from the rapidly growing volume of the biomedical literature is drawing increased attention, while the need for this much diversity also requires both a robust treatment of complex linguistic phenomena and a method to consistently characterize the results. We present a biomedical information extraction system, BioIE, to address both of these needs by utilizing a full-fledged English grammar formalism, or a combinatory categorial grammar, and by annotating the results with the terms of Gene Ontology, which provides a common and controlled vocabulary. BioIE deals with complex linguistic phenomena such as coordination, relative structures, acronyms, appositive structures, and anaphoric expressions. In order to deal with real-world syntactic variations of ontological terms, BioIE utilizes the syntactic dependencies between words in sentences as well, based on the observation that the component words in an ontological term usually appear in a sentence with known patterns of syntactic dependencies.

Abstracting and Indexing↗

PubMed2001

Prediction of drug transport processes using simple parameters and PLS statistics. The use of ACD/logP and ACD/ChemSketch descriptors.

A method of modelling and predicting biopharmaceutical properties using simple theoretically computed molecular descriptors and multivariate statistics has been investigated for several data sets related to solubility, IAM chromatography, permeability across Caco-2 cell monolayers, human intestinal perfusion, brain-blood partitioning, and P-glycoprotein ATPase activity. The molecular descriptors (e.g. molar refractivity, molar volume, index of refraction, surface tension and density) and logP were computed with ACD/ChemSketch and ACD/logP, respectively. Good statistical models were derived that permit simple computational prediction of biopharmaceutical properties. All final models derived had R(2) values ranging from 0.73 to 0.95 and Q(2) values ranging from 0.69 to 0.86. The RMSEP values for the external test sets ranged from 0.24 to 0.85 (log scale).

ATP Binding Cassette Transporter, Subfamily B, Mem↗

PubMed2006

The neurotrophic effects of PACAP in PC12 cells: control by multiple transduction pathways.

Pituitary adenylate cyclase-activating polypeptide (PACAP) and vasoactive intestinal polypeptide (VIP) are closely related members of the secretin superfamily of neuropeptides expressed in both the brain and peripheral nervous system, and they exhibit neurotrophic and neurodevelopmental effects in vivo. Like the index member of the Trk receptor ligand family, nerve growth factor (NGF), PACAP promotes the differentiation of PC12 cells, a well-established cell culture model, to investigate neuronal differentiation, survival and function. Stimulation of catecholamine secretion and enhanced neuropeptide biosynthesis are effects exerted by PACAP at the adrenomedullary synapse in vivo and on PC12 cells in vitro through stimulation of the specific PAC1 receptor. Induction of neuritogenesis, growth arrest, and promotion of cell survival are effects of PACAP that occur in developing cerebellar, hippocampal and cortical neurons, as well as in the more tractable PC12 cell model. Study of the mechanisms through which PACAP exerts its various effects on cell growth, morphology, gene expression and survival, i.e. its actions as a neurotrophin, in PC12 cells is the subject of this review. The study of neurotrophic signalling by PACAP in PC12 cells reveals that multiple independent pathways are coordinated in the PACAP response, some activated by classical and some by novel or combinatorial signalling mechanisms.

Animals↗

PubMed2006

A responder analysis of memantine treatment in patients with Alzheimer disease maintained on donepezil.

OBJECTIVE: The objective of this study was to examine the clinical utility of memantine for moderate-to-severe Alzheimer disease (AD) using responder analyses. METHOD: Data from a previously published 24-week, randomized, double-blind, placebo-controlled trial of 10 mg memantine twice a day in patients with moderate-to-severe AD (N = 404) on stable donepezil therapy were evaluated using three sets of responder criteria. Response rates were calculated and analyzed for the intention-to-treat population using a generalized estimating equations model. The following outcomes were examined separately and in combination: the Alzheimer's Disease Cooperative Study-Activities of Daily Living 19-Item Inventory (ADCS-ADL19), Severe Impairment Battery (SIB), Clinician's Interview-Based Impression of Change Plus Caregiver Input (CIBIC-Plus), and Neuropsychiatric Inventory (NPI). RESULTS: When treatment response required cognitive improvement relative to baseline, memantine yielded higher response rates than placebo. When treatment response was defined as stabilization of individual outcomes, memantine resulted in significantly higher response rates than placebo for all outcomes, with number needed to treat (NNT) ranging from 8-10. More conservative definitions of response that required simultaneous stabilization on multiple outcome measures again favored memantine treatment for six of 10 combinatorial definitions. CONCLUSIONS: These responder analyses may assist clinicians in evaluating the impact of memantine in a relevant clinical scenario, i.e., in patients with AD previously stabilized on a cholinesterase inhibitor. The current results indicate that in this setting, memantine produces both improvement and stabilization of symptoms, across multiple outcomes, and thus provides a clinically important treatment benefit for patients with moderate-to-severe AD.

Activities of Daily Living↗

PubMed2001

Latent semantic structure indexing (LaSSI) for defining chemical similarity.

A novel method for computing chemical similarity from chemical substructure descriptors is described. This new method, called LaSSI, uses the singular value decomposition (SVD) of a chemical descriptor-molecule matrix to create a low-dimensional representation of the original descriptor space. Ranking molecules by similarity to a probe molecule in the reduced-dimensional space has several advantages over analogous ranking in the original descriptor space: matching latent structures is more robust than matching discrete descriptors, choosing the number of singular values provides a rational way to vary the "fuzziness" of the search, and the reduction in the dimensionality of the chemical space increases searching speed. LaSSI also allows the calculation of the similarity between two descriptors and between a descriptor and a molecule.

Algorithms↗