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Results for “target validation”

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PubMed2004

Drugs against superbugs: private lessons from bacteriophages.

Bacterial genomics has provided a plethora of potential targets for antibacterial drug discovery, however, success in the hunt for new antibiotics will hinge on selecting targets with the highest potential. A recent paper by Liu and coworkers describes a new approach to target selection that uncovers strategies used by bacteriophage to disable bacteria. The method uses key phage proteins to identify and validate vulnerable targets and exploits them further in the identification of new antibacterial leads.

Anti-Bacterial Agents↗

PubMed2001

Separate visual representations for perception and action revealed by saccadic eye movements.

Some 30 years ago, Trevarthen [1] introduced the idea of two separate visual systems, a focal system for fine motor acts and an ambient system for gross body movements such as ambulation. More recent developments indicating anatomically and physiologically separate pathways in primate vision [2] have led to a different idea of separate visual systems, one for conscious perception and one for action [3]. It has received empirical support from several studies showing that pointing, reaching, and grasping can remain accurate while the perceived position or size of objects is subject to illusory distortion [4-6]. However, much of this evidence has been challenged on the grounds of methodological flaws, particularly failure to match perfectly the conditions for verbal and motor tasks and failure to replicate results [7-10]. Here we take advantage of the strong compression of perceived position that occurs around the time of saccadic eye movements [11, 12]. Under normal lighting conditions, stimuli flashed briefly over a wide range of spatial positions just before saccadic onset are neither seen nor reached for in their veridical positions, but are compressed toward the saccadic target. We validate the idea of separate systems by showing that, in the dark, subjects are able to point accurately to the correct target position, even though their verbal reports are still subject to compression.

Humans↗

PubMed1995

Spatial orienting and focused attention in attention deficit hyperactivity disorder.

Seventeen children with attention deficit disorder (ADHD) and 10 normal controls performed two tasks while event-related potentials were recorded. ADHD subjects took part in two more sessions under methylphenidate (MP) or placebo. In the spatial orienting task, invalidly cued targets elicited a longer reaction time (RT) and a P3 that was longer in latency and greater in amplitude than did validly cued targets. Performance was similar for both groups, but the early portion of P3 (300-400 ms) was lower in amplitude for invalidly cued targets in ADHD subjects. MP increased accuracy without affecting RT and shortened P3 peak latency and increased the amplitude of its early portion. In the focused attention task, accuracy was greater for controls and MP, but there were no RT differences. Attended stimuli elicited greater amplitude P1, N1, and P3 than did nonattended stimuli, but these measures were unaffected by diagnosis or medication.

Attention↗

PubMed2006

miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes.

Recent work has demonstrated that microRNAs (miRNAs) are involved in critical biological processes by suppressing the translation of coding genes. This work develops an integrated database, miRNAMap, to store the known miRNA genes, the putative miRNA genes, the known miRNA targets and the putative miRNA targets. The known miRNA genes in four mammalian genomes such as human, mouse, rat and dog are obtained from miRBase, and experimentally validated miRNA targets are identified in a survey of the literature. Putative miRNA precursors were identified by RNAz, which is a non-coding RNA prediction tool based on comparative sequence analysis. The mature miRNA of the putative miRNA genes is accurately determined using a machine learning approach, mmiRNA. Then, miRanda was applied to predict the miRNA targets within the conserved regions in 3'-UTR of the genes in the four mammalian genomes. The miRNAMap also provides the expression profiles of the known miRNAs, cross-species comparisons, gene annotations and cross-links to other biological databases. Both textual and graphical web interface are provided to facilitate the retrieval of data from the miRNAMap. The database is freely available at http://mirnamap.mbc.nctu.edu.tw/.

Animals↗

PubMed2005

Transcriptional program controlled by the floral homeotic gene AGAMOUS during early organogenesis.

Floral organs, whose identity is determined by specific combinations of homeotic genes, originate from a group of undifferentiated cells called the floral meristem. In Arabidopsis, the homeotic gene AGAMOUS (AG) terminates meristem activity and promotes development of stamens and carpels. To understand the program of gene expression activated by AG, we followed genome-wide expression during early stamen and carpel development. The AG target genes included most genes for which mutant screens revealed a function downstream of AG. Novel targets were validated by in situ hybridisation and binding to AG in vitro and in vivo. Transcription factors formed a large fraction of AG targets, suggesting that during early organogenesis, much of the genetic program is concerned with elaborating gene expression patterns. The results also suggest that AG and other homeotic proteins with which it interacts (SEPALLATA3, APETALA3, PISTILLATA) are coordinately regulated in a positive-feedback loop to maintain their own expression, and that AG activates biosynthesis of gibberellin, which has been proposed to promote the shift from meristem identity to differentiation.

AGAMOUS Protein, Arabidopsis↗

PubMed2003

Visual search for singleton feature targets across dimensions: Stimulus- and expectancy-driven effects in dimensional weighting.

Four pop-out search experiments investigated whether dimension-based visual attention is top-down modulable. Observers searched for singleton feature targets defined, variably across trials, by a color or an orientation difference to nontargets. Observers were precued to the most probable target-defining dimension (e.g., by the word color) or feature (red) on a given trial. Results revealed expedited reaction times (RTs) for valid-dimension targets relative to neutral-cue conditions, and slowed RTs for invalid-dimension targets. Cue information as to precise target feature yielded some extra effect only for color targets. The dimensional cuing significantly reduced, but did not abolish, the dimension-specific influence of the previous target on detection of the current target (same-dimension RT < different-dimension RT). These findings confirm that top-down dimensional set modulates stimulus-driven dimension processes in the detection of pop-out signals. ((c) 2003 APA, all rights reserved)

Adult↗

PubMed2006

Chemogenomics: drug discovery's panacea?

Chemogenomics aims towards the systematic identification of small molecules that interact with the products of the genome and modulate their biological function. This Opinion article summarizes the different knowledge-based chemogenomics strategies that are followed and outlines the challenges and opportunities that will impact drug discovery. Chemogenomics aims towards the systematic identification of small molecules that interact with the products of the genome and modulate their biological function. While historically the approach is based on efforts that systematically explore target gene families like kinases, today additional knowledge-based systematization principles are followed within early drug discovery projects which aim to biologically validate the targets and to identify starting points for chemical lead optimization. While the expectations of chemogenomics are very high, the reality of drug discovery is quite sobering with very high project attrition rates. This article summarizes the different knowledge-based chemogenomics strategies that are followed and outlines the challenges and potential opportunities that will impact drug discovery.

Chemistry, Pharmaceutical↗

PubMed2005

Prediction and verification of microRNA targets by MovingTargets, a highly adaptable prediction method.

BACKGROUND: MicroRNAs (miRNAs) mediate a form of translational regulation in animals. Hundreds of animal miRNAs have been identified, but only a few of their targets are known. Prediction of miRNA targets for translational regulation is challenging, since the interaction with the target mRNA usually occurs via incomplete and interrupted base pairing. Moreover, the rules that govern such interactions are incompletely defined. RESULTS: MovingTargets is a software program that allows a researcher to predict a set of miRNA targets that satisfy an adjustable set of biological constraints. We used MovingTargets to identify a high-likelihood set of 83 miRNA targets in Drosophila, all of which adhere to strict biological constraints. We tested and verified 3 of these predictions in cultured cells, including a target for the Drosophila let-7 homolog. In addition, we utilized the flexibility of MovingTargets by relaxing the biological constraints to identify and validate miRNAs targeting tramtrack, a gene also known to be subject to translational control dependent on the RNA binding protein Musashi. CONCLUSION: MovingTargets is a flexible tool for the accurate prediction of miRNA targets in Drosophila. MovingTargets can be used to conduct a genome-wide search of miRNA targets using all Drosophila miRNAs and potential targets, or it can be used to conduct a focused search for miRNAs targeting a specific gene. In addition, the values for a set of biological constraints used to define a miRNA target are adjustable, allowing the software to incorporate the rules used to characterize a miRNA target as these rules are experimentally determined and interpreted.

3' Untranslated Regions↗

PubMed2000

Towards 3D structures of G protein-coupled receptors: a multidisciplinary approach.

Current strategies in pharmaceutical research comprise two methodologically different but complementary approaches for lead finding purposes, namely the random screening of compound libraries and the structure-based effort, commonly termed rational drug design. The structure-based approach is aimed to exploit 3D structure data of the molecular components involved in the molecular recognition event that underlies the attempt to therapeutically modulate the biological function of a macromolecular target with proven pathophysiological relevance for a disease state. In this context, G protein-coupled receptors (GPCRs) constitute the most prominent family of validated drug targets within biomedical research, since approximately 60 % of approved drugs elicit their therapeutic effects by selectively addressing members of that target family. From a 3D structure point of view, these transmembrane signal transduction systems represent the most challenging task for structure determination, which is due to the heterogeneous and fine-balanced environment conditions that are necessary for structural and functional integrity of the receptor protein. This contribution will address the different concepts to derive structurally relevant information on the transmemebrane seven-helix protein (7TM) domain of GPCRs with special emphasis laid on the multidisciplinarity of the applied methodologies. The current status of electron-cryo-microscopy on 2D crystals and even high-resolution x-ray crystallography on 7TM proteins will be introduced highlighting the transferability of the emerging structural principles onto the GPCR superfamily. Special techniques from bioinformatics and homology-related molecular modeling in combination with tailor-made protein simulation methodologies complement the experimentally derived data, in that they facilitate the 3D structure generation and structure validation process. This contribution summarises the most recent results of GPCR structure studies with the aim to underline the impact of structure data not only for the purpose of rationalising structure-activity data on low-molecular weight antagonists within the context of a protein binding pocket, but also for a better understanding of e.g. mutagenesis experiments, thus qualifying GPCR structure models as valid communication platforms establishing a functional link between molecular biology, biophysics, bioinformatics and organic chemistry in a highly efficient manner.

Amino Acid Sequence↗

PubMed2005

Reawakening the cellular death program in neoplasia through the therapeutic blockade of IAP function.

Recent studies have shown that members of the inhibitor of apoptosis (IAP) protein family are highly expressed in several classes of cancer. The primary implication of these findings is that the elevated expression of IAPs is not coincidental but actually participates in oncogenesis by helping to allow the malignant cell to avoid apoptotic cell death. This concept, together with the discovery of several IAP-regulatory proteins that use a conserved mode of action, has stimulated a major effort by many research groups to devise IAP-targeting strategies as a means of developing novel antineoplastic drugs. In this Review, we consider the evidence both for and against the IAPs being valid therapeutic targets, and we describe the types of strategies being used to neutralize their functions.

Animals↗

PubMed2000

Prospects for gene therapy for heart failure.

Heart failure represents an enormous clinical challenge in need of effective therapeutic approaches. The possibility of gene therapy for heart failure merits consideration at this time because of improvements in vector technology; cardiac gene delivery; and, most importantly, our understanding of the molecular pathogenesis of heart failure. We will first review recent advances in cardiac gene delivery in animal models and then examine several targets being considered for therapeutic intervention. In this context, gene transfer provides not only a potential therapeutic modality but also an important tool to help validate specific targets. Several interventions, particularly those enhancing sarcoplasmic calcium transport, show promise in animal models of heart failure and in myopathic cardiomyocytes derived from patients. However, bridging the gap between these basic investigative studies and clinical gene therapy remains a formidable task. Early experiments in rodents will need to be extended to large-animal models with clinical-grade vectors and delivery systems to assess both efficacy and safety. On the basis of a foundation of rigorous science and a growing understanding of heart failure pathogenesis, there is reason for cautious optimism for the future.

Animals↗

PubMed2005

Ampicillin/penicillin-binding protein interactions as a model drug-target system to optimize affinity pull-down and mass spectrometric strategies for target and pathway identification.

The identification and validation of the targets of active compounds identified in cell-based assays is an important step in preclinical drug development. New analytical approaches that combine drug affinity pull-down assays with mass spectrometry (MS) could lead to the identification of new targets and druggable pathways. In this work, we investigate a drug-target system consisting of ampicillin- and penicillin-binding proteins (PBPs) to evaluate and compare different amino-reactive resins for the immobilization of the affinity compound and mass spectrometric methods to identify proteins from drug affinity pull-down assays. First, ampicillin was immobilized onto various amino-reactive resins, which were compared in the ampicillin-PBP model with respect to their nonspecific binding of proteins from an Escherichia coli membrane extract. Dynal M-270 magnetic beads were chosen to further study the system as a model for capturing and identifying the targets of ampicillin, PBPs that were specifically and covalently bound to the immobilized ampicillin. The PBPs were identified, after in situ digestion of proteins bound to ampicillin directly on the beads, by using either one-dimensional (1-D) or two-dimensional (2-D) liquid chromatography (LC) separation techniques followed by tandem mass spectrometry (MS/MS) analysis. Alternatively, an elution with N-lauroylsarcosine (sarcosyl) from the ampicillin beads followed by in situ digestion and 2-D LC-MS/MS analysis identified proteins potentially interacting noncovalently with the PBPs or the ampicillin. The in situ approach required only little time, resources, and sample for the analysis. The combination of drug affinity pull-down assays with in situ digestion and 2-D LC-MS/MS analysis is a useful tool in obtaining complex information about a primary drug target as well as its protein interactors.

Ampicillin↗

PubMed2026

Prevalence of Claudin 18.2 Expression in Gastric and Gastroesophageal Junction Adenocarcinoma: A Systematic Review and Meta-Analysis.

BACKGROUND: Claudin 18 isoform 2 (CLDN18.2) has emerged as a clinically validated therapeutic target in gastric and gastroesophageal junction (GEJ) adenocarcinoma following the regulatory approval of zolbetuximab in combination with first-line chemotherapy. Accurate prevalence data at the clinically validated immunohistochemical threshold are essential for patient selection, healthcare resource planning, and treatment strategy. Reported prevalence estimates vary widely across studies due to differences in populations, methodologies, and immunohistochemical protocols. This systematic review and meta-analysis aimed to generate a robust pooled prevalence estimate of CLDN18.2 expression at the threshold used in pivotal phase III trials. METHODS: PubMed, Embase, and the Cochrane Library were searched from database inception through March 12th, 2026. Studies reporting CLDN18.2 expression in gastric or gastroesophageal junction adenocarcinoma using the ≥ 75% moderate-to-strong membranous staining threshold were included. Prevalence proportions were pooled using a random-effects model with logit transformation and restricted maximum-likelihood estimation of between-study variance. Heterogeneity was assessed using the I² statistic and Cochran's Q test, and a 95% prediction interval was calculated. Pre-specified subgroup analyses assessed antibody clone and geographic region, with additional exploratory analyses according to disease setting and specimen type. Sensitivity analyses were performed to assess the robustness of the pooled estimate. RESULTS: Twenty-two predominantly retrospective cohort studies comprising 12,173 patients were included. The pooled prevalence of CLDN18.2 positivity using a random-effects model was 33.99% (95% CI: 30.13%-38.07%; 95% prediction interval: approximately 18%-55%), with high between-study heterogeneity (I² = 92.4%). Subgroup analysis by antibody clone showed no statistically significant difference between studies using the 43-14 A clone (32.79%, 95% CI: 28.86%-36.97%) and those using other reported antibody clones (41.74%, 95% CI: 26.76%-58.42%; p = 0.281). One study with an unreported antibody clone was excluded from this subgroup analysis. Geographic subgroup analysis excluding the multinational Shitara et al. cohort demonstrated a non-significant trend toward higher prevalence in non-Asian populations (37.85%, 95% CI: 31.59%-44.54%) compared with Asian populations (32.10%, 95% CI: 27.28%-37.34%; p = 0.169). All three sensitivity analyses confirmed robustness of the pooled estimate. No significant evidence of publication bias was detected (Egger's test p = 0.56). CONCLUSIONS: Approximately one-third of patients with gastric and GEJ adenocarcinoma express CLDN18.2 at the clinically validated ≥ 75% threshold. However, because the included studies encompassed heterogeneous disease settings and were predominantly HER2-unselected, the pooled estimate should not be interpreted directly as the proportion of patients eligible for zolbetuximab. The estimate was robust across sensitivity analyses and provides an evidence base for understanding CLDN18.2 prevalence and biomarker-testing requirements. Standardisation of immunohistochemical assessment methods is warranted to reduce between-study heterogeneity in future research.

Humans↗

PubMed2006

ViTa: prediction of host microRNAs targets on viruses.

MicroRNAs (miRNAs) are involved in various biological processes by suppressing gene expression. A recent work has indicated that host miRNAs are also capable of regulating viral gene expression by targeting the virus genomes. To investigate regulatory relationships between host miRNAs and related viruses, we present a novel database, namely ViTa, to curate the known virus miRNA genes and the known/putative target sites of human, mice, rat and chicken miRNAs. Known miRNAs are obtained from miRBase. Virus data are collected and referred from ICTVdB, VBRC and VirGen. Experimentally validated miRNA targets on viruses were derived from literatures. Then, miRanda and TargetScan are utilized to predict miRNA targets within virus genomes. ViTa also provides the virus annotations, virus-infected tissues and tissue specificity of host miRNAs. This work also facilitates the comparisons between subtypes of viruses, such as influenza viruses, human liver viruses and the conserved regions between viruses. Both textual and graphical web interfaces are provided to facilitate the data retrieves in the ViTa database. The database is now freely available at http://vita.mbc.nctu.edu.tw/.

Animals↗

PubMed1999

Comparison of three methods to assess therapeutic quality control of treatment with vitamin K antagonists.

During treatment with vitamin K antagonists, International Normalized Ratios (INR) are determined periodically to maintain a therapeutic level of anticoagulation. We evaluated two existing methods for therapeutic quality control (linear interpolation and equidivision), with regard to their validity and reproducibility. In addition, we proposed and evaluated a (hybrid) method that takes into account potential effects of dosage modifications when INRs are far out of the target range. Validity was assessed by deleting intermediary INR results and estimating this INR based on the two surrounding INRs with each of the three methods. The estimated INRs were then compared with the observed INR. Reproducibility of time spent in an INR range was evaluated for each of the three methods by deleting at random increasing proportions of INRs and comparing these estimates with the situation without deletions. We found that estimates of time spent in INR categories obtained with equidivision were most reproducible, but least valid. The hybrid method showed slightly higher validity and reproducibility in comparison with linear interpolation. Since these differences were small, linear interpolation is preferable to the hybrid method, since the calculations involved are easier.

Fibrinolytic Agents↗

PubMed2003

Conclusion. Lessons from the novel D2 dopamine receptor, beta2-adrenoceptor agonist, Viozan: chronic obstructive pulmonary disease and drug development implications.

The development of novel drugs for the treatment of chronic obstructive pulmonary disease (COPD) poses significant challenges. The mechanisms through which the chronic symptoms of COPD arise are poorly understood, making identification of potential therapeutic targets and in vivo evaluation of potential therapies extremely difficult. Despite these challenges, a unique approach of combined D2 dopamine, beta2-adrenoceptor agonism was identified as a valid potential target for the treatment of key COPD symptoms, the therapeutic potential of which was investigated in a series of preclinical evaluations. Subsequent clinical assessment has amassed a wealth of data from over 4000 patients, providing valuable insights into COPD, clinical trial design and the value of patient self-assessment tools.

Adrenergic beta-2 Receptor Agonists↗

PubMed2003

Use of RNA interference to validate Brk as a novel therapeutic target in breast cancer: Brk promotes breast carcinoma cell proliferation.

Brk (PTK6) is a nonreceptor protein tyrosine kinase, which is expressed in over 60% of breast carcinoma tissue samples and breast tumour cell lines, but not normal mammary tissue or benign lesions. Since experimental Brk expression in nontransformed mammary epithelial cells enhances their mitogenic response to epidermal growth factor, it was important to determine the role Brk plays in the proliferation of breast carcinoma cells and validate it as a therapeutic target. We have used RNA interference to efficiently and specifically downregulate Brk protein levels in breast carcinoma cells, and determined that this results in a significant suppression of their proliferation. Additionally, through the expression of a kinase-inactive mutant, we have determined that Brk can mediate promotion of proliferation via a kinase-independent mechanism, potentially functioning as an 'adapter'. These data identify Brk as a novel target for antiproliferative therapy in the majority of breast cancers, and illustrate the power of RNA interference for rapidly validating candidate therapeutic targets.

Breast Neoplasms↗

PubMed2001

Novel agents: clinical trial design.

The development of molecularly targeted anticancer agents has become an attractive therapeutic strategy. However, evaluation of these novel drugs poses special challenges to laboratory and clinical scientists. These include the creation of appropriate models to assess the effect of the agent on its putative target, the validation of new surrogate endpoints, and the use of effective clinical trial designs. An overview of the difficulties in using a new paradigm of drug development for these target-directed compounds is presented and optimal clinical research methodology to determine their efficacy described.

Antineoplastic Agents↗