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Results for “target validation”

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PubMed2001

Real-time molecular and cellular analysis: the new frontier of drug discovery.

The pharmaceutical industry is currently facing the challenge of maintaining increased efficiency and productivity while contending with a deluge of genomic and high-throughput screening data. To ease the bottlenecks at target validation and lead optimization, the industry must look to the living cell, the ultimate target of all drugs, as a source of new biological knowledge. This new 'cell-centric' perspective must integrate reagents that report on the state of molecular processes within the cell, automated detection and analysis of these processes, and cellular knowledge, building into a single platform.

Cells↗

PubMed2006

Pharmacological targeting of adipocytes/fat metabolism for treatment of obesity and diabetes.

Obesity is now recognized as a rapidly increasing worldwide threat to health, largely as a result of causing diabetes. Thus, considerable efforts are underway in the pharmaceutical industry to find drugs to treat this condition. Target validation in various academic and industrial laboratories has revealed a number of potential molecular targets in fat cells or adipocytes. By definition, obesity is too much fat, and we here review efforts to treat obesity and, by proxy, diabetes by modulating the metabolic state of adipocytes.

Adipocytes↗

PubMed2005

Recognition of chromosomal DNA in human cells by peptide nucleic acids and small duplex RNAs.

Inhibition of translation by duplex RNA (siRNA) complementary to mRNA is a powerful approach to silencing genes in mammalian cells and RNA interference (RNAi) is an important natural biological mechanism for controlling gene expression. Anti-mRNA duplexes are widely used for laboratory studies, target validation, and therapeutic development. Endogenously expressed duplex RNAs (microRNAs, miRNAs) have been shown to target mRNA and be natural regulators of expression. Recently, we have shown that peptide nucleic acids (PNAs) or duplex antigene RNAs (agRNAs) that target DNA sequences can also inhibit gene transcription. These findings extend gene silencing to targets within chromosomal DNA.

Alternative Splicing↗

PubMed2005

Non-insulin dependent diabetes mellitus: present therapies and new drug targets.

Type 2 Diabetes Mellitus (DM) or Non-Insulin Dependent Diabetes Mellitus (NIDDM) accounts for 90-95% of all diabetes cases and has become a major health concern over the years. This disease has assumed frightening proportions due to unhealthy food habits and sedentary life style. About a decade ago, due to the absence of defined molecular targets or an understanding of disease pathophysiology, treatment of this disease was mostly focused on insulin secretion or administration of external insulin. During the past decade however, advent of genomics and proteomics has helped in understanding the molecular alteration characteristics of NIDDM. Untreated type 2 diabetes leads to several complications such as hyperlipidemia, hypertension and atherosclerosis--collectively known as Syndrome X. Though United Kingdom Prospective Diabetes Study (UKPDS) showed that normalization of hyperglycemia could prevent majority of diabetes complications, the available treatment regime does not adequately normalize the blood glucose level in type 2 diabetic patients. Currently, four distinct classes of oral hypoglycemic agents are available, some of which can act as lipid lowering agents as well. The efficacy and side effect profiles of these drugs are still to be optimized, so there is an unmet need for better candidates. Several new targets as well as better drugs for old targets are under investigation across the world. Availability of such drugs, based on the validated targets, may lead to a new therapeutic paradigm for the prevention of diabetes as well as complications arising out of it. The current review will deal with existing oral therapies for type 2 diabetes as well as the emerging therapeutic targets.

AMP-Activated Protein Kinases↗

PubMed2001

Prevention of human prostate tumor metastasis in athymic mice by antisense targeting of human angiogenin.

PURPOSE: Angiogenin is a potent positive mediator of neovascularization, a process required for both primary tumor growth and metastasis. In the present study, the effect of a fully phosphorothioated antisense oligodeoxynucleotide, designated JF2S, targeting the AUG translation initiation codon region of human angiogenin, on human prostate tumor development and metastasis in athymic mice was examined. EXPERIMENTAL DESIGN: JF2S was evaluated for its capacity to affect in vitro synthesis of angiogenin and subsequent tumorigenicity of transiently transfected prostate tumor cells in mice. In vivo treatment experiments were then conducted in which JF2S was used to prevent formation of tumors in an ectopic model and metastasis in an orthotopic model. RESULTS: Transient transfection of tumor cells with JF2S inhibited both angiogenin gene expression in vitro and tumorigenicity of these transfected cells in athymic mice. In therapy experiments, local treatment with JF2S completely protected mice from developing prostate tumors after s.c. injection of PC-3 human prostate tumor cells (P < 0.0001, survivor analysis). Most importantly, systemic prophylactic administration of JF2S prevented, in 47% of mice, formation of regional iliac lymph node micrometastases arising from primary tumors growing in the more natural orthotopic prostate setting (P = 0.0003, Fisher's exact test). Furthermore, total protection from regional metastasis occurred in those mice in which JF2S treatment successfully diminished human angiogenin expression in vivo. Tumor-associated angiogenesis was also impaired by JF2S treatment. When therapy was delayed until all of the mice harbored primary tumors in the prostate, the incidence of regional metastasis was still significantly decreased (P < 0.005, survivor analysis). CONCLUSIONS: These findings demonstrate that human prostate cancer establishment and spread in athymic mice is extremely susceptible to targeted disruption of tumor-derived human angiogenin gene expression. Therefore, angiogenin is a valid target against which to devise preventative strategies for prostate cancer metastasis.

Animals↗

PubMed2005

Discovery and validation of drug targets for tumour angiogenesis.

The formation of blood vessels is a key process in the progression of solid tumours, providing the means for tumour growth and metastasis. A number of drugs are currently being developed to exploit inhibition of angiogenesis in the therapy of cancer. An even greater number of genes that are regulated in models of in vitro angiogenesis have been identified. These genes present potential drug targets for the development of novel, more efficient, drugs that will enable the judicious design of drug cocktails that may be able to account for the many different cancer pathologies and their drug resistance properties. Dealing with the validation of hundreds of potential angiogenesis drug targets requires the utilisation of experimental technology platforms that enable concomitant and dynamic target selection filtering and validation. Such platforms should act as a funnel-like medium-to-low throughput processes that enable the sequential short-listing of hundreds of candidates culminating in the selection of only a small number of well-validated targets that are manageable by drug screening regimes.

Angiogenesis Inhibitors↗

PubMed2025

From genetic causality to druggable targets: A multiomics framework identifies ZSCAN16 in gout pathogenesis.

ObjectiveGout is a prevalent form of inflammatory arthritis in which many patients respond suboptimally to current therapies. Drug development is hampered by a lack of genetically validated targets, leading to high clinical trial attrition. This study aimed to systematically identify and prioritize novel, druggable targets for gout via a multilayered genetic and functional genomics approach.MethodsWe performed two-sample Mendelian randomization (MR) using cis-expression quantitative trait locus (cis-eQTL) data and dual independent gout genome-wide association study (GWAS) cohorts (openGWAS and FinnGen). The candidate genes were subjected to a rigorous validation pipeline including Bayesian colocalization, phenome-wide association studies (PheWASs) to assess pleiotropy and on-target safety, and single-cell RNA sequencing (scRNA-seq) to delineate the cellular context. Molecular docking was used to evaluate the structural druggability of prioritized targets.ResultsMR analysis revealed 15 genes causally associated with gout. Colocalization analysis (PPH4 > 0.8) prioritized two targets: ZSCAN16 (risk-increasing, OR = 1.04, 95% CI [1.02-1.06]) and TRIM10 (protective, OR = 0.96, 95% CI [0.94-0.98]). Crucially, PheWAS revealed that ZSCAN16 is highly specific to gout, whereas TRIM10 exhibited extensive pleiotropy with hematological and cardiometabolic traits, indicating significant safety risks. Single-cell analysis provided orthogonal validation, demonstrating flare-specific upregulation of ZSCAN16 in cytotoxic T/NK cells. Molecular docking confirmed ZSCAN16 as a structurally druggable target, showing high-affinity binding with known compounds (e.g. digoxin, binding energy = -9.6 kcal/mol).ConclusionsOur study identifies ZSCAN16 as a high-potential, druggable therapeutic target for gout, highlighting its genetic influence on specific immune cell activities during acute flares. Conversely, TRIM10 was deprioritized owing to substantial pleiotropic liabilities and poor chemical tractability. These findings suggest that ZSCAN16 could play a crucial role in the pathogenesis of gout and may provide a valuable lead for future drug discovery efforts.

Humans↗

PubMed1999

The role of the E6-p53 interaction in the molecular pathogenesis of HPV.

Human papillomaviruses (HPVs) are associated with a number of clinical conditions, of which the most serious is cervical carcinoma. The E6 protein of the oncogenic, mucosal-specific HPV types has been shown to complex with p53 and, as a result, target it for rapid proteasome-mediated degradation. As a consequence, p53's growth-arrest and apoptosis-inducing activities are abrogated. Since p53 is frequently wild type in cervical cancers, unlike other cancers in which it is often mutated, the notion has arisen that E6's activity with respect to p53 is equivalent to an inactivating mutation of p53. In addition, several studies have shown that the pathways both upstream and downstream of p53 are intact in cervical cancers; this suggests the potential importance of the E6 - p53 interaction for therapeutic intervention. However, like all viral oncoproteins, E6 is a multifunctional protein and a plethora of other cellular targets has been identified. Indeed, E6's interactions with some of these additional targets appear to be equally important in the pathogenesis of HPV, and may also represent valid targets for therapeutic intervention.

Alternative Splicing↗

PubMed2004

Haplotype structure and genotype-phenotype correlations of the sulfonylurea receptor and the islet ATP-sensitive potassium channel gene region.

The genes for the sulfonylurea receptor (SUR1; encoded by ABCC8) and its associated islet ATP-sensitive potassium channel (Kir6.2; encoded by KCNJ11) are adjacent to one another on human chromosome 11. Multiple studies have reported association of the E23K variant of Kir6.2 with risk of type 2 diabetes. Whether and how E23K itself-or other variant(s) in either of these two closely linked genes-influences type 2 diabetes remains to be fully determined. To better understand genotype-phenotype correlation at this important candidate gene locus, we 1) characterized haplotype structures across the gene region by typing 77 working, high-frequency markers spanning 207 kb and both genes; 2) performed association studies of E23K and nearby markers in >3,400 patients (type 2 diabetes and control) not previously reported in the literature; and 3) analyzed the resulting data for measures of insulin secretion. These data independently replicate the association of E23K with type 2 diabetes with an odds ratio (OR) in the new data of 1.17 (P = 0.003) as compared with an OR of 1.14 provided by meta-analysis of previously published, nonoverlapping data (P = 0.0002). We find that the E23K variant in Kir6.2 demonstrates very strong allelic association with a coding variant (A1369S) in the neighboring SUR1 gene (r(2) > 0.9) across a range of population samples, making it difficult to distinguish which gene and polymorphism in this region are most likely responsible for the reported association. We show that E23K is also associated with decreased insulin secretion in glucose-tolerant control subjects, supporting a mechanism whereby beta-cell dysfunction contributes to the common form of type 2 diabetes. Like peroxisome proliferator-activated receptor gamma, the SUR1/Kir6.2 gene region both contributes to the inherited risk of type 2 diabetes and encodes proteins that are targets for hypoglycemic medications, providing an intriguing link between the underlying mechanism of disease and validated targets for pharmacological treatment.

ATP-Binding Cassette Transporters↗

PubMed2003

Inhibitors of sialyltransferases: potential roles in tumor growth and metastasis.

For over thirty years it has been evident that there is altered glycosyltransferase activity in neoplastic tissue when compared to healthy tissue. It has also long been speculated that disruption of the neoplastic expression of sialic acid on cellular glycoconjugates, is a valid target in anti-metastatic therapeutic development. Over the years attempts have been made to synthesize inhibitors of sialyltransferases in a effort to assist in the validation or dissolution of these enzymes as potential therapeutic targets.

Enzyme Inhibitors↗

PubMed2003

The crystal structure of Trypanosoma brucei enolase: visualisation of the inhibitory metal binding site III and potential as target for selective, irreversible inhibition.

The glycolytic enzymes of the trypanosomatids, that cause a variety of medically and agriculturally important diseases, are validated targets for drug design. Design of species-specific inhibitors is facilitated by the availability of structural data. Irreversible inhibitors, that bound covalently to the parasite enzyme alone, would be potentially particularly effective. Here we determine the crystal structure of enolase from Trypanosoma brucei and show that two cysteine residues, located in a water-filled cavity near the active-site, are modified by iodoacetamide leading to loss of catalytic activity. Since these residues are specific to the Trypanosomatidae lineage, this finding opens the way for the development of parasite-specific, irreversibly binding enolase inhibitors. In the present structure, the catalytic site is partially occupied by sulphate and two zinc ions. Surprisingly, one of these zinc ions illustrates the existence of a novel enolase-binding site for divalent metals. Evidence suggests that this is the first direct visualization of the elusive inhibitory metal site, whose existence has hitherto only been inferred from kinetic data.

Amino Acid Sequence↗

PubMed2002

Selecting targets for therapeutic validation through differential protein expression using chromatography-mass spectrometry.

The identification of potential targets for therapeutic intervention can be accomplished on a systematic basis by a variety of techniques that include quantitative analysis of gene-specific mRNA levels and expressed proteins in normal and diseased cells. Differences in the expression levels of nucleic acid and protein gene products could suggest protein drug targets that are directly causative of disease, or reveal biochemical pathways that could be modulated by therapeutic molecules. Any effort based on mRNA or protein expression level comparisons could be confounded by a number of factors: level in steady-state may not be correlated with actual encoded protein levels; differentially expressed protein levels might be a result of disease process, and not causative of the process, and therapeutic intervention based on such a difference will be unproductive and the differential expression of mRNA or protein may be the result of biological variation unrelated to the disease process under study. In order to address these possibly confounding factors, it is necessary to validate potential targets by establishing their firm association with disease, and their minimal distribution in non-diseased tissues of any type. This requirement suggests that emphasis on true and reproducible quantitation of protein expression levels in a variety of samples will be an effective and highly efficient method of generating drug targets with a high degree of utility. To achieve this aim, we have established an industrial-scale proteomics-based discovery platform consisting of cell biology, protein chemistry, and mass spectrometry technical groups together with bioinformatics groups. The analytical method used for quantitation employs isotope labeling for differential analysis (ICATTM, Applied Biosystems, Inc.). With this technique, tryptic peptides are generated from labeled proteins that have been specifically captured from various subcellular locations or protein families. The resulting peptides are identified and quantified by mass spectrometry. To evaluate this approach on a large-scale, we have applied it to a study of continuous cell lines derived from human pancreatic adenocarcinomas. We have been able to establish processes for target discovery for small molecule drug targets as well as therapeutic antibody target identification for cell surface proteins. In addition, we have developed a process for identification of serum markers of this disease based upon standardized fractionation procedures. The results of these analyses will be presented together with the some of the issues from both the wet and dry (computational) lab that need to be addressed in such an undertaking.

Biomarkers, Tumor↗

PubMed1999

Cysteine protease inhibitors as chemotherapy for parasitic infections.

Analysis of the evolution, localization and biologic function of papain family cysteine proteases in metazoan and protozoan parasites has provided important and often surprising insights into the biochemistry and cellular function of this diverse enzyme family. Furthermore, the relative lack of redundancy of cysteine proteases in parasites compared to their mammalian hosts makes them attractive targets for the development of new antiparasitic chemotherapy. The treatment of experimental models of parasitic diseases with cysteine protease inhibitors has provided an important 'proof of concept' for the use of cysteine protease inhibitors in vivo. Evidence has now accumulated that cysteine protease inhibitors can selectively arrest replication of a microbial pathogen without untoward toxicity to the host. Furthermore, this can be achieved with reasonable dosing schedules and oral administration of the drug. Initial studies have confirmed the efficacy of cysteine protease inhibitors in treatment of Trypanosoma cruzi, Plasmodium falciparum and Leishmania major. Work on Trypanosoma brucei, the agent of African trypanosomiasis, is preliminary but also promising. Target validation studies have shown that biotinylated or radiolabeled irreversible inhibitors specifically bind to the cysteine protease targets thought to represent the major activity within the parasite. In the case of T. cruzi, the effect of inhibitors appears to be predominantly in blocking protease processing. Transfection studies using variant constructs have supported this model. Finally, the generation of null mutants for the multiple protease genes in Leishmania mexicana has provided the first genetic support for the key role of this enzyme family in parasite virulence. Safety studies in rodents and analysis of uptake of inhibitors by parasites and host cells suggest that the selectivity of inhibitors for the parasite targets may reside in the lack of redundancy of parasite proteases, the higher concentration of host proteases in intracellular compartments, and differential uptake of inhibitors by parasites. Attempts to elicit resistance to cysteine protease inhibitors in parasite cultures suggest that mechanisms of induced resistance are independent of resistance to the traditional antiparasitic agents. This suggests that cysteine protease inhibitors may provide an alternative to traditional therapy in drug-resistant organisms.

Animals↗

PubMed2003

Current targets for anticancer drug discovery.

The call for the discovery of less toxic, more selective, and more effective agents to treat cancer has become more urgent. Inhibition of angiogenesis continues to be one of the main streams in the current cancer drug discovery activity. Insights into tumor angiogenesis biology have led to the identification of a number of molecules, which are important for the progression of these processes. Of particular interest is a group of growth factors including fibroblast growth factor, platelet-derived growth factor, and vascular endothelial growth factor. These growth factors and their corresponding receptor tyrosine kinases have become important targets for inhibition of the proliferation of endothelial cells, the main component of blood vessels. The validated targets for inhibition of angiogenesis also include a family of matrix metalloproteinases and cell adhesion molecules. In the closely related area, protein kinases have emerged as one of the most important targets for drug discovery. Besides growth factor receptor tyrosine kinases, numerous other protein kinases implicated in malignancies have been identified including non-receptor kinases such as Bcl-Abl and Src kinases. In addition, the cell cycle regulators (cyclin-dependent kinases, p21 gene) and apoptosis modulators (Bcl-2 oncoprotein, p53 tumor suppressor gene, survivin protein, etc) have also attracted renewed interest as potential targets for anticancer drug discovery. Other molecular targets include protein farnesyltransferase (FTase), histone deacetylase (HDAC), and telomerase, which have essential roles in cellular signal transduction pathways (FTase, HDAC) and cell life-span (telomerase). This review presents a comprehensive summary and discussion on the most important targets currently attracting a great deal of interest in contemporary anticancer drug design and discovery. Recent advances complementing these targets are also highlighted.

Animals↗

PubMed2004

Affinity-based screening techniques for enhancing lead discovery.

Contemporary, rational small-molecule lead discovery methods, comprising target identification, assay development, high-throughput screening (HTS), hit characterization and medicinal chemistry optimization, dominate early-stage drug discovery strategies in many pharmaceutical companies. There is a growing disparity between the increasing cost of funding these methods and the decreasing number of new drugs reaching the market. New strategies must be adopted to reverse this trend. The use of genomics- and proteomics-based target discovery efforts can aid the process by dramatically increasing the number of novel, more highly validated targets entering the discovery process, but HTS must meet this increased demand with faster, cheaper technologies. Although activity-based screening strategies are typically efficient, allowing one scientist to interrogate tens of thousands of compounds per day, affinity-based screening strategies can allow much greater efficiency in the overall process. Affinity-based methods can play a role in both facilitating the screening of a greater number of targets and in efficiently characterizing the primary hits discovered.

Drug Design↗

PubMed1994

Electrophysiological correlates to cued attentional shifts in the visual and auditory modalities.

Reaction time (RT) is usually speeded and slowed to correctly and incorrectly cued target stimuli, respectively, in experiments on attention shift (Posner, 1988). When targets occur in a spatial location different from the cue, shifting attention from the cued location to the target location involves interrupt of ongoing activity, move attention to the new location, and reengage attention. The present study investigated whether the cognitive operations involved in cued vs uncued attentional shifts also were detectable in the event-related potentials (ERPs). Two experiments are reported, one with visual and one with auditory stimuli. In the visual modality, the cue and target were a lit-up square and an asterisk, respectively, shown on a computer screen. In the auditory modality, the cue was a tone in either the left or right ear, followed by the target noise in either the same or the opposite ear. The results from the visual experiment showed shorter RTs to correctly cued (Valid) targets and longer RTs to incorrectly cued (Invalid) targets. Invalidly cued targets elicited enhanced P3 amplitudes, with a frontocentral distribution. Reduced P3 amplitudes were observed on Valid trials, largest reduction for parietooccipital leads. The auditory experiment showed P3 enhancement frontally and reduced amplitudes at temporal and parietal leads. No RT differences were seen to Valid and Invalid trials. The existence of an anterior attention system involved in interrupt and disengage of attention, and a posterior attention facilitation system related to cue presentation is discussed.

Adult↗

PubMed2006

Targeting transcription factors for cancer gene therapy.

A high proportion of oncogenes and tumor suppressor genes encode transcription factors. Deregulated expression or activation and inactivation of transcription factors as well as mutations and translocations play critical roles in tumorigenesis. Furthermore, the majority of oncogenic signaling pathways converge on sets of transcription factors that ultimately control gene expression patterns resulting in tumor formation and progression as well as metastasis. Under normal physiological conditions whole sets of genes with similar functions are regulated by highly specific, tightly regulated upstream transcriptional regulators, whereas in cancer aberrant activation of these transcription factors leads to deregulated expression of multiple gene sets associated with tumor development and progression. The activity of these transcription factors can be modulated by multiple mechanisms including posttranslational modifications. Activation or inactivation of transcription factors promote cancer development, cell survival and proliferation and induce tumor angiogenesis. Since many of these transcription factors are inactive under normal physiological conditions and their expression and activities are tightly regulated, these transcription factors represent highly desirable and logical points of therapeutical interference in cancer development and progression. Three major families of transcription factors have emerged as important players in human cancer and are validated targets in drug discovery for cancer therapy: 1) the NF-kappaB and AP-1 families of transcription factors, 2) the STAT family members and 3) the steroids receptors. This review aims to elucidate the divergent molecular mechanisms involved in the deregulated activation of transcription factor signaling in malignant transformation, although additional transcription factor families such as the Ets factors, ATF family members, basic helix-loop-helix transcription factors etc. are additional critical transcriptional regulators in human cancer. We explore new approaches to specifically inhibit these transcription factors in cancer in order to validate them as a drug targets. Efforts to develop novel viral vectors for therapeutic applications are also discussed.

Animals↗

PubMed2026

Mitochondrial Function-Related Genes in Sleep Disorders: A Multi-Omics Mendelian Randomization Study.

Mitochondrial dysfunction is linked to sleep disorders in previous report, but the potential roles of specific genes remain unclear. This study aimed to dissect different subtype-specific genetic associations and their underlying mechanisms. A multi-omics Summary-data-based Mendelian Randomization (SMR) approach was performed to identify potential causal links between mitochondrial function-related genes and sleep disorders. We integrated GWAS data from FinnGen database (the discovery set), independent GWAS datasets (covering different sleep-disorder subtypes and used for validation), and cis-QTLs (including mQTLs, eQTLs, and pQTLs) to perform systematic exploration. Specially, we performed targeted validation of tissue-specific effects, leveraging gene expression data from disease-relevant brain regions within the GTEx database. Our SMR analysis identified mitochondrial function-related genes potentially modulating sleep disorders across biological layers, initially identifying 102 genes at the methylation level, 48 at the gene expression level, and 6 at the protein abundance level. Integrative analysis subsequently prioritized DCXR and ACADVL and revealed their distinct, subtype-specific associations. DCXR exhibited a protective role in sleep apnea while ACADVL showed a paradoxical risk conferring role in daytime sleepiness. In addition, the analysis identified an epigenetic regulatory mechanism for DCXR in which its expression and protein levels are modulated by DNA methylation. Finally, validation in brain-hypothalamus tissue confirmed DCXR as a significant potential protective factor (OR = 0.929, 95% CI: 0.887-0.973, P_HEIDI = 0.999, FDR = 0.2449). Our findings implicate key mitochondrial genes, particularly DCXR and ACADVL, in the pathophysiology of specific sleep disorder subtypes, highlighting potential avenues for precision medicine. Clinical trial number: Not applicable.

Humans↗