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PubMed2002

Full-speed mammalian genetics: in vivo target validation in the drug discovery process.

The completion of the Human Genome Project has signaled the beginning of the post-genome era, with a corresponding shift in focus from the sequencing and identification of genes to the exploration of gene function. A rate-limiting step in deriving value from this gene sequence information is determining the potential pharmaceutical applications of genes and their encoded proteins. This validation step is crucial for focusing efforts and resources on only the most promising targets. Strategies using reverse mouse genetics provide excellent methods for validating potential targets and therapeutic proteins in vivo in a mammalian model system.

Animals↗
PubMed2004

Target validation of cytochrome P450 CYP1B1 in prostate carcinoma with protein expression in associated hyperplastic and premalignant tissue.

PURPOSE: To investigate the localization and distribution of cytochrome P450 CYP1B1 protein expression in patients diagnosed with prostate carcinoma compared to those with bladder carcinoma. To validate CYP1B1 as a molecular target for the development of selective cancer therapeutics for use in combination with radiation. METHODS AND MATERIALS: Prostatectomy specimens (n = 33) of moderate Gleason grade (3 + 3 and 3 + 4) were analyzed immunohistochemically for CYP1B1 protein expression using a specific monoclonal antibody for the enzyme. The intensity of CYP1B1 staining was assessed both semiquantitatively using visual scoring and quantitatively by spectral imaging microscopy using reference spectra and compared with bladder carcinoma (n = 22). RESULTS: CYP1B1 protein expression was present in 75% of prostate carcinomas (n = 27) compared to 100% of bladder carcinomas (n = 22). In both cases, CYP1B1 protein expression was heterogeneous and localized in the cytoplasm of the tumor cells but absent from the surrounding stromal tissue. CYP1B1 was also detected in premalignant prostatic intraepithelial neoplasia (n = 2, 100%), as well as noncancerous tissues, including benign prostatic hyperplasia (n = 27, 82%), metaplastic prostatic urothelium (n = 8, 100%), and hyperplastic prostatic urothelium (n = 14, 100%). Higher CYP1B1 protein expression in bladder vs. prostate carcinoma was confirmed by their corresponding average normalized absorbances (+/- standard deviation), measured as 1.40 +/- 0.44 and 0.55 +/- 0.09, respectively. Overall CYP1B1 staining intensity in prostate carcinoma was similar to that in prostatic intraepithelial neoplasia, benign prostatic hyperplasia, and hyper-/metaplastic urothelial tissue. No CYP1B1 was detected in normal prostate tissue. CONCLUSIONS: CYP1B1 is overexpressed in prostate carcinoma at a high frequency and is also detectable in the associated premalignant and hyperplastic tissue, implicating a possible link with malignant progression and CYP1B1 as a suitable target for therapy. Spectral imaging microscopy has highlighted differences in CYP1B1 protein expression between different cancers.

Aged↗
PubMed2004

Antisense and RNA interference approaches to target validation in pain research.

In recent years numerous potential new targets for the development of novel drugs to treat chronic pain have been identified. Antisense strategies provide a straightforward approach to validate and further analyze their function. Furthermore, they offer the possibility of investigating a single member of a closely related family of proteins that cannot be easily targeted using small-molecule pharmacological tools. The recent discovery that short double-stranded RNA molecules can be employed to induce RNA interference in mammalian systems has opened exciting new roads for functional genomics. Gene silencing by small interfering RNAs has been demonstrated in neurons, and several targets involved in pain perception have been addressed. Furthermore, promising in vivo results have recently been obtained with small interfering RNAs.

Animals↗
PubMed2003

Exploring genetic influences on cognition: emerging strategies for target validation and treatment optimization.

Genomic research has produced an abundance of new candidate targets that remain to be validated as potential treatments for neuropsychiatric disorders. Functional neuroimaging, meanwhile, has provided detailed new insights into the neural circuits involved in emotional and cognitive control. At the growing interface between these independent lines of progress, new efforts are underway to unify our understanding of regional brain function with that of genetic and biochemical influences on behavior. Such a unified understanding of the mechanisms involved in cognitive and emotional control may open up new avenues for therapeutic intervention at the pharmacological and behavioral levels. In line with this, a new initiative sponsored by the National Institutes of Mental Health (NIMH) aims to bridge gaps between clinical diagnostics and the molecular processes that influence susceptibility to psychiatric disorders. A major goal of this initiative is to identify the neural and neurochemical substrates of basic cognitive processes that are disrupted in psychiatric disorders and to examine the influence of genetic factors at the cognitive level. This review describes some well-known findings that are at the forefront of this interface. The progress already made indicates that the goals of the new initiative are well founded and achievable.

Animals↗
PubMed2001

Functional genomics and target validation approaches using antisense oligonucleotide technology.

The recent increase in the amount and rate of accumulation of genomic information has created new challenges for the pharmaceutical industry. These include how best to rapidly and efficiently identify key genes responsible for complex disease phenotypes and how to use this information to develop new and specific classes of drugs. Antisense technology offers a powerful approach to identify novel cellular networks and signaling "cassettes" and provides a method to validate genes in vivo as attractive drug targets.

Drug Design↗
PubMed2006

Screening the receptorome: an efficient approach for drug discovery and target validation.

The receptorome, comprising at least 5% of the human genome, encodes receptors that mediate the physiological, pathological and therapeutic responses to a vast number of exogenous and endogenous ligands. Not surprisingly, the majority of approved medications target members of the receptorome. Several in silico and physical screening approaches have been devised to mine the receptorome efficiently for the discovery and validation of molecular targets for therapeutic drug discovery. Receptorome screening has also been used to discover, and thereby avoid, the molecular targets responsible for serious and unforeseen drug side effects.

Animals↗
PubMed2003

siRNA-mediated antitumorigenesis for drug target validation and therapeutics.

Application of siRNA to knockdown a specific gene requires target mRNA accessibility, effective intracellular delivery of siRNA into target cells and potent siRNA inhibition of target mRNA. Use of siRNA as a tool is advancing in almost every field of biomedical research, but some of the most dynamic and exciting applications of siRNA are in cancer research. This review summarizes the results obtained with siRNA in cancer, in particular functional validation of tumorigenic genes in cell culture and animal tumor models, effective siRNA delivery systems, efficiency of siRNA agents compared with antisense oligonucleotides and efforts for potential therapeutic development. Along with the rapidly growing literature on using siRNA as a functional genomic tool, there is emerging evidence that siRNA may represent a novel therapeutic modality for cancer treatment when optimized local and systemic delivery systems are available.

Animals↗
PubMed1999

Development of cysteine protease inhibitors as chemotherapy for parasitic diseases: insights on safety, target validation, and mechanism of action.

Cysteine proteases have been identified as promising targets for the development of antiparasitic chemotherapy. An attractive aspect of these enzymes is their widespread importance in both protozoan and helminth parasites of domestic animals and humans. Concerns about the ability to selectively inhibit parasite proteases without affecting host homologues have been addressed in recent studies of Trypanosoma cruzi and Plasmodium falciparum. Significant data on half-life, metabolism, pharmacokinetics and safety have been accumulated. Differential uptake of proteases by parasitic organisms versus host cells, and relatively less redundancy in parasite protease gene families, may be two factors which contribute to the successful treatment of animal models of infection.

Animals↗
PubMed2004

One-week 96-well soft agar growth assay for cancer target validation.

Soft agar growth, used to measure cell anchorage-independent proliferation potential, is one of the most important and most commonly used assays to detect cell transformation. However, the traditional soft agar assay is time-consuming, labor-intensive, and plagued with inconsistencies due to individual subjectivity. It does not, therefore, meet the increasing demands of today's oncology drug target screening or validation processes. This report describes an alternative 96-well soft agar growth assay that can function as a replacement for the traditional method and overcomes the aforementioned limitations. It offers the following advantages: a shortened assay duration (1 week instead of 4 weeks) that makes transient transfection or treatment possible; plate reader quantification of soft agar growth (measuring cloning efficiency and colony size); and a significant reduction in required labor. Higher throughput also makes it possible to process large numbers of samples and treatments simultaneously and in a much more efficient manner, while saving precious workspace and overall cost.

Agar↗
PubMed2007

Antisense oligonucleotides: target validation and development of systemically delivered therapeutic nanoparticles.

Antisense oligonucleotides (ASO) against specific molecular targets (e.g., Bcl-2 and Raf-1) are important reagents in cancer biology and therapy. Phosphorothioate modification of the ASO backbone has resulted in an increased stability of ASO in vivo without compromising, in general, their target selectivity. Although the power of antisense technology remains unsurpassed, dose-limiting side effects of modified ASO and inadequate penetration into the tumor tissue have necessitated further improvements in ASO chemistry and delivery systems. Oligonucleotide delivery systems may increase stability of the unmodified or minimally modified ASO in plasma, enhance uptake of ASO by tumor tissue, and offer an improved therapy response. Here, we provide an overview of ASO design and in vivo delivery systems, and focus on preclinical validation of a liposomal nanoparticle containing minimally modified raf antisense oligodeoxynucleotide (LErafAON). Intact rafAON (15-mer) is present in plasma and in normal and tumor tissues of athymic mice systemically treated with LErafAON. Raf-1 expression is decreased in normal and tumor tissues of LErafAON-treated mice. Therapeutic benefit of a combination of LErafAON and radiation or an anticancer drug exceeds radiation or drug alone against human prostate, breast, and pancreatic tumors grown in athymic mice. Further improvements in ASO chemistry and nanoparticles are promising avenues in antisense therapy of cancer.

Animals↗
PubMed2026

GFPT1 as a cross-ancestry validated target for degenerative spinal disease: genetic association in a Chinese cohort and functional characterization in zebrafish.

Degenerative spinal disease (DSD), including spinal stenosis and spondylosis, lacks effective pharmacological treatment. To identify druggable targets and assess cross-ancestry applicability, we integrate multi-omics analyses using Summary-data-based Mendelian Randomization (SMR), colocalization, and two-sample Mendelian randomization with European whole-blood, peripheral-blood, and CSF eQTL/pQTL datasets, followed by whole-genome sequencing (WGS) validation in a Chinese cohort. We identify 7 genes/proteins associated with spinal stenosis and 5 with spondylosis, with GFPT1, GPX1, and SERPINA1 shared by both. Two-sample MR further supports the causal associations of these targets with DSD. Phenome-wide MR prioritization selects GFPT1 and GPX1 as favorable candidates with no predicted adverse effects and potential beneficial effects on hypertension. In the Chinese cohort (67 lumbar spinal stenosis patients and 100 controls), WGS identifies 4 GFPT1 cis-eQTL loci (rs13016371, rs35392088, rs12997521, and rs13019789) associated with lumbar spinal stenosis risk; all risk alleles are linked to increased GFPT1 expression, and all 24 variant carriers show L4/L5 stenosis on imaging. Druggability analysis identifies IOX1 as the sole preclinical-stage compound targeting GFPT1, and molecular docking supports robust binding to GFPT1 (- 6.39 kcal/mol). Functional assays show that IOX1 directly inhibits GFPT1 enzymatic activity and induces fructose-6-phosphate accumulation. In zebrafish, IOX1 significantly rescues GFPT1-induced degenerative phenotypes. These findings establish GFPT1 as a cross-ancestry validated therapeutic target for DSD and nominate IOX1 as a promising disease-modifying candidate.

Animals↗
PubMed2007

Target validation using RNA interference in solid tumors.

Reverse genetics is one strategy that is currently used to establish a link between a target gene and a disease phenotype. In this process, the function of a gene is inhibited and the consequence of its loss on a desired biological function, such as tumor growth and metastasis, is monitored. RNA interference (RNAi) has been found to be the most effective method to specifically inhibit gene expression. Notably, interactions between cancer cells, stromal cells, and the extracellular matrix (ECM) are crucial to angiogenesis and tumorigenesis. Tumor cells and the surrounding stroma are the principle source of growth factors and cytokines, which induce remodeling of the ECM mediated by metalloproteases (MMPs) secreted by macrophages. The production of macrophages is regulated by colony-stimulating factor (CSF)-1, which is overexpressed in several tumors. When short-interfering RNAs (siRNAs) targeting either the CSF-1 or its receptors were delivered into colon and breast cancer xenografts in mice, tumor growth was inhibited. Associated with this suppression, we observed decreased tumor vascularity, reduced expression of angiogenic factors and MMPs, and decreased macrophage recruitment to the tumors. The suppression of CSF-1 by RNA interference is therefore a powerful tool to block gene function and influence tumor-stroma interactions in solid tumor development.

Animals↗
PubMed2002

Target validation and drug discovery using genomic and protein-protein interaction technologies.

After the successful completion of the human genome project, mapping of the human proteome has become the next important challenge facing the biotech and pharmaceutical industries. Identification of the 'right' target(s) is now a critical part of the process because of the cost of drug discovery. Compounding this situation is the fact that the pharmaceutical industry faces a further challenge of being able to sustain current and historical growth rates. Hence, the discovery of new drug targets is important for developing new drug leads that can become preclinical drug candidates. Proteomics is the next phase of the effort whereby the human genome can be understood. However, mapping the human proteome presents a daunting challenge. Proteomics involves several essential components with the most significant being the discovery and description of all protein-protein interactions. Once this compendium is available, a secondary and equally important initiative will be to decipher proteins that are differentially expressed in any given disease condition. At this point, the critical focus will be to select the most relevant proteins, understand their partner interactions and then further winnow them to the point where they are relevant pharmaceutical target candidates. This paradigm can be compared to finding the relevant 'needle in the proteome haystack'. This review describes the use of genomic and protein-protein interaction technologies to identify and validate these 'needles' as the first step in the drug discovery process.

Animals↗
PubMed2000

Pharmacogenomics and therapeutic target validation in cerebral vasospasm.

One of the most important pharmacogenomic technologies is transcriptome analysis. We used this method to study the change of gene expression profiles in animal models of cerebral vasospasm. We found novel drug target candidates in cerebral vasospasm through pharmacogenomics. By using differential display and quantitative reverse transcriptase-polymerase chain reaction, we found that heme oxygenase-1 (HO-1) mRNA was prominently induced in the basilar artery and modestly in brain tissue in a murine vasospasm model. There was a significant correlation between the degree of vasospasm and HO-1 mRNA levels in the basilar arteries exhibiting vasospasm. Antisense HO-1 oligodeoxynucleotides (ODN) inhibited HO-1 induction in the basilar arteries, but not in the whole brain tissue. This phenomenon was not observed in the nontreatment, sense HO-1 ODN and scrambled ODN treatment arteries. We report, for the first time, the protective effects of HO-1 gene induction by endogenous or clinical compounds in cerebral vasospasm after subarachnoid hemorrhage, a finding that should provide a novel therapeutic target for cerebral vasospasm.

Animals↗
PubMed2001

Peptide deformylase as an antibacterial drug target: target validation and resistance development.

New inhibitors of peptide deformylase (PDF) which are very potent against the isolated enzyme and show a certain degree of antibacterial activity have recently been synthesized by our group. Several lines of experimental evidence indicate that these inhibitors indeed interfere with the target enzyme in the bacterial cell. (i) The inhibition of Escherichia coli growth could be counteracted by overexpression of PDF from different organisms, including E. coli, Streptococcus pneumoniae, and Haemophilus influenzae. Conversely, reduced expression of PDF in S. pneumoniae resulted in an increased susceptibility to the inhibitors. (ii) Proteome analysis on two-dimensional gels revealed a shift for many proteins towards lower pI in the presence of PDF inhibitors, as would be expected if the proteins still carry their N-formyl-Met terminus. (iii) PDF inhibitors show no antimicrobial activity against E. coli under conditions that make growth independent of formylation and deformylation. The antibacterial activity in E. coli was characterized as bacteriostatic. Furthermore, the development of resistance in E. coli was observed to occur with high frequency (10(-7)). Resistant mutants show a reduced growth rate, and DNA sequence analysis revealed mutations in their formyl transferase gene. Taking all these aspects into account, we conclude that PDF may not be an optimal target for broad-spectrum antibacterial agents.

Amidohydrolases↗
PubMed2002

Clinical and functional target validation using tissue and cell microarrays.

Expression levels of thousands of genes or proteins can be readily determined using microarray techniques. However, this represents only the first step in understanding the biological and medical significance of these molecules. New high-throughput techniques, such as tissue and cell microarrays, will facilitate clinical and functional analysis of molecular targets.

Animals↗