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Structure-Based Target Druggability Assessment

The focus of this chapter is on the important concepts behind the in silico techniques that are used today to assess target druggability. The first step of the assessment consists of finding cavity space in the protein using 2D and/or 3D topological concepts. These concepts underlie the geometry ...

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PARP Inhibition as a Prototype for Synthetic Lethal Screens

Although DNA damaging chemotherapy and radiation therapy remain the main stay of current treatments for cancer patient, these therapies usually have toxic side effect and narrow therapeutic window. One of the challenges in cancer drug discovery is how to identify drugs that selectively ...

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CellProfiler and KNIME: Open Source Tools for High Content Screening

High content screening (HCS) has established itself in the world of the pharmaceutical industry as an essential tool for drug discovery and drug development. HCS is currently starting to enter the academic world and might become a widely used technology. Given the diversity of problems tack ...

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Integration of RNAi and Small Molecule Screens to Identify Targets for Drug Development

Cellular models for siRNA and small molecule high throughput screening have been widely used in the last decade to identify targets for drug discovery. As an example, we present a two-fold readout approach based on cell viability and multipolar phenotype. To maximize the discovery of potenti ...

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High-Throughput RNAi Screening for the Identification of Novel Targets

Gene silencing through RNA interference has provided researchers with an effective way to study gene function. High-throughput RNA interference (HT-RNAi) screening has further permitted researchers to identify functionally relevant mediators of cellular response on a large ...

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Western Blot Evaluation of siRNA Delivery by pH-Responsive Peptides

Gene silencing, via RNA interference (RNAi) technologies using small interfering RNA (siRNA), has been developed as an important tool for target identification and validation in drug discovery and has huge therapeutic potential. However, effective delivery into cells presents a ma ...

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siRNA Design Principles and Off-Target Effects

Short interfering RNAs (siRNAs) are a major research tool that allows for knock-down of target genes via selective mRNA destruction in almost all eukaryotic organisms. siRNAs typically consist of a synthetic ∼21 nucleotide (nt) RNA-duplex where one strand is designed with perfect compl ...

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The Design and StructureFunctional Properties of DNA-Based Immunomodulatory Sequences

DNA-based immunomodulatory sequences (DIMS) are promising compounds for the treatment of different diseases, including inflammation and cancer. They act through the interaction with TLR9, a member of the Toll-like receptor family whose essential role in innate immunity was recen ...

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Identification of Aptamers as Specific Binders and Modulators of Cell-Surface Receptor Activity

In recent years, the SELEX (Systematic Evolution of Ligands by EXponential enrichment) technology has established itself as a powerful tool in basic research with promising applications in diagnostics and therapeutics. Oligonucleotides with high-affinities to their target ...

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The Path to Oncology Drug Target Validation: An Industry Perspective

The advent of a variety of genomic, proteomic and other system-based scientific approaches has raised the expectations of identifying novel targets for oncology drug discovery. However, the complexity of human genome cancer alterations requires a careful analysis of the function of c ...

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ChIPing Away at Global Transcriptional Regulation

The regulation of gene expression impacts all aspects of cell biology and biochemistry. As we gain a greater understanding of the mechanisms involved in this process, we also begin to unveil its complexities. The delicate balancing act played out by the multitude of DNA interacting proteins c ...

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RIP-CHIP in Drug Development

Microarrays are extensively used to evaluate the effects of compounds on gene expression in the cells. Most of the studies so far have analyzed the transcriptome of the cell. The basic assumption of this approach is that the changes in gene expression occur at the level of transcription of a gene. Howe ...

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HELP (HpaII Tiny Fragment Enrichment by Ligation-Mediated PCR) Assay for DNA Methylation Profiling of Primary Normal and Malignant B Lymphocytes

The role of cytosine methylation in the regulation of gene expression during normal development and malignant transformation is currently under intense investigation. An ever increasing body of evidence demonstrates that carcinogenesis is associated with aberrant DNA meth ...

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High-Throughput Screening of Metalloproteases Using Small Molecule Microarrays

The promise of rapid and cost-effective drug screening assays on solid support is one that may now be realized with the advent of small molecule microarrays. Many of the initial hurdles in library design and microarray fabrication have been overcome over the last decade, allowing this platform ...

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Metabolic Enzyme Microarray Coupled with Miniaturized Cell-Culture Array Technology for High-Throughput Toxicity Screening

Due to poor drug candidate safety profiles that are often identified late in the drug development process, the clinical progression of new chemical entities to pharmaceuticals remains hindered, thus resulting in the high cost of drug discovery. To accelerate the identification of safer ...

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Production and Application of Glycan Microarrays

Glycans are vital elements of living organisms and are involved in recognition, communication, cell growth and development, motility, and other significant processes. The interactions of glycans with the proteins that bind them provide valuable information about protein inter ...

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Small Molecule Selectivity and Specificity Profiling Using Functional Protein Microarrays

Small molecules interact with proteins to perturb their functions, a property that has been exploited both for research applications and to produce therapeutic agents for disease treatment. Commonly utilized approaches for identifying the target proteins for a small molecule have ...

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Use of Tissue Microarray to Facilitate Oncology Research

HPV-positive oropharyngeal squamous cell carcinomas (OSCC) represent a distinct disease entity from traditional OSCC. We hypothesized that for HPV DNA-positive cases, p16 expression status differentiates the biologically relevant ones. We determined HPV16DNA viral load in a ...

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Multicenter Clinical Sample Collection for Microarray Analysis

In this chapter, we describe numerous methods to extract RNA, DNA, and protein from tissue, represented by kidney transplant biopsies, and from peripheral blood cells collected at various clinical sites. Gene expression profiling and SNP-based genome-wide association studies are do ...

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Isolation of Total RNA from Transgenic Mouse Melanoma Subsets Using Fluorescence-Activated Cell Sorting

The majority of tumors, including melanoma, are phenotypically heterogeneous in that they contain various cell populations with differential expression of cell surface antigens such as CD133/Prominin-1. We have used fluorescence-activated cell sorting (FACS) technology to ...

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