Novartis Institutes for BioMedical Research - Articles and news items

Lead discovery for targeting G protein-coupled receptors

Issue 5 2011 / 19 October 2011 / Sandra Siehler and Sandra W. Cowan-Jacob, Novartis Institutes for BioMedical Research

G protein-coupled receptors (GPCRs) control a plethora of key physiological functions in every cell of an organism. GPCRs are therefore involved in many diseases, since altered ligand or receptor levels and genetic or epigenetic modifications can lead to GPCR dysfunction and hence a pathophysiological phenotype. About one third of currently marketed drugs target GPCRs. The human genome contains 720-800 predicted GPCRs, and about half of them respond to olfactory/sensory signals, whereas the others are known or predicted to be activated by endogenous ligands and many of these represent potential drug targets. Seventy seven per cent of these non-sensory GPCRs belong to the class A (rhodopsin-like) family, whereas 14 per cent represent class B (secretin-like) GPCRs, less than one per cent belong to the class C (metabotropic receptor-like) or the atypical frizzled-/smoothened receptor class, and the remaining 25 per cent are orphan receptors1,2.

All of these families share a common overall structure consisting of an extracellular aminoterminus, a seven helical transmembrane domain and an intracellular carboxy-terminus3 (Figure 1). The diverse class A family is generally activated by small molecules binding to a pocket in the transmembrane domain (TMD), while in class B the natural ligands are peptides which use the TMD pocket and the large N-terminal domain, and in family C the ligands bind to the N-terminal domain alone, causing conformational changes that trigger receptor signalling. (more…)

Maldi-mass spectrometry imaging applied to drug discovery and development

Issue 5 2011 / 19 October 2011 / Brendan Prideaux, Dieter Staab, Gregory Morandi, Nicole Ehrhard and Markus Stoeckli, Novartis Institutes for BioMedical Research

Since its introduction in the field of biomedical imaging over 10 years ago1, matrixassisted laser desorption/ionisation mass spectrometry imaging (MALDI-MSI) has played an ever increasing role in drug discovery and development and is now utilised in laboratories of many leading pharmaceutical companies and collaborating academic institutions.

The need for mass spectrometry imaging in drug discovery is founded on the shortcomings of current technologies. Traditional methods of spatially mapping the distribution of compounds in tissue involved a combination approach of autoradiography (WBA) with metabolite information obtained from LC/MS analysis of tissue homogenate2. Autoradio – graphy methods only monitor the radiolabel and therefore are not able to distinguish the parent drug from its metabolites. The addition of LC/MS allows for conclusive determination of metabolites. However, this only produces spatial information at the whole organ level and not the spatial detail that can be routinely achieved using MSI. (more…)

The evolution of RNAi technologies in the drug discovery business

Issue 5 2010 / 29 October 2010 / Jason Borawski and L. Alex Gaither, Novartis Institutes for Biomedical Research

In the past decade, the pharmaceutical industry has exploited the naturally occurring cellular RNAi pathway to enhance drug discovery research. The RNAi pathway, triggered by dsRNA, selectively, although not always specifically, degrades mRNA leading to substantial decreases in post-transcriptional gene expression1. Researchers have capitalised on this intrinsic pathway by synthesising RNAi reagents to modify the expression of any desired gene. RNAi libraries consisting of synthetic siRNAs or plasmid based shRNAs are amendable to largescale genome-wide screening campaigns to search for new therapeutic targets. Such loss of function screens can reveal novel targets and synthetic lethal interactions for cancer therapy2,3. These screens have also been used to identify novel host factors for diseases such as Hepatitis C4-7 and HIV8-14. Selective gene silencing can deconvolute molecular pathways implicated in disease onset and progression15. (more…)

Indirect modulation of cardiac ion channels and implications for preclinical safety assessment

Issue 4 2010 / 19 August 2010 / Gül Erdemli & Dmitri Mikhailov, Center for Proteomic Chemistry, Novartis Institutes for BioMedical Sciences and Albert M Kim, Translational Medicine, Novartis Institutes for BioMedical Sciences

The preclinical assessment of a small molecule’s liability for QT interval prolongation is an essential part of the drug discovery process. Patch clamp assays for heterologously expressed recombinant cardiac ion channels are widely used in the pharmaceutical industry to evaluate potential drug-channel interactions. These assays are generally acute assessments and are not designed to detect indirect channel modulations that may result in QT prolongation. Despite the abundant literature demonstrating potential transcriptional, translational and post-translational mechanisms for indirect ion channel modulation, contribution of these mechanisms to drug-induced QT prolongation and/or arrhythmia propensity is not well understood. In this brief review, we discuss some potential mechanisms through which indirect ion channel modulation can produce QT prolongation and strategies for their early detection and mitigation. (more…)

The changing role of automation in High Throughput Screening

Industry Focus 2009, Past issues / 10 January 2009 /

Among the challenges for the pharmaceutical industry, declining research productivity and increasing research costs take a prominent position. This is often put in the context of efforts in the pharmaceutical industry to automate and “industrialise” research activities, combinatorial chemistry and High Throughput Screening being the most prominent examples. An argument is being put forward that the industry replaced scientists with robots and scientists’ ingenuity with mindless screening. It is then concluded that the investments into automation were misguided and led to a decline in research productivity. (more…)

MALDI FT-ICR MS platform for proteomics: Rationale for an offline approach and optimised implementation

Issue 3 2008, Past issues / 19 July 2008 /

MALDI FT-ICR MS platform for proteomics: Rationale for an offline approach and optimised implementation
A number of sophisticated approaches have been developed to study the structure and function of genes, including the whole-scale sequencing of entire organisms[1], global transcriptional profiling[2], and forward genetic studies[3]. However, these techniques are ultimately limited by the fact that they only assess intermediates on the way to the protein products of genes that ultimately regulate biological processes[4,5].

Processes such as RNA processing, proteolytic activation, and hundreds of possible post-translational modifications (PTMs) can result in the production of numerous proteins of unique structure and function from a limited number of genes. Additionally, biological activity often results from the assembly of numerous proteins into an active complex, the nature and composition of which can only be explored at the protein level. Therefore, proteomic studies should be able to answer many questions about cellular processes and diseases that cannot be answered by genomic methods alone6.

However, such studies are far harder to perform than their genomic counterparts, and any general analysis platform must possess high sensitivity, be tolerant of a wide range of experimental and analytical conditions, and be able to process and display massive amounts of information. More importantly, these analysis systems must be able to perform extremely high-throughput measurements, since unlike the relatively fixed nature of the genome, the expression and interactions of proteins are in a constant state of flux, varying over time, tissue type, and in response to environmental changes. (more…)

Antibody-based proteomics to study cellular signalling networks

Issue 2 2008, Past issues / 19 March 2008 /

The complexity of drug discovery faces many challenges; principally, the failure of drug candidates during the development process as a result of adverse effects or lack of efficacy. A key reason for this high attrition rate is that we are only just beginning to understand the complexity of the response(s) from a biological system to perturbations, such as a disease state or drug treatment. Subsequently, a deeper insight into the molecular mechanisms underlying both disease processes and drug action will ultimately contribute to increased productivity through the drug discovery process[1,2].

In recent years, progress has been made in ascribing pathological conditions to defects in molecular pathway components, for example, linking dysregulation of signalling pathways to cancer and inflammatory diseases.

Kinases and phosphatases are key regulators in signalling pathways, so it is not surprising that across the pharmaceutical industry, a substantial percentage of drug discovery efforts are focused on targeting these enzyme classes. In particular, the modulation of cellular kinase activities, which is one of the most rapidly growing areas in the development of novel drugs. (more…)

High content screening as improved lead finding strategy

Issue 2 2008, Past issues / 19 March 2008 /

High content screening (HCS) is based on subcellular imaging using automated microscopy, in combination with automated image analysis. High content screening was first introduced over a decade ago as one of the promising new technologies, intended to address the bottleneck of secondary assays in the development of new drugs. Since then, the application has rapidly expanded throughout the entire drug discovery process, from target identification and validation, through to lead optimisation and detailed investigation of the mode of action.[1,2,3]

One main characteristic of HCS is its capability of multiplexing, meaning not only several additional reagents creating several read outs, but also gives the ability to analyse different parameters of each individual cell, within an array of cells. Temporary cellular events which can be analysed via live cell and population analysis deliver sensitive results of rare events within the cell population.

An area where HCS shows its benefits is in the high throughput screening of small molecules for lead finding. Increasingly, pharmaceutical companies successfully screen their full collection; however, the throughput is limited by the assay procedure, including washing and fixation steps4,5. Image collection and data analysis time can be another throughput limiting factor, depending on instrument setup and complexity of the biology to be analysed. (more…)

MicroRNAs and their relatives – new avenues in biomedical research

Issue 6 2007, Past issues / 23 November 2007 /

Non-coding RNAs (ncRNAs) consist of a growing heterogeneous class of transcripts defined as RNA molecules that lack any extensive “Open Reading Frame” (ORF) and function as structural, catalytic or regulatory entities rather than serving as templates for protein synthesis. While non-coding sequences make up only a small fraction of the DNA of prokaryotes, among eukaryotes, the proportion of DNA that does not code for protein increases with their complexity, underscoring the likelihood of a “hidden layer” of gene regulation in animal genomes₁.

Although previously being classified as “junk”, recent studies strongly indicate that ncRNAs play central roles in regulating gene expression at multiple levels including; transcription, alternative splicing, RNA modification, such as RNA editing, RNA stability and translation and chromatin modification. Still, there is an ongoing debate on whether ncRNAs are important functional contributors to an organism’s complexity or rather represent transcriptional “background” or “noise”₂. NcRNAs can be subdivided into two main classes: “housekeeping” RNAs such as transfer RNAs (tRNAs), ribosomal RNAs (rRNAs), small nuclear RNAs (snRNAs) and regulatory RNAs (“riboregulators”), such as small nucleolar RNAs (snoRNAs), and microRNAs (miRNAs), which are expressed at certain stages of organism development or cell differentiation and can modulate expression of other genes on the levels of transcription or translation. In particular, miRNAs represent a class of ncRNAs which has recently attracted major attention within the scientific community. Although information on the function of miRNAs is still sparse, an increasing body of evidence suggests that these molecules play major roles in important biological processes and may contribute to the pathogenesis of human diseases₃. Consequently, an increasing number of research scientists who have traditionally worked on proteins, are beginning to move their focus towards studying the world of these tiny RNA molecules. The potential and prospects of miRNAs and other newly discovered ncRNA family members as a new class of therapeutic are reviewed, and the constraints associated with current miRNA target validation approaches are discussed. (more…)

In vitro safety pharmacology profiling

Issue 1 2006, Past issues / 2 February 2006 / Jacques Hamon, Kamal Azzaoui, Steven Whitebread, Laszlo Urban, Edgar Jacoby, Bernard Faller, Novartis Institutes for BioMedical Research

One major cause of the late failure of drugs in development (i.e. attrition) is the lack of clinical safety of the compounds (accounting for approximately 30% of failures together with toxicology)1. One of the key elements is the off-target effects of the compounds, causing adverse drug reaction (ADRs).

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The promise and pitfalls

Issue 3 2005, Past issues / 22 August 2005 / Craig S. Mickanin, Research Investigator and Mark A. Labow, Executive Director, Genomic and Proteomic Sciences, Novartis Institutes for BioMedical Research

Perhaps the most significant technological advancement in the study of gene function in the post-genome era has been the discovery that RNA interference (RNAi) can be exploited for depletion of endogenous mRNA in mammalian cells. As the pharmaceutical industry has fallen under intense pressure to both identify and validate high-quality drug targets, the lure of bona fide genome-wide functional analysis and target identification using small interfering RNA (siRNA) has fueled the interest in what can now be truly called ‘functional’ genomics.

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Dosing and weighing in the pharmaceutical laboratory

Issue 1 2005, Past issues / 7 March 2005 / Dr. Ulrich Schopfer, Global Head of Compound Management, Dr. Frank Hoehn, Laboratory Head, Automation, Matthieu Hueber, Automation Engineer, Novartis Institutes for BioMedical Research

Dispensing of solids is still a demanding task in laboratory automation. The solubilisation of High Throughput Screening (HTS) libraries is one of the most challenging problems in this area, since millions of different substances have to be processed by the same technology.

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