Issue 4 2007

In vivo drug target validation using RNAi

Issue 4 2007 / 21 July 2007 / Jost Seibler, Head of Technology Development, Artemis Pharmaceuticals and Frieder Schwenk, Principal Scientist, University of Applied Science, Department of Applied Natural Sciences, Gelsenkirchen, Germany

Among the genetic model organisms, the laboratory mouse (Mus musculus) has a predominant role in the study of human disease and in pre-clinical drug development. Apart from the high degree of sequence homology of mouse and human genomes, and similarities in many physiological aspects, advanced targeting technologies make the crucial difference; providing unique tools for elucidating gene function in vivo.

The ability to manipulate the genome in ES cells and mice was developed in the late 1980s; since then, gene targeting has been used extensively to study gene function in genetically modified mouse strains. As initially designed; the technique allows the disruption of a target gene in the murine germline by the insertion of a selectable marker. About 4.000 “knock-out” (KO) mice have been described in the literature, demonstrating the wide use of this approach. The application of Cre/loxP recombination has refined the tools for manipulating the mouse genome; detecting site and timing of gene alteration in the living animal1-3. An inherent feature of these recombinase-based approaches, however, is a non-reversible gene switch that does not allow modulating gene expression in a given cell. In addition, the derivation of conditional mouse mutants is costly and time consuming due to extensive vector construction, ES cell manipulation, and breeding. The finding that RNAi can mediate potent gene knockdown in transgenic animals provides the opportunity to significantly reduce time and effort for the generation of genetically modified mouse models4-6. (more…)

Tagged with: Artemis Pharmaceuticals, Frieder Schwenk, Functional genomics, Jost Seibler, RNAi, Transgenesis

How will MicroRNAs affect the drug discovery landscape?

Issue 4 2007 / 21 July 2007 / Dr. Neil Clarke and Dr. Mark Edbrooke, GlaxoSmithKline Research and Development, Hertfordshire, UK

The archetypal microRNAs, lin-4 and let-7, were discovered in the nematode worm Caenorhabditis elegans over a decade ago and, at that time, no one would have predicted that they would be anything other than an interesting feature of worm developmental biology. However, in recent years there has been an explosion of research activity in the field of microRNAs (miRNAs), so much so that the number of publications has almost doubled every year over the last five years (see Figure 1).

Fuelling this activity was the identification of miRNAs in many more organisms including humans, and especially the discovery that they are linked to human disease. In this article we review recent progress and developments that are advancing our understanding of the role of miRNAs in several human disease settings and therapeutic arenas, and how this may affect the drug discovery landscape.

MicroRNAs are evolutionarily conserved, noncoding RNA molecules, approximately 22 nucleotides in size, that negatively regulate target gene expression at the post-transcriptional level1-3. Originally ignored as that fraction of the genome colloquially termed “Junk DNA”, examples are now known in many species. Almost 40% of miRNAs are encoded in introns, 50% are intergenic and 10% are in exons. Release 9.2 (May 2007) of miRBase (the miRNA sequence database) http://microrna.sanger.ac.uk/4-6, contains 4584 entries representing hairpin precursor miRNAs, expressing 4430 mature miRNA products in primates, rodents, birds, fish, worms, flies, plants and viruses. The database contains 475 human miRNA sequences, just under half of which have been experimentally verified. The number of miRNA encoding genes is rapidly expanding, and this number may constitute between 1-4% of expressed genes in the genome7-9. Recent literature suggests that between 20-30% of all human genes may be subject to regulation by miRNAs and that each miRNA may, on average, contribute to the regulation of 200 or more mRNA targets10. Most miRNAs bind the 3’UTR of their target genes with imperfect sequence complementarities and repress translation initiation, though perfect complementarity can lead to mRNA cleavage in a process similar to that mediated in RNA interference (RNAi). (more…)

Tagged with: Dr. Mark Edbrooke, Dr. Neil Clarke, Drug discovery, Functional genomics, GlaxoSmithKline, microRNA, RNAi

Industry Insight: Biology and data capture in the life sciences industry

Issue 4 2007 / 21 July 2007 / Neil Kipling, CEO, IDBS

Neil Kipling, CEO of leading advanced software solutions provider for the life sciences industry, IDBS, talks to us about current and future functions of biology and data capture within the life sciences industry. (more…)

Tagged with: CEO, Data capture, IDBS, Neil Kipling

Academic contribution to high-content screening for functional and chemical genomics

Issue 4 2007 / 21 July 2007 / Kerstin Korn and Eberhard Krausz (Corresponding author), Head, HT-Technology Development Studio (TDS), Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG)

High-content screening (HCS) is defined as multiplexed functional screening based on imaging multiple markers (e.g. nuclei, mitochondria etc.) in the physiologic context of intact cells by extraction of multicolour fluorescence information1. It is based on a combination of advanced fluorescence-based reagents, modern liquid handling devices, automated imaging systems and data processing, as well as sophisticated image analysis software.

Initially, HCS was mainly used by pharmaceutical and biotech companies to discover new therapeutic targets and characterize new chemical leads against those targets. As this technology provides not only morphological, phenotypic and genotypic information, but functional data, it has been established as a powerful tool in modern research and drug development. Today, HCS has the potential to be used in a wide range of applications, such as target identification and validation, primary and secondary screening, mode-of-action studies, the hit-to-lead process, the identification of biomarkers, the exploitation of cytotoxicity and genotoxicity, and the tracking of cellular processes applying living cells to support basic research as well as pharmaceutical R&D. While the primary HCS literature still remains rare, a considerable number of review articles summarizing strategies, progress and developments in HCS have been already published, e.g.2-7. Within this review we are going to be focusing on HCS screens published by academic groups; moreover we would like to give a short overview of new technology developments driven by academic groups. (more…)

Tagged with: Chemical genomics, Eberhard Krausz, Functional genomics, HCS (High Content Screening), HT-Technology Development Studio (TDS), Kerstin Korn, Max Planck Institute

The impact of automation on drug discovery

Issue 4 2007 / 21 July 2007 / William P. Janzen, President and COO, Amphora Discovery

Automated systems and modern pharmaceuticals have both had a hugely positive impact on human life. While these technologies developed in parallel with one another during roughly the same time period in the early 20th century, they didn’t interact until automation found its way into the laboratory in the 1970s.

Since that time highly automated robotic systems such as High Throughput Screening (HTS) operations, compound repositories and parallel synthesis chemistry labs have become ubiquitous in core laboratories and are increasingly being found in academic and institutional environments. However, it is surprisingly difficult to measure the impact of automation as an isolated entity; as they have always incorporated automated systems, the settings that employ robotics on a large scale must either be assessed holistically by looking at the impact of the combined technology, or at a lower level by utilizing productivity measures that are less global. This problem is compounded by the fact that the details of core operations in pharmaceutical companies are closely held as a matter of proprietary. (more…)

Tagged with: Amphora Discovery, Drug discovery, Lab Automation, Laboratory information management systems (LIMS), William P. Janzen

Implementation of an enterprise ELN: a case study

Issue 4 2007 / 21 July 2007 / Dr. Simon Weston, Programme Delivery Leader, Discovery, AstraZeneca

The paper notebook has played a central role in the recording of the methods and results of scientific research for centuries. It has some strengths: portability, flexibility and (to some degree) incontrovertibility but in an enterprise environment it has many weaknesses. Chief among these is that the vast majority of information entered is lost to the enterprise unless substantial processes and governance structures are created to ensure its dissemination. However, even if these are in place, searching for relevant information is likely to be time-consuming and difficult since there is no automated search capability below the level of the physical book.

In chemistry in particular, the relentless spread of automated, high-throughput synthetic approaches and the attendant growth in related analytical data outputs cast doubt on the suitability of the book format itself; there simply isn’t room to accommodate all the data. Indeed, analytical data print-outs are commonly bound into a book form and signed and stored separately from the laboratory notebook itself. (more…)

Tagged with: AstraZeneca, Dr. Simon Weston, ELNs, LIMS

Implementing Near Infrared Spectroscopy as a PAT tool in the biopharmaceutical industries

Issue 4 2007 / 21 July 2007 / Payal Roy-Choudhury, PhD Student, Fermentation Centre, Strathclyde Institute of Pharmacy & Biomedical Science, Glasgow, UK

Biopharmaceuticals are the fastest growing sector of the pharmaceutical industry[1]; with monoclonal’s being the key biopharmaceutical products representing a significant proportion of the current business focus. It is anticipated that this new generation of biopharmaceuticals will revolutionise clinical medicine over the next 5-10 years.

The Food and Drug Administration (FDA) announced their guidance document on Process Analytical Technology (PAT) in 2004[2]; this prompted many pharmaceutical companies to re-evaluate their future requirements for bioprocess analysis. The PAT initiative specifically encourages the development of improved process monitoring technology in the manufacturing environment. This has effectively led the investigation of a number of novel technologies in a biomanufacturing context, and much attention has been focused on near infrared (NIR) spectroscopy. Potentially, NIR offers the prospect of real-time control of the physiology of cultured cells in fermenters; leading to marked improvements in authenticity, purity and production efficiency. (more…)

Tagged with: Near Infrared Spectroscopy, PAT, Payal Roy-Choudhury, Strathclyde Institute of Pharmacy & Biomedical Science

A “PAT” on the back for Rapid Microbiological Methods

Issue 4 2007 / 21 July 2007 / Robert Johnson, Director, Dialogue

The modern microbiological laboratory needs to change and become more innovative in its approach to microbial detection, enumeration and identification. (more…)

Tagged with: Dialogue, PAT, Robert Johnson

PAT in the pharmaceutical industry

Issue 4 2007 / 21 July 2007 / Don Arnone, Teraview / Gawayne Mahboubian-Jones, Optimal Automation / Vinod Mehta, Carl Zeiss / Christian Woelbeling, Werum Software & Systems AG / Denise Root, Foss / Ingrid Maes, Siemens / Chris Hobbs, ABB

European Pharmaceutical Review brings you a comprehensive guide to the current developments and possible future innovations within Process Analytical Technologies. (more…)

Tagged with: ABB, Abbott, ASTM International, AstraZeneca, Carl Zeiss, Chris Hobbs, Christian Woelbeling, David Littlejohn, Denise Root, Don Arnone, Eli Lilly and Co., Foss, Ingrid Maes, Novartis, Optimal Automation, PAT, Pat Picariello, Siemens, Staffan Folestad, Steve Doherty, University of Stratchclyde, Vinod Mehta, Werum Software & Systems AG, Yatindra Joshi