Current Drug Discovery Technologies , Volume 1, No. 1, 2004
Contents
About
the Editor-in-Chief
Function Oriented Synthesis: The Design, Synthesis, PKC Binding and Translocation
Activity of a New Bryostatin Analog Pp.1-11
Paul
A. Wender, Jeremy L. Baryza, Stacey E. Brenner, Michael O. Clarke, Madeleine
L.Craske, Joshua C. Horan, Tobias Meyer
[Abstract]
Genetically Engineered Mouse Models for Drug
Discovery: New Chemical Genetic Approaches Pp.13-26
Susanne
Heck, Xiaobing Qian, and Mark Velleca
[Abstract]
Experiences in Implementing uHTS - Cutting
Edge Technology Meets the Real World Pp.27-35
Philip
Gribbon, Sabine Schaertl, Malcolm Wickenden, Gareth Williams, Rachel Grimley,
Frank Stuhmeier, Hartwig Preckel, Christian Eggeling, Joachim Kraemer, Jeremy
Everett, Wilma W. Keighley, Andreas Sewing
[Abstract]
Systematic Analysis of Large Screening Sets
in Drug Discovery Pp.37-47
Paul
E. Blower, Jr., Kevin P. Cross, Michael A. Fligner, Glenn J. Myatt, Joseph S.
Verducci, and Chihae Yang
[Abstract]
The FlexX Database Docking Environment — Rational
Extraction of Receptor Based Pharmacophores Pp.49-60
Holger
Claussen, Marcus Gastreich, Volker Apelt, Jonathan Greene, Sally A. Hindle, and
Christian Lemmen
[Abstract]
Assessment of the Health Effects of Chemicals
in Humans: I. QSAR Estimation of the Maximum Recommended Therapeutic Dose
(MRTD) and No Effect Level (NOEL) of Organic Chemicals Based on Clinical Trial
Data1 Pp.61-76
Edwin
J. Matthews, Naomi L. Kruhlak, R. Daniel Benz, and Joseph F. Contrera
[Abstract]
Development of Immunopharmacotherapy Against
Drugs of Abuse Pp.77-89
Michael M. Meijler, Masayuki Matsushita, Peter Wirsching and Kim D. Janda
[Abstract] [Full text article]
Ion Channel Drug Discovery and Research: The
Automated Nano-Patch- Clamp© Technology Pp.91-96
A. Brueggemann, M. George, M. Klau, M. Beckler, J. Steindl, J.C. Behrends and N. Fertig
[Abstract] [Full text article]
The Isolated Perfused Rat Kidney Model: A
Useful Tool for Drug Discovery and Development Pp.97-111
David
R. Taft
Abstracts
[Back to top] Function Oriented Synthesis: The Design,
Synthesis, PKC Binding and Translocation Activity of a New Bryostatin Analog
Paul
A. Wender, Jeremy L. Baryza, Stacey E. Brenner, Michael O. Clarke, Madeleine
L.Craske, Joshua C. Horan, Tobias Meyer
[Full text article]
Bryostatin 1 represents a novel and potent therapeutic lead with a unique activity profile. Its natural and synthetic availability is severely limited. Function oriented synthesis provides a means to address this supply problem through the design of synthetically more accessible simplified structures that at the same time incorporate improved functional activity. Pharmacophore searching and a new computer aided visualization of a possible binding mode are combined with an understanding of function and knowledge of synthesis to design and prepare a new and simplified compound with bryostatin-like function in biological systems. This new compound is a potent ligand for protein kinase C in vitro (Ki = 8.0 nM). More significantly, the described molecule retains the functional ability to translocate a PKCd-GFP fusion protein in RBL cells. The extent of protein translocation and the sub-cellular localization induced by this new compound is similar to that seen in response to bryostatin 1, indicating that the new molecule retains the functional activity of the natural product but is simpler and can be synthesized in a practical fashion.
[Back to top] Genetically Engineered Mouse Models for Drug
Discovery: New Chemical Genetic Approaches
Susanne
Heck, Xiaobing Qian, and Mark Velleca
[Full text article]
While standard transgenic and knockout mouse technologies have provided a wealth of information for target selection and validation, there have been great advances in using more sophisticated modeling techniques to achieve temporal and spatial regulation of individual genes in adult animals. Recent developments in RNA interference (RNAi) technology in in vivo models promise to further improve upon the static and irreversible features of gene knockouts. Chemical genetic approaches create novel functional alleles of targets and allow fine modulation of protein function in vivo by small molecules, providing the most pharmacologically relevant target validation. Using these advanced models, one can not only ask whether the function of the target is critical for the initiation and maintenance of the disease, but also whether therapies designed to alter the function of the target would be safe and efficacious. In this review, we describe various in vivo tools for target validation in mouse models, discuss advantages and disadvantages of each approach, and give examples of their impact on drug discovery.
[Back to top] Experiences in Implementing uHTS - Cutting
Edge Technology Meets the Real World
Philip
Gribbon, Sabine Schaertl, Malcolm Wickenden, Gareth Williams, Rachel Grimley,
Frank Stuhmeier, Hartwig Preckel, Christian Eggeling, Joachim Kraemer, Jeremy
Everett, Wilma W. Keighley, Andreas Sewing
[Full text article]
Driven by growing corporate compound files, the demands of target biology, and attempts to cut cost, the number of solutions to HTS has spiralled. In quick succession new assay technologies and screening platforms are appearing on the market, with the promise of screening faster than ever in low volume high density formats whilst providing high quality data. Within this world of rapid change, Pfizer has applied cutting edge technology to HTS by introducing screening in 1 ml formats utilising single molecule detection technology. Instead of resource intensive in-house development, Pfizer entered into a collaboration with Evotec OAI / Evotec Technologies and introduced their Mark-II EVOscreenTM platform. In this article we will outline the benefits of the approach taken at Pfizer, Sandwich, and introduce the Mark-II EVOscreenTM platform, illustrating the potential but also possible pitfalls of HTS miniaturisation.
[Back to top] Systematic Analysis of Large Screening Sets
in Drug Discovery
Paul
E. Blower, Jr., Kevin P. Cross, Michael A. Fligner, Glenn J. Myatt, Joseph
S. Verducci, and Chihae Yang
[Full text article]
Each year large pharmaceutical companies produce massive amounts of primary screening data for lead discovery. To make better use of the vast amount of information in pharmaceutical databases, companies have begun to scrutinize the lead generation stage to ensure that more and better qualified lead series enter the downstream optimization and development stages. This article describes computational techniques for end to end analysis of large drug discovery screening sets. The analysis proceeds in three stages: In stage 1 the initial screening set is filtered to remove compounds that are unsuitable as lead compounds. In stage 2 local structural neighborhoods around active compound classes are identified, including similar but inactive compounds. In stage 3 the structure-activity relationships within local structural neighborhoods are analyzed. These processes are illustrated by analyzing two large, publicly available databases.
[Back to top] The FlexX Database Docking Environment — Rational Extraction of
Receptor Based Pharmacophores
Holger
Claussen, Marcus Gastreich, Volker Apelt, Jonathan Greene, Sally A. Hindle,
and Christian Lemmen
[Full text article]
We present an integrated docking environment that allows for iterative and interactive detailed analysis of many docking solutions. All docking information is stored in an ORACLE database. New scoring schemes (e.g. target-specific scoring functions) as well as various types of filters can be easily defined and tested within this environment.
As an example application we investigated the validity of the following hypothesis: If a docking procedure can lead to enrichments significantly better than random then a bias towards (partially) correct placements should be detectable. Such bias in terms of a preference for certain interacting groups within the active site can be used to select a set of receptor-based pharmacophore constraints, which in turn might be used to enhance the docking procedure.
As a proof of concept for this approach we performed docking studies on three targets: thrombin, the cyclin-dependent kinase 2 (CDK2) and the angiotensin converting enzyme (ACE). We docked a set of known active compounds with standard FlexX and derived three sets of target-specific receptor-based pharmacophore constraints by statistical analysis of the predicted placements. Applying these receptor-based constraints in a virtual screening protocol utilizing FlexXPharm led to significantly improved enrichments.
[Back to top] Assessment of the Health Effects of Chemicals
in Humans: I. QSAR Estimation of the Maximum Recommended Therapeutic Dose
(MRTD) and No Effect Level (NOEL) of Organic Chemicals Based on Clinical Trial
Data1
Edwin
J. Matthews, Naomi L. Kruhlak, R. Daniel Benz, and Joseph F. Contrera
[Full text article]
The primary objective of this investigation was to develop a QSAR model to estimate the no effect level (NOEL) of chemicals in humans using data derived from pharmaceutical clinical trials and the MCASE software program. We believe that a NOEL model derived from human data provides a more specific estimate of the toxic dose threshold of chemicals in humans compared to current risk assessment models which extrapolate from animals to humans employing multiple uncertainty safety factors. A database of the maximum recommended therapeutic dose (MRTD) of marketed pharmaceuticals was compiled. Chemicals with low MRTDs were classified as high-toxicity compounds; chemicals with high MRTDs were classified as low-toxicity compounds. Two separate training data sets were constructed to identify specific structural alerts associated with high and low toxicity chemicals. A total of 134 decision alerts correlated with toxicity in humans were identified from 1309 training data set chemicals. An internal validation experiment showed that predictions for high- and low-toxicity chemicals were good (positive predictivity >92%) and differences between experimental and predicted MRTDs were small (0.27–0.70 log-fold). Furthermore, the model exhibited good coverage (89.9–93.6%) for three classes of chemicals (pharmaceuticals, direct food additives, and food contact substances). An additional investigation demonstrated that the maximum tolerated dose (MTD) of chemicals in rodents was poorly correlated with MRTD values in humans (R2 = 0.2005, n = 326). Finally, this report discusses experimental factors which influence the accuracy of test chemical predictions, potential applications of the model, and the advantages of this model over those that rely only on results of animal toxicology studies.
This report is not an official U.S. Food and Drug Administration guidance or policy statement. No official support or endorsement by the U.S. Food and Drug Administration is intended or should be inferred.
[Back to top] Development of Immunopharmacotherapy Against Drugs of Abuse
Michael
M. Meijler, Masayuki Matsushita, Peter Wirsching and Kim D. Janda
[Full text article]
Drug addiction is a major worldwide medical and social problem that continues to escalate. The addiction syndrome is remarkably similar between different drugs of abuse, and can be characterized as a chronic relapsing brain disorder with neurobiological changes that lead to a compulsion to take a drug with loss of control over drug intake. Presently used medications for the treatment of dependence disorders are based on drugs that are either agonists or antagonists of drugs of abuse, and have yielded only limited success. Immunopharmacotherapy is based on the generation or administration of antibodies that are capable of binding the targeted drug before it can reach the brain, whereas replacement strategies based on agonists or antagonists of these drugs generally cause many undesired side effects. A large amount of data has been gathered in recent years on the effects of active and passive immunization against cocaine, nicotine, PCP and methamphetamine in animal models, suggesting potential efficacy of these treatments in humans; and clinical trials are currently underway for vaccines against cocaine and nicotine.
[Back to top] Ion Channel Drug Discovery and Research: The Automated Nano-Patch-
Clamp© Technology
A.
Brueggemann, M. George, M. Klau, M. Beckler, J. Steindl, J.C. Behrends and N. Fertig
[Full text article]
Unlike the genomics revolution, which was largely enabled by a single technological advance (high throughput sequencing), rapid advancement in proteomics will require a broader effort to increase the throughput of a number of key tools for functional analysis of different types of proteins. In the case of ion channels -a class of (membrane) proteins of great physiological importance and potential as drug targets- the lack of adequate assay technologies is felt particularly strongly. The available, indirect, high throughput screening methods for ion channels clearly generate insufficient information. The best technology to study ion channel function and screen for compound interaction is the patch clamp technique, but patch clamping suffers from low throughput, which is not acceptable for drug screening. A first step towards a solution is presented here. The nano patch clamp technology, which is based on a planar, microstructured glass chip, enables automatic whole cell patch clamp measurements. The Port-a-Patch© is an automated electrophysiology workstation, which uses planar patch clamp chips. This approach enables high quality and high content ion channel and compound evaluation on a one-cell-at-a-time basis. The presented automation of the patch process and its scalability to an array format are the prerequisites for any higher throughput electrophysiology instruments.
[Back to top] The Isolated Perfused Rat Kidney Model: A Useful Tool for Drug
Discovery and Development
David
R. Taft
[Full text article]
Over the past three decades, the Isolated Perfused Rat Kidney (IPK) has been used to study numerous aspects of renal drug disposition. Among the available ex-vivo methods to study renal transport, the IPK allows for elucidation of the overall contributions of renal transport mechanisms on drug excretion. Therefore, IPK studies can provide a bridge between in vitro findings and in vivo disposition. This review paper begins with a detailed overview of IPK methodology (system components, surgical procedure, study design). Various applications of the IPK are then presented. These applications include characterizing renal excretion mechanisms, screening for clinically significant drug interactions, studying renal drug metabolism, and correlating renal drug disposition with drug-induced changes in kidney function. Lastly, the role of IPK studies in drug development is discussed. Demonstrated correlations between IPK data and clinical outcomes make the IPK model a potentially useful tool for drug discovery and evaluation.