Enabling New Targets by Integrated Lead Discovery

Advances in biomedical science and technology are directing attention to drug targets that were previously deemed difficult or even "un-druggable". At Novartis, we have re-designed our approach to lead discovery to exploit these opportunities. Placing biological understanding of disease at the center of lead discovery strategies, we make extensive use of focussed screening in complex biologically relevant models. We emphasize methods that build confidence also in hits with weak activity and build on synergies between different technologies to answer key scientific questions in projects. Here we describe the scientific, cultural and organizational changes that had to be implemented to introduce this concept of "Integrated Lead Discovery"

Theoretical and Experimental Relationships between %-Inhibition and IC50 Data observed in HTS

The 4-parameter logistic Hill equation models the theoretical relationship between inhibitor concentration and %-inhibition in response, and is used to derive IC50 values as a measure of compound potency. This relationship is the basis for screening strategies that first measure %-Inhibition at a single, uniform concentration, and then determine IC50 values for compounds above a threshold. In screening practice, however, a “good” correlation between %-inhibition values and IC50 values is not always observed, and in literature there seems confusion about what correlation even to expect. We examined the relationship between %-inhibition data and IC50 data in a HDAC4 HTS data set and compared our findings to a series of numerical simulations that allowed the investigation of the influence of various parameters including uncertainties in the screening concentration and in Hill model parameters as well as influences of assay data quality parameters

How phenotypic screening influenced drug discovery – lessons from 5 years practice

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Molecular diversity management strategies for building and enhancement of diverse and focused lead discovery compound screening collections.

This publication describes processes for the selection of chemical compounds for the building of a high-throughput screening (HTS) collection for drug discovery, using the currently implemented process in the Discovery Technologies Unit of the Novartis Institute for Biomedical Research, Basel Switzerland as reference. More generally, the currently existing compound acquisition models and practices are discussed. Our informatics, chemistry and biology-driven compound selection consists of two steps: 1) The individual compounds are filtered and grouped into three priority classes on the basis of their individual structural properties. Substructure filters are used to eliminate or penalize compounds based on unwanted structural properties. The similarity of the structures to reference ligands of the main proven druggable target families is computed, and drug-similar compounds are prioritized for the following diversity analysis. 2) The compounds are compared to the archive compounds and a diversity analysis is performed. This is done separately for the prioritized, regular and penalized compounds with increasingly stringent dissimilarity criterion. The process includes collecting vendor catalogues and monitoring the availability of samples together with the selection and purchase decision points. The development of a corporate vendor catalogue database is described. In addition to the selection methods on a per single molecule basis, selection criteria for scaffold and combinatorial chemistry projects in collaboration with compound vendors are discussed

The Novartis compound archive -- from concept to reality.

As HTS technologies come of age, pharmaceutical companies are focusing increasingly on the quality of their screening collections. Storage conditions and their influence on compound stability and solubility are debated intensely. At Novartis, a strategy was developed that is different to most other companies: (1) compounds unsuitable for storage in solution are excluded by computational methods; (2) compounds are stored at 4 degrees C/20% relative humidity in a DMSO/water mixture to avoid freeze-thaw cycles and water uptake and to allow rapid plate replication; (3) resolubilisation of compounds at regular intervals

Screening for Mevalonate Pathway Inhibitors using sensitized bacteria strains

A simple, optical density based assay for mevalonate pathway inhibitors was developed, that relies on sensitized S. aureus strains and that is fully compatible with high-density screening in 1536-well format. S. aureus strains were constructed in which the mevalonate pathway genes are regulated by an IPTG (isopropyl--D-thiogalactopyranoside)-inducible promoter. Inhibitors of the target enzyme appeared more potent under low IPTG conditions, where a lower amount of enzyme is available to the bacteria, than under high IPTG conditions. This effect was used to bias the hits towards specific inhibitors. Screens were run against the enzymes HMG-CoA synthase (MvaS) and mevalonate kinase (mvaK1), mevalonate diphosphate decarboxylase (mvaD) and phosphomevalonate kinase (mvaK2). The later three enzymes are regulated as an operon. These assays allowed the discovery of potent antibacterial leads that led to an active lead optimization program. The example presented here demonstrates that a sensitization strategy can be successfully applied to > 1 Mio compound HTS in a high density 1536-well format

Stability of screening compounds in wet DMSO.

The impact of storage conditions on compound stability and compound solubility has been debated intensely over the past 5 years. At Novartis, the authors decided to opt for a storage concept that can be considered controversial because they are using a DMSO/water (90/10) mixture as standard solvent. To assess the effect of water in DMSO stocks on compound stability, the authors monitored the purity of a subset of 1404 compounds from ongoing medicinal chemistry projects over several months. The study demonstrated that 85% of the compounds were stable in wet DMSO over a 2-year period at 4 degrees C. This result validates the storage concept developed at Novartis as a pragmatic approach that takes advantage of the benefits of DMSO/water mixtures while mediating the disadvantages. In addition, the authors describe how purity data collected over the course of the chemical validation of high-throughput screening actives are used to improve the analytical quality of the Novartis screening deck

Closing the gap between centralized and decentralized compound management approaches.

The demand for organized storage concepts to maintain, collect and distribute compounds has grown not only at pharmaceutical companies, but also at smaller research organizations and academic laboratories where there is the demand to store and retrieve substances systematically. However, budget limitations have prevented these smaller groups from buying costly storage systems offered by specialized commercial vendors. On the other hand, within pharmaceutical companies a need for inexpensive and flexible storage concepts has developed and complements the existing automated archives. For reasons of efficiency, most companies have built centralized facilities holding large collections of internal medicinal chemistry compounds to assist various, globally distributed research programs. This standardization and centralization though is not always ideal for a global organization. Therefore, site specific and localized requirements need to be addressed to ensure quick on site access to compounds without losing the global accessibility to them. In this article, we describe an approach towards a low cost and highly flexible store concept with manual compound stores of variable design addressing local needs, created to complement the existing automated stores. A key component of our implementation is the Compound Store Manager software which is capable of administering the different global stores. The developed backend system and centralized data management facilitates the operation and integration of the stores into an existing store environment