Towards a comprehensive strategy to target identification and mode of action elucidation for bioactive small molecules

Recorded On: 02/06/2018

Target identification and the elucidation of mechanism of action (MoA) for bioactive small molecules are key steps in phenotypic and
pathway-centric approaches to drug discovery. In recent years, various strategies have been introduced and refined that address these
questions from different angles and provide glimpses of different aspects of the often complex physical and functional interactions of
a compound when exerting its biological effects in vivo: Affinity-based approaches aim to describe the (protein) interactome of drug
candidates which constitutes the full spectrum of potential efficacy and off-targets. These include quantitative chemoproteomics such
the combinations of small molecule affinity chromatography or photo-affinity labeling with mass spectrometry-based protein
identification and quantitation, as well as large scale implementations of biophysical approaches in vitro such as size-exclusion
chromatography. On the other hand, a variety of functional genetic and genomic strategies have been introduced that include
(unbiased or targeted) generation of compound-resistant cells followed by identification of the resistance-conferring genetic changes
by next generation sequencing as well as the utilization of genome-wide knock-down and deletion approaches including RNAi and
CRISPR. In these cases, the generation of target/MoA hypotheses is based on the elucidation of functional relationships between a
gene and the compound-induced phenotype. In contrast to the individual protein or gene resolution provided by these former
strategies, cellular profiling approaches interrogate the overall cellular response to compound treatment at the level of signaling, gene
expression, viability or metabolism. Finally, knowledge-based approaches rely on empirical and computational approaches and a
reference collection of compounds with known targets and MoA to make inferences. Since the various approaches provide orthogonal
information and have unique strengths, multipronged strategies are best suited to provide a comprehensive picture of the target/MoA
space of a bioactive compound and ultimately enable successful elucidation of the efficacy target and its functional link to the
phenotype under investigation. The various classes of target ID platforms will be presented and discussed in the context of real-life
applications.

Markus Schirle

Novartis Institutes for Biomedical Research

Markus Schirle received his master’s degree in biochemistry at University of Tubingen, Germany and his Ph.D. in 2001 for his work with H.G. Rammensee/Tubingen on the identification of disease-associated MHC peptides by mass spectrometry-based approaches. After postdoctoral studies in proteomics with Alfred Nordheim/Tubingen, he joined Cellzome (Heidelberg, Germany, now part of GSK) from 2001 – 2007 where his work focused on protein and small molecule affinity proteomics for target identification (ID) and mechanism of action (MoA) studies. Since joining Novartis in 2007, he established a platform for chemical and affinity proteomics for target ID and MoA studies; since 2013 he is group leader for the ChemGx hub which also covers biophysical and biochemical in vitro methods for studying protein–compound interactions. The hub is responsible for affinity-based approaches to target ID/MoA and hit finding for Novartis drug discovery projects globally.

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