Evotec has established a world-leading platform to support the discovery and validation of innovative disease modifying targets across different therapeutic areas, as well as to aid target deconvolution following a phenotypic screen.
Our capabilities to identify and validate targets comprises:
- Dedicated transcriptomic and proteomic profiling across cells and tissues followed by bioinformatics-driven data mining and hypothesis building
- Gene knock-out, knock-down and over-expression studies both in vitro and in vivo using relevant disease models
- Ex vivo imaging technology platform using tissue sections to study cellular and molecular events
- Phenotypic screening using complex cellular models to mimic disease
- Target deconvolution expertise using methods such as chemical biology (proteomics-based), transcriptomics, metabolomics, cell painting and CRISPR screening
Gene expression profiling
Gene activity is regulated very precisely and dynamically in cells, tissues or whole organisms. Observing changes in gene expression can give valuable insight into physiology, disease states, or drug action in biological systems. From early target identification to mode of action studies and biomarker identification the analysis of gene expression data supports the drug discovery processes.
Key activities include:
- In vitro or in vivo design and execution of transcriptomics studies, choosing the relevant technology for the question at hand. Evotec routinely uses a broad range of methods – from the monitoring of single genes in high-throughput screening with targeted approaches to full transcriptome methods like RNA-Seq or single cell RNA-Seq
- Bioinformatics analysis is performed by a team of experienced bio-informaticians and data scientists routinely assessing differential gene expression, pathway and interaction networks by analysis of raw data from transcriptomics studies and providing expert biological insight
- Considerable experience with the major repositories of expression data and signatures is available. Depending on project needs we also run customised in silico workflows, e.g. meta-analyses or integration of transcriptomics and predictive pharmacology data
Data handling and analysis tools
To analyse large datasets generated from deep RNA sequencing, Evotec has developed a powerful and user-friendly data analysis platform called PanHunter. Based on peer reviewed algorithms, the Evotec transcriptomics platform allows scientists to work interactively with gene expression data and to use state-of-the-art statistics and application tools.
In vitro target modulation capabilities
Evotec offers a variety of approaches, principally based on AAV and Lentivirus delivery systems for in vitro target modulation, including the powerful CRISPR technology. This genetic toolbox allows for target manipulation in a broad spectrum of disease related models and can be coupled to a broad range of relevant read-outs. Evotec uses CRISPR-Cas9 gene editing technology licensed under ERS Genomics, Merck/Millipore and the Broad Institute.
Evotec’s genetic screening platform applies whole-genome wide CRISPR and shRNA screening to aid target identification in a variety of cellular systems. Pooled and arrayed screening coupled to relevant read-outs aim to deconstruct complex biological phenotypes. An integrated bioinformatics pipeline enables relevant hit identification and biological annotation.
In the context of identifying relevant targets of hits from phenotypic screenings, CRISPR technology allows for assessing the contribution of each gene in the genome to compound activity. This offers a broad spectrum analysis of compound biology including identifying direct compound targets.
CRISPR and related technologies offer straight forward solutions for target validation. Evotec offers basic loss-of function and over-expression models but also more elaborate genome editing approaches in disease relevant models including primary cells and iPS-derived systems to confirm target contribution to disease phenotypes.
In vivo target validation
Targets arising from either disease relevant animal models, in vitro genetic experiments or the public domain need careful validation and confirmation, ideally prior to initiating a small molecule discovery programme. Evotec has developed a number of in vivo and ex vivo models across numerous therapeutic indications to help answer these questions.
Target engagement and modulation with small molecules or antibodies
Using a variety of techniques ranging from microdialysis to pharmacodynamic modelling with biomarker detection to transcriptomics/proteomics, Evotec aims to demonstrate early physiological function of the target in disease biology. This embraces a number of end points such as monitoring secreted factors, slice electrophysiology or signalling cascade modulation.
In vivo knockdown experiments
In the absence of suitable tool compounds alternative genetic approaches embracing stereotactic delivery of AAV-shRNA is routinely used to modulate in vivo expression levels and activity of the host protein, to investigate the effects this protein has on cell physiology and disease progression.
To maximise the efficiency and robustness of in vivo target modulation, Evotec has implemented an automated histology platform leveraging the expertise in image analysis and quantification.
The ability to study small molecules, biologics or genetic targets in the context of disease biology can only be truly leveraged through the application of phenotypic screening in a disease setting. With over 15 years of experience, Evotec offers a wide selection of phenotypic assays suitable for HTS and mechanism of action studies.
A variety of read-outs
From high-content imaging through to flow cytometry the most appropriate read-out for the mechanism of interest is applied.
Disease relevant in vitro models
Using target agnostic approaches, Evotec emphasises the use of disease relevance from the perspective of target tissue and cellular model through to stimuli and read-outs.
Primary cells and iPS models
Where possible Evotec employs primary cells or cell lines appropriate for the disease of interest : via the implementation of iPS cell lines and bespoke differentiation approaches, through the patient in a dish approach, Evotec aims to address human translation as early as possible.
Phenotypic screening at Evotec is complemented by genetic screening approaches to maximise the value of complex phenotypic assays to not only enable hit identification, but unbiased de-novo target identification and target deconvolution.
Chemical Proteomics and Target Identification
Evotec scientists have pioneered chemical proteomics applications to support target deconvolution of bioactive compounds emerging from phenotypic screens. Cellular target identification is the crucial step to enable further drug optimisation and development.
Evotec Cellular Target Profiling™ is a powerful technology to identify specific cellular compound targets in lysates from any cell type or tissue. Evotec’s chemical proteomics offering further comprises photoaffinity labelling for covalent target capture in live cells.
- Evotec’s chemical proteomics approaches use high-end quantitative mass spectrometry to reveal and verify specific cellular targets of a drug
- Evotec Cellular Target Profiling™ determines target-specific dissociation constants for the compound studied, ranking targets according to their likely physiological relevance
In silico target identification and druggability assessment
Evotec uses industry standard target interaction databases which combined with other ‘omics’ data can be used to construct target interaction maps. These networks can be significantly enhanced using our predictive pharmacology tools. Over 200 million bioassay datapoints are currently sourced for model building. Pathway analysis can be used to identify new and novel targets proposed to modulate a disease hypothesis. Such approaches are fundamental in target deconvolution and drug repurposing.
Evotec can run structure-based assessment studies for novel targets to provide an additional read on druggability when no/few druglike compounds are known. New 2D sequence based “switchability” calculations projected onto 3D structures have successfully been used for predicting allosteric sites for modulation, surfaces for PPIs and mAb binding.