Multi-omics for next-generation therapy development

Next-generation drugs, such as antibodies, targeted protein degraders, and cell and gene therapies, offer substantial promise for treating diseases. However, their development and production involve significant complexity and challenges. 

Image Credit: Shutterstock.com/PreciousJ 

From high expenses and lengthy development timelines to regulatory hurdles, the journey from discovery to market is demanding.

A major hurdle in developing next-generation treatments is their high biological complexity; a thorough understanding of disease biology is needed to target specific cells or molecular components and produce a desirable therapeutic result.

As a result, limited understanding of the underlying molecular mechanisms has prevented the identification of an appropriate target.

Consequently, to ensure effective pharmaceutical development and production, biological complexity must be taken into consideration. Starting as early as therapeutic discovery, researchers must use model systems and screening assays that better reflect human biology, capturing subtle molecular alterations that can impact safety and effectiveness.

Using innovative technologies from the outset

During pharmaceutical discovery, physiologically relevant disease models, including patient-derived induced pluripotent stem cells (iPSCs) and organoids, should be employed to help capture human diversity.

With this in mind, Evotec relies on industrialized iPSC-based platforms for therapeutic discovery, using them from early lead optimization through to regulatory safety research.

This includes using novel “clinical-trial-in-a-dish” models designed to mimic diverse patient responses in vitro. The strong efficacy of these models helps identify candidates while flagging those with possible toxicity.

In addition, iPSCs are laying the foundation for scalable, off-the-shelf treatments by enabling affordable, high-throughput cell therapy production. However, due to their biological complexity, the true potential of iPSCs can only be realized when next-generation technologies, including omics, are used to guide the development workflow.

Driving therapeutic discovery with omics

Over the past few decades, molecular biology methods have advanced significantly. Researchers once studied just a handful of proteins requiring large quantities of input biological material (such as Western blots).

Now, the rise of low-input and high-throughput omics technologies enables the simultaneous analysis of thousands of genes, transcripts, proteins, and metabolites. Multi-omics methods have become a valuable part of therapeutic discovery, offering the capacity to rapidly produce huge quantities of relevant biological data.

More recently, the following omics strategies have helped fuel further progress in therapeutic discovery:

  1. Single-cell and spatial resolution: Transitioning from conventional bulk omics to single-cell and spatial strategies (e.g., single-cell transcriptomics, spatial transcriptomics, spatial proteomics, high-sensitivity proteomics) is transforming therapeutic discovery, delivering insights into the molecular states and spatial organization of individual cells or cell types.
  1. Time-resolved multi-omics: Merging omics data, including genomics, transcriptomics, proteomics, and metabolomics over a time course (e.g., from longitudinal patient data), provides deeper insights into disease progression, enabling the development of therapies that act prior to symptom onset. 

    On the other hand, in cell culture experiments, linking the omics readouts at different time points can support the understanding of causal biological relationships, e.g., between transcript and protein levels.
  1. AI/ML-driven data evaluation: The use of machine learning (ML) and artificial intelligence (AI) strategies is increasing in multi-omics evaluation, supporting complex dataset integration and pattern identification. These innovative strategies significantly improve both accuracy and speed, while enabling a deeper, more comprehensive understanding of disease mechanisms.

Integrating omics into the drug discovery pipeline

Evotec embraces innovative omics advancements with its PanOmics platform. The company’s proprietary E.MPD (Evotec Molecular Patient Database) is central to this platform, producing data from thousands of patient samples. This technology helps to understand complex disease biology and fuels progress in therapeutic discovery.

Implemented omics methods include mass-spectrometry-based proteomics, which is a highly effective strategy for discovering hits for previously “undruggable” proteins and identifying new protein biomarkers that are inaccessible by antibody-based technologies. This whitepaper provides more information on the power of MS-based proteomics.

In addition to hit identification, Evotec’s PanOmics platform is transforming other aspects of therapeutic discovery, including both in vitro and in vivo disease modeling, target identification, biomarker discovery, and patient stratification.

The smooth integration of multi-omics throughout the drug discovery pipeline ultimately boosts the likelihood of success, ensuring more effective candidate selection, reducing attrition rates, and accelerating the path to the clinic. 

Increasing the versatility of drug discovery

To speed up the discovery of next-generation treatments, agnostic technologies, including omics, are growing in importance. Rather than being restricted to specific diseases or pharmaceutical modalities, these technologies focus on revealing the underlying molecular mechanisms.

Many omics technologies are classified as agnostic, meaning they are unbiased and do not require any domain-related knowledge regarding the drug modality or therapeutic area.

Experiments can be developed without forming an a priori hypothesis regarding the target proteins, providing versatility in pharmaceutical discovery and development. An example of a versatile agnostic technology applicable in pharmaceutical discovery is mass-spectrometry-based proteomics, which replaces conventional targeted immuno-based assays to help capture the complete complexity of the biological system.

Drug repurposing is another growing trend increasing flexibility in drug discovery. This strategy uses innovative computational techniques, including transcriptomics and AI, to investigate promising novel applications for therapies already on the market.

Collaborations fuel innovation, from discovery through to market

For organizations seeking to develop state-of-the-art modalities, collaborating with a CRO/CDMO such as Evotec is essential for success. Evotec provides standardized, quality-assured platforms that seamlessly integrate innovative technologies, helping organizations remain at the forefront of pharmaceutical discovery and development.

The company also recognizes integration as a critical factor for success. It offers a completely integrated drug discovery and development program, INDiGO®, helping to de-risk candidates and guarantee a seamless transition from initial concept to final product. 

As treatments become more complicated and individualized, the demand for affordable production with higher success rates continues to grow. Lower prices and reduced risks can be achieved by having cell-line development, process development, and clinical and commercial production under one roof, as is the case with Evotec’s Just – Evotec Biologics’ J.POD facilities.

Located in the United States (Toulouse J.POD now belongs to Sandoz), this facility offers the infrastructure for continuous production, setting the stage for scalable and cost-effective biotherapeutics. 

In addition to Evotec’s technical abilities, the people behind the partnerships play an equally valuable role. The company’s dedicated research team collaborates closely with its partners to advance each project, leveraging broad, cross-disciplinary expertise in technological and therapeutic areas, while also valuing communication, adaptability, and flexibility.

About Evotec

Evotec is a life science company that is pioneering the future of drug discovery and development. By integrating breakthrough science with AI-driven innovation and advanced technologies, we accelerate the journey from concept to cure – faster, smarter, and with greater precision. Our expertise spans small molecules, biologics, cell therapies and associated modalities, supported by proprietary platforms such as Molecular Patient Databases, PanOmics and iPSC-based disease modeling.

With flexible partnering models tailored to our customers’ needs, we work with all Top 20 Pharma companies, over 800 biotechs, academic institutions, and healthcare stakeholders. Our offerings range from standalone services to fully integrated R&D programs and long-term strategic partnerships, combining scientific excellence with operational agility.

Through Just – Evotec Biologics, we redefine biologics development and manufacturing to improve accessibility and affordability. With a strong portfolio of over 100 proprietary R&D assets, most of them being co-owned, we focus on key therapeutic areas including oncology, cardiovascular and metabolic diseases, neurology, and immunology.

Evotec’s global team of more than 4,500 experts operates from sites in Europe and the U.S., offering complementary technologies and services as synergistic centers of excellence. Learn more at www.evotec.com and follow us LinkedIn and X/Twitter @Evotec


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Last updated: Aug 19, 2026 at 11:48 AM

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