Navigating Phase 1: Target Identification and Validation in Drug Discovery

Drug discovery is a journey defined by high stakes and complex challenges. From the initial identification of a target to the rigorous demands of human trials, the path to a successful therapeutic is often fragmented, leading to high attrition rates where promising compounds fail to translate into effective medicines.

This blog series outlines a comprehensive strategy to overcome these hurdles. By leveraging human-relevant models and advanced translational tools early and consistently, researchers can bridge the gap between the laboratory and the patient.

We’ll explore this journey through three phases – foundation and discovery, preclinical optimization, and translational execution.

Phase 1 establishes the groundwork for successful drug development by identifying disease-relevant targets, confirming their biological roles, and assessing early compound activity. Modern genetic tools, high-throughput screening, and advanced in vitro models support faster, more precise decisions, advancing the most promising targets and compounds to later development stages.

Target Identification: Confirming Target Relevance with CRISPR/Cas9 and 2D Cell Line Models

Target identification aims to pinpoint molecular drivers of disease that can be targeted by therapeutics. Advances in gene-editing platforms, particularly clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9), have significantly strengthened target discovery strategies. (The Art of Finding the Right Drug Target: Emerging Methods and Strategies - PMC).

CRISPR-based functional screening enables systematic gene perturbation to demonstrate the roles of specific genes in disease pathways. By observing phenotypic consequences of CRISPR-mediated knockout (CRISPR-KO), inhibition (CRISPRi), or activation (CRISPRa), researchers gain mechanistic insights to guide rational target selection. Guide RNAs direct the Cas nuclease to precise genomic locations, allowing precise gene disruption or transcriptional modulation. These screens are often combined with multi-omics technologies and high-throughput sequencing to map disease-driving pathways.

Orthogonal approaches, such as combining RNA interference (RNAi) with CRISPR, further strengthen confidence in target selection. They ensure that observed effects in two-dimensional (2D) cell line models accurately reflect modulation of the intended gene and confirm target relevance before progressing to more complex systems. (A Pipeline for Drug Target Identification and Validation - PMC).

By integrating CRISPR functional genomics with validated 2D cell line models, researchers can efficiently confirm target relevance, reduce false-positive rates, and establish a robust foundation for downstream discovery activities.

Early Screening: Accelerating Hit Identification through High-Throughput Platforms

Once validated targets are prioritized, early screening identifies compounds showing initial activity. High-throughput platforms enable efficient evaluation of large compound libraries in relevant cellular systems.

OmniScreen™

OmniScreen is a large-scale cancer cell line screening platform that enables cost-effective assessment of compound efficacy across deeply characterized cancer cell lines. It provides flexible panel selection and supports gene expression and biomarker analyses. The platform also integrates with matched xenograft models and real-time analytics to facilitate smooth progression from in vitro findings to in vivo evaluation.

MuScreen

MuScreen provides complementary in vivo insights by evaluating immunotherapeutic agents or combinations in syngeneic and tumor homograft models. The platform integrates RNA sequencing, immune profiling, and histopathology to identify responder populations and early pharmacodynamic markers, enhancing the assessment of immunomodulatory mechanisms.

OrganoidXplore™

OrganoidXplore enables high-throughput screening across patient-derived organoid (PDO) models. These organoids retain the genetic, molecular, and phenotypic features of the original tumors, allowing clinically relevant assessment of drug sensitivity, resistance, and biomarker expression. PDOs provide a powerful system for assessing drug responses in patient-specific tumor models, supporting the identification of effective drug combinations and predicting patient prognosis.

Together, OmniScreen, MuScreen, and OrganoidXplore form an integrated early screening ecosystem, evaluating compounds across multiple model systems to increase confidence in hit identification and guide subsequent target validation.

Target Validation: Enhancing Translational Relevance through Advanced In Vitro Models

Target validation confirms the mechanism of action (MOA) and biological relevance of lead compounds before preclinical development. Advanced three-dimensional (3D) in vitro models improve predictive accuracy by replicating tissue architecture, cellular heterogeneity, and human-specific responses.

Organoids derived from tumor tissues or patient samples organize into structures that preserve the genetic, molecular, and phenotypic features of the original tumor. These organoids enable assessment of target engagement, downstream signaling, and drug responses in a human-relevant context. By capturing aspects of tumor heterogeneity, they provide a robust platform for validating mechanisms of action and supporting early data-driven decisions in oncology drug discovery.

3D bone marrow models extend these capabilities to hematological malignancies. Scaffold- and hydrogel-based systems incorporating mesenchymal stem cells, osteoblasts, and adipocytes recreate physiological gradients, hypoxia, and stromal interactions. These models reveal mechanisms driving tumor growth and drug resistance. They also support evaluation of bone remodeling and therapeutic efficacy in clinically relevant systems for diseases such as multiple myeloma (MM) and leukemia.

High-content imaging complements these models by capturing morphological, functional, and molecular changes, allowing detailed analysis of compound effects. When combined with pharmacology and bioanalytical services, this integrated approach provides human-relevant, data-rich insights that strengthen early decision-making and increase confidence before progressing to preclinical and clinical studies.

Specialized Solutions: Leveraging Expertise for Complex Targets and Disease Contexts

Some targets and disease settings require highly specialized model systems. KRAS-driven cancers are challenging to treat due to activating mutations, complex signaling dynamics, and pronounced tumor heterogeneity. Advanced preclinical models, including PDOs and three-dimensional microphysiological systems (MPS), allow detailed evaluation of KRAS-targeted therapies, ranging from small molecules to antibody-drug conjugates and combination regimens.

Antibody-drug conjugates (ADCs) require careful assessment of binding specificity, internalization, and cytotoxic payload delivery. The 3D spheroids and tumoroids provide physiologically relevant environments to evaluate selectivity, internalization kinetics, and tumor cell killing. Off-target binding assessments, high-content imaging, and in vivo models, including patient-derived xenografts (PDX), humanized systems, and syngeneic models, support ADC pharmacology, pharmacokinetics, and efficacy studies. Bioanalytical assays, such as drug-to-antibody ratio measurements and stability analyses, generate regulatory-ready data to guide early decision-making.

Acute myeloid leukemia (AML) presents additional challenges due to genetic complexity, rapid disease progression, and treatment resistance. Advanced 3D bone marrow models recreate microenvironmental interactions that shape AML biology, enabling evaluation of MOA, resistance mechanisms, and therapeutic efficacy in physiologically relevant systems. PDOs and MPS platforms support testing of targeted agents, immunotherapies, and combination strategies, enhancing translational relevance and facilitating personalized therapy development.

Conclusion

Phase 1 of drug discovery, encompassing target identification and validation, establishes the foundation for successful therapeutic development. Combining CRISPR and validated 2D cell line systems for target identification, high-throughput platforms such as OmniScreen, MuScreen, and OrganoidXplore for early hit discovery, and advanced 3D in vitro models for rigorous target validation allows researchers to make confident, data-driven decisions. These insights support informed progression to preclinical and clinical studies.