CRISPR & Drug Discovery: An Overview

Introduction to CRISPR & Drug Discovery

Drug discovery is the process by which new candidate medications are identified and optimized with the aim of treating or curing diseases. This scientific and often interdisciplinary field involves a series of methodical steps – the drug discovery workflow stages - that are designed to identify effective and safe compounds that can modulate biological targets in a desired way to alleviate or eliminate symptoms of diseases. The entire process aims to validate the efficacy, safety, and pharmacokinetics (how the drug is absorbed, distributed, metabolized, and excreted) of the candidate compounds. Given the complexity and high standards for both safety and efficacy, drug discovery is a long, laborious, and expensive process, often requiring many years and substantial financial investment (10+ years and >1 bio $). Thus, optimizing drug discovery workflows for scientists, to reduce time, costs and increase the efficiency of drug development, is primordial. Despite the challenges, it is a critical process that has led to the development of numerous medications that have dramatically improved human health. A standard drug discovery workflow is composed of five steps, as represented, in Figure 1.

CRISPR Drug Discovery Workflow Stages by Cytosurge

Figure 1 - Drug discovery workflow and its five stages by Cytosurge.

The drug discovery workflow is usually initiated by a disease or clinical condition lacking suitable treatment options. In most cases, observations from basic academic or clinical research provide the initial hypothesis that modulation of the activity of a protein or pathway might result in a therapeutic effect in a disease state. Subsequently, a target is identified and further validated before it progresses into the lead identification phase. During this phase, millions of compounds are screened to determine substances that act on the identified target. 

The identified compounds that show activity (100s) are further characterized using a plethora of assays. After the hit validation process, the potential therapeutics are narrowed down (10s) and the best candidates are further validated and optimized. In the next step, toxicity and efficacy are characterized in disease models (animal and organoid). Usually, after this process, a unique candidate is identified that will move to the pre-clinical and clinical studies. However, most drugs fail in the clinical phase due to two main reasons: 1. They do not work or 2. They are not safe. Therefore, the process of target identification and validation is crucial in drug development to address point 1. 

Do you want to learn more about gene editing techniques

The Impact of CRISPR on Drug Discovery Stages

Genome engineering has the potential to significantly advance the field of drug discovery, and CRISPR is rapidly emerging as the go-to tool for this purpose. Known for its precise editing capabilities and minimal off-target effects, CRISPR can streamline the drug discovery pipeline, ultimately leading to a greater number of rigorously validated drugs entering clinical trials.

Precision & Efficiency


Fasten Discovery Process

From identifying and validating genetic targets to constructing biologically relevant disease models, CRISPR genome engineering offers a fast, accurate, and cost-effective solution to accelerate your research. In pre-clinical research, genome manipulation is crucial for studying gene functions. While early assays like RNA interference (RNAi) screens were limited by partial gene silencing and high off-target risks, first-generation gene editing tools like zinc finger nucleases (ZNFs) and transcription activator-like effector nucleases (TALENs) offered more precision but were time-consuming and expensive. CRISPR-Cas systems overcome these limitations, offering an easier, more efficient approach to gene editing.

The development of the CRISPR-Cas systems as a genome engineering tool initiated a revolution in modern biology. In combination with the rapid expansion of reference genomes as well as personalized genomic sequence information, CRISPR-Cas based technologies enable nearly unlimited genetic manipulation, even in formerly difficult to target context such as human cells. The focus of CRISPR-Cas in the clinical context is centered on curing Mendelian diseases. However, the system holds great promises in accelerating the drug discovery process, to treat complex heritable and somatic diseases. 

The first step of the drug discovery workflow involves identifying and confirming a 'target' that plays a role in a disease condition. Targets can range from proteins and genes to entire pathways or disease-related metabolites. A target must be clinically, and commercially viable, and above all, druggable in an effective and safe way. 

Druggability” refers to a target's accessibility to potential drug molecules and its ability to produce a measurable biological response upon interaction. Targets are identified through various methods such as loss and gain of function assays (e.g., RNAi, CRISPR-ko, CRISPRa, CRISPRi screens), bioinformatic analyses like genome-wide association studies, or hypothesis-driven approaches.

Yet, target identification using screens or data base mining provides only correlative information between the observed phenotype and the genotype. As an example, it remains difficult to understand the link between genetic variation and disease predisposition, phenotypic disease development and treatment response. In addition, traditional methods for studying the link between genotype and phenotype have limitations, such as the difficulty in obtaining matched samples and the time required to perform such studies.

To perform target validation, monoclonal cell lines were employed to clarify relationships between genotype and phenotype. The advent of CRISPR-Cas technology has revolutionized this area by facilitating the creation of isogenic cell lines. This technology allows for precise targeting of genes, splice variants, or even multiple genes within a pathway (multiplex editing), making it highly effective for studying diseases and potential drug targets. CRISPR-Cas can also be used to generate models for studying point mutations or single nucleotide polymorphisms (SNPs) in genes that are linked to specific diseases. These cellular models enable comprehensive studies using a variety of biochemical, molecular, and cellular assays, supplemented by more advanced models like organoids and transgenic animals. 

In compound screening, large libraries of small molecules or proteins are screened for their biological activity, specifically their impact on a validated target phenotype. Compounds that show promise in initial screenings are called 'hits.' Transgenic reporter cell lines, generated by CRISPR-Cas and HDR, are a cost-effective tool for this. These cell lines contain a genetic element that produces a detectable signal, such as fluorescence, when the target is affected. Alternatively, in vitro methods are used, especially when the target is a well-understood protein. Here, the protein is produced and purified, and its interaction with the compounds is quantified. Often, both approaches are combined for comprehensive screening.

These hits are then validated through further tests to confirm their potential as drug candidates. After multiple rounds of screening, a few hundred compounds undergo further validation, often using a different read-out or the previously used isogenic cell lines.  Compounds that significantly alter or reverse the phenotype are considered strong candidates. The 'hit' compounds are then chemically engineered and tested to improve their stability, solubility, selectivity, efficacy, and pharmacokinetic properties, resulting in 'lead' compounds. Lead compounds undergo rigorous testing in vitro (in test tubes - "in cellulo") and in vivo (in animal models) to evaluate their safety, efficacy, and pharmacokinetics. Ultimately, only a handful, often just 1-2, proceed to the next stage of drug discovery.

Prior to clinical trials are pre-clinical development. This stage of the drug discovery process consists mainly of in-depth phenotypic validation using cellular and animal models. Furthermore, the toxicity, the efficacy and the pharmacokinetics are assessed. At this stage of the drug discovery process, only one compound will enter the clinical phase. In the clinical phase, the toxicity is assessed again in healthy volunteers before the drug will be tested in broad clinical studies. Clinical trials are carried out in several phases (Phase I, II, III, and sometimes IV) to test the drug's safety, optimal dosage, and efficacy in humans.

  • Phase I: Primarily focuses on safety in a small number of healthy volunteers.
  • Phase II: Looks at the drug's efficacy and optimal dosage in a larger number of patients.
  • Phase III: Further assesses efficacy and monitors adverse reactions in a large cohort of patients.
  • Phase IV: Post-marketing studies after the drug is approved and released.

The final stages comprise FDA approval, drug production, and further monitoring. 

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Hughes, James P., et al. "Principles of early drug discovery." British journal of pharmacology 162.6 (2011): 1239-1249.

Fellmann, Christof, et al. "Cornerstones of CRISPR–Cas in drug discovery and therapy." Nature reviews Drug discovery 16.2 (2017): 89-100.

Genetic Engineering & Biotechnology News - Short news article how CRISPR is accelerating drug discovery consulted in September 2023. URL:

Salame, Natasha, et al. "Recent Advances in Cancer Drug Discovery Through the Use of Phenotypic Reporter Systems, Connectivity Mapping, and Pooled CRISPR Screening." Frontiers in Pharmacology 13 (2022): 852143.

Karki, Roshan, et al. "Defining “mutation” and “polymorphism” in the era of personal genomics." BMC medical genomics 8 (2015): 1-7.