How to mitigate the risk of low success rate in clinical trials

Three-Dimensional in Vitro Cell Culture Models in Drug Discovery

Drug development is a time-consuming and expensive process that proceeds through several stages from target identification to lead discovery and optimization, preclinical validation, and clinical trials, ending up in approval for clinical use. It is well known that 90 percent of drugs that reach clinical stage development never make it to FDA approval and commercialization. The cost of a failed drug is between $800m and £1.4bn. With this low success rate in clinical trials, drug discovery remains a slow and costly business. Hence, there is an urgent need for new technologies which can mitigate the risk of failures. Two of the most promising areas expected to improve the success rates in drug development are the development of novel biomarkers and the availability of new preclinical models that better imitate in vivo biology.  It is now well-accepted that culturing cells in three-dimensional (3D) systems that can mimic key factors of tissue is much more representative of the in vivo environment.

Cell-based assays are simple, fast and cost-effective as well as versatile and easily reproducible compared to cost-intensive animal models. To date, the majority of cell cultures used in drug discovery are two-dimensional (2D). However, it has become clear that 2D cultures do not necessarily reflect the complex microenvironment cells encounter in a tissue. One of the biggest influences shaping our understanding of the limited physiological relevance of 2D cultures is the growing awareness of the interconnections between cells and the extracellular matrix (ECM) surrounding them. The ECM is characterized not only by its biochemical composition, but also its physical and mechanical properties, with tissue stiffness being important for the maintenance of homeostasis. The composition of the ECM along with its physical properties can influence a cell’s response to drugs by either enhancing drug efficacy, altering a drug’s mechanism of action (MOA) or by promoting drug resistance. Moreover, traditional 2D cell cultures are not amenable to studies of oxygen or nutrient gradients as all cells are homogeneously exposed to the tissue culture medium. In contrast, cells encapsulated into 3D matrices provide opportunities to understand oxygen, growth factor and nutrient-mediated mechanisms leading to changes in cell phenotype and alterations in drug response.

Most 3D culture techniques are categorized into non-scaffold, anchorage-independent and scaffold-based 3D culture systems as well as hybrid 3D culture models. In scaffold-based 3D cultures, cells are embedded into the matrix and the chemical and physical properties of the scaffold material will influence cell characteristics. Thus, when selecting a 3D cell culture scaffold for a certain application, one will need to consider properties of the material that define physical factors such as porosity, stiffness, and stability in culture as well as biological properties such as cell compatibility or adhesiveness.

Animal-derived versus Synthetic Hydrogel Scaffolds

Whilst hydrogels display solid-like material properties, they are comprised of over 95% water by volume, and thus can provide a cell-liquid interface. Hydrogels may come from natural sources or can be synthetic, with the possibility of mixing different hydrogel materials to obtain hybrid hydrogels possessing new physical and biological properties. Hydrogels from natural sources are biocompatible and facilitate cell attachment through integrin receptors which leads to the activation of cell signaling pathways. Therefore, they can control cell survival, growth, and differentiation and can modulate the response to therapeutic approaches, including chemotherapy, immunotherapy, and radiation. However, hydrogels processed from natural sources have batch-to-batch variability of the purified scaffold which may interfere with pharmacological studies of drug response. Often, in addition to their major constituents, they contain many other components and are therefore poorly chemically defined. In contrast to animal-derived, the synthetic hydrogels are chemically and physically well-defined and often have tunable mechanical properties to achieve a desired stiffness or porosity. Well-designed, synthetic hydrogels, such as BiogelxTMpeptide hydrogels, are ideal materials to use as 3D cell culture scaffolds as they can mimic biological properties of ECM, be functionalized with defined adhesive moieties, and encapsulate growth factors. They have the advantage of being comparatively inexpensive, have reproducible material properties that are usually easy to tune through synthesis or crosslinking, and are reproducible, thereby supporting the acquisition of consistent results.

Additional peptide hydrogels currently being used in 3D culture are the yeast-derived peptides EAK16 and RADA16, peptide amphiphiles Fmoc-FF (Fluorenylmethoxycarbonyl- diphenylalanine) and Fmoc-RGD (Fluorenylmethoxycarbonylarginine-glycine-aspartic acid), the peptide hydrogel h9e based on the fusion of functional domains from a silk protein and a human calcium channel, FEFK and FEFKEFK which form hydrogels in the presence of a metalloprotease, and the MAX1 peptide which gelates under physiological conditions, and like h9e, has shear-thinning properties.

Applications of 3D Cultures in Drug Discovery

In recent years, 3D cell culture systems that model the in vivo microenvironment, and are therefore expected to yield results with higher predictive value for clinical outcome, are becoming more prominent in drug discovery. In addition, 3D cell culture models using human cells can circumvent drawbacks of mouse models that, aside from the high cost and ethical considerations, are not always able to accurately recapitulate human diseases or capture side effects of drugs such as liver toxicity. 3D cell culture technology with primary patient-derived tumor cells, and molecular profiling data, may open the door for preclinical screening of a personalized panel of drug candidates to improve outcome and reduce side effects of cancer therapy.



Langhans SA (2018) Three-Dimensional in Vitro Cell Culture Models in Drug Discovery and Drug Repositioning. Front. Pharmacol. 9:6. doi: 10.3389/fphar.2018.00006

Clinical Development Success Rates Report 2006-2015, Biotechnology Innovation Organisation & Biomedtracker


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