3D Cell Culture Tools and Techniques: Building Better Models for Drug Discovery

The way we model human biology in the lab is rapidly changing. For decades, traditional two-dimensional (2D) cell cultures have been considered the gold standard for preclinical drug testing. Yet over 95% of drug candidates identified in 2D systems fail when tested in animals or humans because they lack the structural and functional complexity of real tissues.

With the passage of the FDA Modernization Act 2.0, alternatives to animal testing, collectively known as New Approach Methodologies (NAMs), are gaining momentum. Among these, three-dimensional (3D) cell culture models are emerging as powerful tools for creating predictive, physiologically relevant platforms for drug discovery and toxicology.

What Are 3D Cell Culture Models?

3D cell culture allows cells to grow and interact in environments that mimic the architecture, mechanics, and signaling of human tissues. Unlike flat 2D monolayers, 3D cultures support cell–cell and cell–matrix interactions, better replicating in vivo biology.

There are three main classes of 3D models:

      •   Spheroids: Simple aggregates of cells that form through self-assembly. Applications: tumor modeling, drug                     screening, immunotherapy testing.
      •   Organoids: Self-organized structures derived from pluripotent stem or progenitor cells that recapitulate organ-               specific architecture and function. Applications: developmental biology, precision medicine, disease modeling.
      •   Bioprinted Tissue Constructs: Engineered 3D constructs created by layer-by-layer deposition of bioinks (cells +             hydrogels). Applications: regenerative medicine, tissue engineering, advanced drug testing.

How Are 3D Structures Formed?

Scaffold-Free Methods

      •   Hanging drop plates – Rely on gravity to aggregate cells into spheroids.
      •   Ultralow attachment (ULA) plates – Prevent cells from sticking, forcing them to form aggregates.
      •   Spinner flasks / rotating bioreactors – Keep cells suspended for dynamic aggregation.
      •   Magnetic levitation – Uses magnetic nanoparticles to guide cell assembly.

Scaffold-Based Methods

      •   Hydrogels (e.g., collagen, Matrigel, alginate, PEG) provide an ECM-like environment.
      •   Decellularized ECM retains native biological cues for tissue-specific functions.
      •   Porous scaffolds (e.g., PLGA, ceramics) support vascularization and nutrient diffusion.