Small molecule drugs

Precise cell counting at every process step for reliable results

Small molecule drugs (SMDs) or pharmaceutical drugs are developed to interact with larger molecules in the cell, e.g. receptors. When serving as cell signaling activators, inhibitors or moderators, SMDs can be used to regulate cellular events and steer disease outcomes to benefit the patient.

Whether derived from biological compounds or synthesized, SMDs are used in disease treatment and prevention in a multitude of ways. A more recent approach is to develop SMDs to suit each patient’s specific variation of a disease. This approach is known as personalized or precision medicine, and tests drugs on cells from the individual patient. Precision drugs become important in the treatment of illnesses where the disease is based on different genetic mutations with the same phenotypic presentation e.g. cystic fibrosis1,2, or where the genetic make-up of the disease changes over time e.g. cancers3-5.

To best direct the efficacy of SMDs, they are often administered in vivo as small molecule drug conjugates (SMDCs), where a small molecule is linked to a ligand. This ensures a better stability of the SMD (e.g. within the bloodstream) and a potent linkage to the target cell within which the molecule is released to exert its effect6.

Close-up of a person wearing a blue glove who is about to pipette into a 96-well plate.

Another way to deliver drugs is by using the antibody-drug conjugates (ADCs), which have become a much-used method in developing precision medicine for disease treatments such as cancer. More recently, mesoporous silica nanoparticles (MSNs) are used for their biocompatibility to deliver therapeutic agents for cell targeting7.

Small molecule drug discovery is based on rigorous screening setups

When developing SMDs, the first step is to synthesize candidate drugs for the disease/disorder of focus, based on specific bioinformatics and protein-drug structural interaction studies8. Next, it is important to have/use an efficient screening system to test multiple drug candidates using microtiter plates on a large scale. Since this method involves working with very small volumes for testing, rigorous cell seeding density control becomes a crucial parameter for success and limiting variation in screening outcomes.

Often, depending on the disease in focus, a single quantitative screen is performed to determine the efficacy of the drug in a functional test. For example, the Forskolin-induced swelling of colonic organoids was used to test every single cystic fibrosis patient in the Netherlands to develop personalized drugs and thus provide them with a better treatment outcome nationwide9.

Next, several qualitative tests are useful in determining a range of concentration for testing the drug in further studies, to ensure doses are effective with the least number of negative side-effects. When there are only a few drug candidates, the next stage requires animal testing, and once the clinical trials once the lead drug candidate has been identified, clinical trials can begin.

Why is cell counting important during drug screening?

When seeding cells for adherent cultures and large-scale microtiter screening, it is important to have precise cell numbers in every setup to obtain reliable results. To achieve this, a robust cell counting method without human bias is desirable. The NucleoCounter® NC-202™ automated cell counter provides a 30-second cell count and viability assay which is robust and with the lowest variation in the market.

The NC-202™ is GMP (and 21 CFR Part 11) compliant and effortless to operate. This makes process scale-up and technology transfer for downstream development easier. The instrument needs no calibration, focus or adjustments, providing consistent results across instruments, users and sites.

The unique Via2-Cassette™ provides an all-in-one sample pipetting, staining and loading into the instrument and helps eliminate human error in cell counting. No pipettes, no exposure to (toxic) reagents and minimal clean-up qualifies the NucleoCounter® system as a very safe and easy to use option.

Functional tests for cancer drug candidates

Woman pipetting a sample into a NC-Slide A8™ 8-chamber sampling device next to a NucleoCounter® NC-3000™.

When shortlisting drug candidates, it is important to use a fast and reliable method to discern which work well and which do not. The NucleoCounter® NC-3000™ comes with several cancer assays, including a two-minute Cell Cycle Assay, Caspase 3/7, 8 and 9 Assay (apoptosis), Cell Vitality Assay (redox state by glutathione), and several more. The FlexiCyte™ Assay allows for setting up a user-defined assay to test up to eight samples at a time within minutes.

As a GMP/21 CFR Part 11-compliant instrument, the NC-3000™ can be used across drug development and manufacturing and also for QC validation of production batches.


  1. G Berkers, R v/d Meer, H Heijerman et al.: Lumacaftor/ivacaftor in people with cystic fibrosis with an A455E-CFTR mutation J Cyst Fibros. 2020; 25;S1569-1993(20)30910
  2. C Hine, P Nagakumar and M Desai: Small molecule drugs in cystic fibrosis. Arch Dis Child Educ Pract Ed. 2020; 19;edpract-2020-319009. Online print.
  3. M Barok, M Puhka, N Yazdi et al.: Extracellular vesicles as modifiers of antibody-drug conjugate efficacy. Barok: J Extracell Vesicles. 2021; 10(4):e12070.
  4. T Jiang, G Wang, Y Liu et al.: Development of small-molecule tropomyosin receptor kinase (TRK) inhibitors for NTRK fusion cancers. Acta Pharm Sin B. 2021; 11(2):355-372.
  5. Y Chen, Z Li, X Chen et al.: Long non-coding RNAs: From disease code to drug role. Acta Pharm Sin B. 2021; 11(2):340-354.
  6. C Zhuang, X Guan, H Ma et al.: Small molecule-drug conjugates: A novel strategy for cancer-targeted treatment. Eur J Med Chem. 2019; 163:883-895.
  7. S Stephen, B Gorain, H Choudhury et al.: Exploring the role of mesoporous silica nanoparticle in the development of novel drug delivery systems. Drug Deliv Transl Res. 2021; Online ahead of print.
  8. S Yuan, Y-Q Luo et al.: New drug approvals for 2020: Synthesis and clinical applications. Eur J Med Chem. 2021; 12;215:113284.
  9. AM Vonk, P van Mourik, AS Ramalho et al: Protocol for Application, Standardization and Validation of the Forskolin-Induced Swelling Assay in Cystic Fibrosis Human Colon Organoids. STAR Protocols 1, 100019. 2020.