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How are small molecule drugs developed?

How are small molecule drugs developed?

Small molecule drugs are organic compounds that affect a variety of molecular pathways, primarily by targeting key proteins. Such compounds have a low molecular weight, allowing them to easily penetrate cells. Small drugs are developed from leads that derive from rational drug design or isolated from nature. 

The discovery of small molecule drugs is a complex process that requires interdisciplinary expertise. Small molecules can be obtained through:

  • Rational drug design or the development of medications based on the study of the structure and function of target molecules. This is a methodological approach rather than a brute force approach conducted through a high volume of tests and experiments.

  • Isolated from natural sources, where a multidisciplinary approach is taken by using natural sources as pharmacological leads against many different diseases.

  • Phenotypic screening using cell-based assays. These assays measure a phenotype in physiological systems, which includes all preclinical assays formats using physiological systems. 

  • Target-based drug discovery, which involves target identification and validation, assay development, hit identification, hit to lead, lead optimization, and candidate selection and development.

What are small molecules used for? 

Small molecules have enormous biological and medicinal applications, most importantly being their potential as novel cancer therapies. Small molecules are one category of drugs that are defined by their production by chemical synthesis. Some examples include:

  • Aspirin

  • Felbamate

  • Varenicline

Small molecules are typically between 0.1 and 1 kDa in size and have relatively simple structures that do not trigger an immune response. One such key area for their application includes the identification and development of molecular entities capable of targeting RNA, offering almost endless biochemical applications such as: 

  • Regulation of polymerase reactions

  • Viral infectivity

  • Gene expression and storage


Dotmatics small molecule discovery software can help transform small molecule discovery by making your chemistry flow.