Small molecule

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In the fields of pharmacology and biochemistry, a small molecule is a low molecular weight organic compound which is by definition not a polymer. The term small molecule, especially within the field of pharmacology, is usually restricted to a molecule that also binds with high affinity to a biopolymer such as protein, nucleic acid, or polysaccharide and in addition alters the activity or function of the biopolymer. The upper molecular weight limit for a small molecule is approximately 800 Daltons which allows for the possibility to rapidly diffuse across cell membranes so that they can reach intracellular sites of action. In addition, this molecular weight cutoff is a necessary but insufficient condition for oral bioavailability.

Small molecules can have a variety of biological functions, serving as cell signaling molecules, as tools in molecular biology, as drugs in medicine, as pesticides in farming, and in many other roles. These compounds can be natural (such as secondary metabolites) or artificial (such as antiviral drugs); they may have a beneficial effect against a disease (such as drugs) or may be detrimental (such as teratogens and carcinogens).

Biopolymers such as nucleic acids, proteins, and polysaccharides (such as starch or cellulose) are not small molecules, although their constituent monomers — ribo- or deoxyribonucleotides, amino acids, and monosaccharides, respectively — are often considered to be. Very small oligomers are also usually considered small molecules, such as dinucleotides, peptides such as the antioxidant glutathione, and disaccharides such as sucrose.



Most drugs are small molecules, although some drugs can be proteins, e.g. insulin. Many proteins are degraded if administered orally and most often cannot cross the cell membranes. Small molecules are more likely to be absorbed, although some of them are only absorbed after oral administration if given as prodrugs.

Many dietary supplements are small molecules (but not herb extracts, such as ginkgo).

Primary and Secondary metabolites

For organisms to produce small molecules they need one or more specialized enzymes (to create and destroy), which as a result are not that varied in vertebrates (recent and small + slow population size), but very common in soil bacteria (such as streptomyces) and fungi, which in particular secrete antibiotics.

Plants also have several secondary metabolites, which play a role in cell signalling, pigmentation or in defence, several of which have also been used as drugs (medical and recreational):

Research tools

A further example, Cell culture example of small molecules as a tool instead of a protein. in cell culture to obtain a pancreatic lineage from mesodermal stem cells the retinoic acid signalling pathway must be activated while the sonic hedgehog pathway inhibited, which can be done by adding to the media anti-shh antibodies, Hedgehog interacting protein or cyclopamine, the first two are protein and the last a small molecule.[1]

Enzymes and receptors are often activated or inhibited by endogenous protein, but can be also inhibited by endogenous or exogenous small molecule inhibitors or activators with can bind to the active site or on the allosteric site.

An example is the teratogen and carcinogen phorbol 12-myristate 13-acetate which is a plant terpene which activates protein kinase C promoting cancer, making it a very useful investigative tool.[2] There is also interest in creating small molecule artificial transcription factors to regulate gene expression, examples include wrenchnol (a wrench shaped molecule).[3]

Binding of ligand can be characterised using a variety of analytical techniques such as surface plasmon resonance or dual polarisation interferometry to quantify the reaction affinities and kinetic properties and also any induced conformational change.

See also


  1. Mfopou JK, De Groote V, Xu X, Heimberg H, Bouwens L (May 2007). [Expression error: Missing operand for > "Sonic hedgehog and other soluble factors from differentiating embryoid bodies inhibit pancreas development"]. Stem Cells 25 (5): 1156–65. doi:10.1634/stemcells.2006-0720. PMID 17272496. 
  2. Voet, Judith G.; Voet, Donald (1995). Biochemistry. New York: J. Wiley & Sons. ISBN 0-471-58651-X. 
  3. Koh JT, Zheng J (September 2007). [Expression error: Missing operand for > "The new biomimetic chemistry: artificial transcription factors"]. ACS Chem. Biol. 2 (9): 599–601. doi:10.1021/cb700183s. PMID 17894442. 

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