In molecular biology and pharmacology, a small molecule is a low molecular weight (<900 Daltons) organic compound that may help regulate a biological process, with a size on the order of 10−9 m. Most drugs are small molecules.
The upper molecular weight limit for a small molecule is approximately 900 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. Finally, a lower molecular weight cutoff of 500 Daltons (as part of the "rule of five") has been recommended for small molecule drug development candidates based on the observation that clinical attrition rates are significantly reduced if the molecular weight is kept below this 500 Dalton limit.
Pharmacology usually restricts the term to a molecule that binds to a specific biopolymer—such as protein or nucleic acid—and acts as an effector, altering the activity or function of the biopolymer. Small molecules can have a variety of biological functions, serving as cell signaling molecules, 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 and proteins, and polysaccharides (such as starch or cellulose) are not small molecules—though their constituent monomers—ribo- or deoxyribonucleotides, amino acids, and monosaccharides, respectively—are often considered small molecules. Very small oligomers are also usually considered small molecules, such as dinucleotides, peptides such as the antioxidant glutathione, and disaccharides such as sucrose.
Small molecules may also be used as research tools to probe biological function as well as leads in the development of new therapeutic agents. Some can inhibit a specific function of a multifunctional protein or disrupt protein–protein interactions.
Most drugs are small molecules, although some drugs can be proteins (e.g., insulin and other biologic medical products). Many proteins are degraded if administered orally and most often cannot cross cell membranes. Small molecules are more likely to be absorbed, although some of them are only absorbed after oral administration if given as prodrugs. One advantage small molecule drugs (SMDs) have over "large molecule" biologics is that many SMDs can be taken orally whereas biologics generally require injection or another parenteral administration.
A wide variety of organisms including bacteria, fungi, and plants, produce small molecule secondary metabolites also known as natural products, which play a role in cell signalling, pigmentation and in defense against predation. Secondary metabolites are a rich source of biologically active compounds and hence are often used as research tools and leads for drug discovery. Examples of secondary metabolites include:
- Nonribosomal peptides, such as actinomycin-D
- Natural phenols (including flavonoids)
- Terpenes, including steroids
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 that activates protein kinase C, which promotes cancer, making it a useful investigative tool. There is also interest in creating small molecule artificial transcription factors to regulate gene expression, examples include wrenchnolol (a wrench shaped molecule).
Binding of ligand can be characterised using a variety of analytical techniques such as surface plasmon resonance, microscale thermophoresis or dual polarisation interferometry to quantify the reaction affinities and kinetic properties and also any induced conformational change.
- Macielag MJ (2012). "Chemical properties of antibacterials and their uniqueness". In Dougherty TJ, Pucci MJ. Antibiotic Discovery and Development. p. 801–2. ISBN 978-1-4614-1400-1. "The majority of [oral] drugs from the general reference set have molecular weights below 550. In contrast the molecular weight distribution of oral antibacterial agents is bimodal—between 340 and 450 Da but with another group in the 700–900 molecular weight range."
- Veber DF, Johnson SR, Cheng HY, Smith BR, Ward KW, Kopple KD (June 2002). "Molecular properties that influence the oral bioavailability of drug candidates". J. Med. Chem. 45 (12): 2615–23. doi:10.1021/jm020017n. PMID 12036371.
- Lipinski CA (December 2004). "Lead-and drug-like compounds: the rule-of-five revolution". Drug Discovery Today: Technologies 1 (4): 337–341. doi:10.1016/j.ddtec.2004.11.007.
- Leeson PD, Springthorpe B (November 2007). "The influence of drug-like concepts on decision-making in medicinal chemistry". Nature Reviews Drug Discovery 6 (11): 881–90. doi:10.1038/nrd2445. PMID 17971784.
- Arkin MR, Wells JA (April 2004). "Small-molecule inhibitors of protein-protein interactions: progressing towards the dream". Nature Reviews Drug Discovery 3 (4): 301–17. doi:10.1038/nrd1343. PMID 15060526.
- Samanen J (2013). "Chapter 5.2 How do SMDs differ from biomolecular drugs?". In Ganellin CR, Jefferis R, Roberts SM. Introduction to Biological and Small Molecule Drug Research and Development: theory and case studies (Kindle ed.). New York: Academic Press. ASIN B00CXO99RG. doi:10.1016/B978-0-12-397176-0.00005-4. ISBN 978-0-12-397176-0. "Table 5.13: Route of Administration: Small Molecules: oral administration usually possible; Biomolecules: Usually administered parenterally"
- Atta-ur-Rahman, ed. (2012). Studies in Natural Products Chemistry 36. Amsterdam: Elsevier. ISBN 978-0-444-53836-9.
- Mfopou JK, De Groote V, Xu X, Heimberg H, Bouwens L (May 2007). "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.
- Voet JG, Voet D (1995). Biochemistry. New York: J. Wiley & Sons. ISBN 0-471-58651-X.
- Koh JT, Zheng J (September 2007). "The new biomimetic chemistry: artificial transcription factors". ACS Chem. Biol. 2 (9): 599–601. doi:10.1021/cb700183s. PMID 17894442.
- Wienken CJ, Baaske P, Rothbauer U, Braun D, Duhr S (2010). "Protein-binding assays in biological liquids using microscale thermophoresis". Nat Commun 1: 100. doi:10.1038/ncomms1093. PMID 20981028.