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Small molecule

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Title: Small molecule  
Author: World Heritage Encyclopedia
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Subject: Biochemistry, Hit selection, Small Molecule Pathway Database, Biomolecule, Polymer
Collection: Drug Discovery, Drugs, Induced Stem Cells, Plant Physiology
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Small molecule


External links

  1. ^ a b Macielag MJ (2012). "Chemical properties of antibacterials and their uniqueness". In Dougherty TJ, Pucci MJ. Antibiotic Discovery and Development. pp. 801–2.  
  2. ^ 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.  
  3. ^ Lipinski CA (December 2004). "Lead-and drug-like compounds: the rule-of-five revolution". Drug Discovery Today: Technologies 1 (4): 337–341.  
  4. ^ 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.  
  5. ^ 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.  
  6. ^ 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.  
  7. ^ Atta-ur-Rahman, ed. (2012). Studies in Natural Products Chemistry 36. Amsterdam: Elsevier.  
  8. ^ 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.  
  9. ^ Voet JG, Voet D (1995). Biochemistry. New York: J. Wiley & Sons.  
  10. ^ Koh JT, Zheng J (September 2007). "The new biomimetic chemistry: artificial transcription factors". ACS Chem. Biol. 2 (9): 599–601.  
  11. ^ Wienken CJ, Baaske P, Rothbauer U, Braun D, Duhr S (2010). "Protein-binding assays in biological liquids using microscale thermophoresis". Nat Commun 1: 100.  
  12. ^ Levine DS (2003). "Bio-defense company re-ups". San Francisco Business Times. Retrieved September 6, 2006. 


See also

Small molecule anti-genomic therapeutics, or SMAT, refers to a biodefense technology that targets DNA signatures found in many biological warfare agents. SMATs are new, broad-spectrum drugs that unify antibacterial, antiviral and anti-malarial activities into a single therapeutic that offers substantial cost benefits and logistic advantages for physicians and the military.[12]

Anti-genomic therapeutics

Binding of ligand can be characterised using a variety of analytical techniques such as surface plasmon resonance, microscale thermophoresis[11] or dual polarisation interferometry to quantify the reaction affinities and kinetic properties and also any induced conformational change.

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.[9] There is also interest in creating small molecule artificial transcription factors to regulate gene expression, examples include wrenchnolol (a wrench shaped molecule).[10]

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 which can bind to the active site or on the allosteric site.

Cell culture example of a small molecule 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.[8]

Research tools

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.[7] Examples of secondary metabolites include:

Secondary metabolites

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.[6]



  • Drugs 1
  • Secondary metabolites 2
  • Research tools 3
  • Anti-genomic therapeutics 4
  • See also 5
  • References 6
  • External links 7

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.[5]

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.

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.[1][2] 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.[3][4]

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