Fragment-based DRUG discovery


Fragment-based lead discovery (FBLD) also known as fragment-based drug discovery (FBDD) is a method used for finding lead compounds as part of the drug discovery process. It is based on identifying small chemical fragments, which may bind only weakly to the biological target, and then growing them or combining them to produce a lead with a higher affinity. FBLD can be compared with high-throughput screening (HTS). In HTS, libraries with up to millions of compounds, with molecular weights of around 500 Da, are screened, and nanomolar binding affinities are sought. In contrast, in the early phase of FBLD, libraries with a few thousand compounds with molecular weights of around 200 Da may be screened, and millimolar affinities can be considered useful.

Library design

In analogy to the rule of five, it has been proposed that ideal fragments should follow the ‘rule of three’ (molecular weight < 300, ClogP < 3, the number of hydrogen bonddonors and acceptors each should be < 3 and the number of rotatable bonds should be < 3).[1] Since the fragments have relatively low affinity for their targets, they must have high water solubility so that they can be screened at higher concentrations.

Advantages over traditional libraries

Advantages of screening low molecular weight fragment based libraries over traditional higher molecular weight chemical libraries are several.[2] These include:

  • More hydrophilic hits in which hydrogen bonding is more likely to contribute to affinity (enthalpically driven binding). It is generally much easier to increase affinity by adding hydrophobic groups (entropically driven binding), starting with a hydrophilic ligand increases the chances that the final optimized ligand will not be too hydrophobic (log P < 5).
  • Higher ligand efficiency so that the final optimized ligand will more likely be relatively low in molecular weight (MW < 500).
  • Since two to three fragments in theory can be combined to form an optimized ligand, screening a fragment library of N compounds is equivalent to screening N2 – N3compounds in a traditional library.
  • Fragments are less likely to contain sterically blocking groups that interfere with an otherwise favorable ligand-protein interaction, increasing the combinatorial advantage of a fragment library even further.


  1.  Congreve M, Carr R, Murray C, Jhoti H (October 2003). “A ‘rule of three’ for fragment-based lead discovery?”. Drug Discov. Today 8 (19): 876–7. doi:10.1016/S1359-6446(03)02831-9PMID 14554012.
  2.  Erlanson DA, McDowell RS, O’Brien T (July 2004). “Fragment-based drug discovery”. J. Med. Chem. 47 (14): 3463–82. doi:10.1021/jm040031vPMID 15214773.

  • Folkers G, Jahnke W, Erlanson DA, Mannhold R, Kubinyi H (2006). Fragment-based Approaches in Drug Discovery (Methods and Principles in Medicinal Chemistry). Weinheim: Wiley-VCH. ISBN 3-527-31291-9.
  • Everts S (2008-07-21). “Piece By Piece”. Chemical and Engineering News 86 (29): 15–23. doi:10.1021/cen-v086n029.p015.
  • Kuo LC (2011). Fragment Based Drug Design, Volume V493: Tools, Practical Approaches, and Examples (Methods in Enzymology). Boston: Academic Press. ISBN 0-12-381274-7.
  • Erlanson DA (June 2011). “Introduction to Fragment-Based Drug Discovery”. Top Curr Chem 317: 1–32. doi:10.1007/128_2011_180PMID 21695633.
  • Edward Zartler, Michael Shapiro (2008). Fragment-based drug discovery a practical approach. Wiley.

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  One Response to “Fragment-based DRUG discovery”

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