Fragment-based lead 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 bond donors 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.

Library screening and quantification

In fragment-based drug discovery, the low binding affinities of the fragments pose significant challenges for screening. Many biophysical techniques have been applied to address this issue. In particular, ligand-observe nuclear magnetic resonance (NMR) methods such as water-ligand observed via gradient spectroscopy (waterLOGSY), saturation transfer difference spectroscopy (STD-NMR), ¹⁹F NMR spectroscopy and inter-ligand Overhauser effect (ILOE) spectroscopy,^[2][3] protein-observe NMR methods such as ¹H-¹⁵N heteronuclear single quantum coherence (HSQC) that utilises isotopically-labelled proteins,^[4] surface plasmon resonance (SPR)^[5] and isothermal titration calorimetry (ITC)^[6] are routinely-used for ligand screening and for the quantification of fragment binding affinity to the target protein.

Once a fragment (or a combination of fragments) have been identified, protein X-ray crystallography are used to obtain structural models of the protein-fragment(s) complexes.^[7][8] Such information can then be used to guide organic synthesis for high-affinity protein ligands and enzyme inhibitors.^[9]

Advantages over traditional libraries

Advantages of screening low molecular weight fragment based libraries over traditional higher molecular weight chemical libraries are several.^[10] 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 - N³ compounds 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.

See also

• Druglikeness
• Protein-directed dynamic combinatorial chemistry
• Lipinski's rule of five

References

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)02831-9. PMID 14554012.
2. Ma R, Wang P, Wu J, Ruan K (July 2016). "Process of Fragment-Based Lead Discovery — A Perspective from NMR". Molecules. 21 (7): 854. doi:10.3390/molecules21070854.
3. Norton RS, Leung EW, Chandrashekaran IR, MacRaild CA (July 2016). "Applications of ¹⁹F-NMR in Fragment-Based Drug Discovery". Molecules. 21 (7): 860. doi:10.3390/molecules21070860.
4. Harner MJ, Frank AO, Fesik SW (June 2013). "Fragment-based drug discovery using NMR spectroscopy". J. Biomol. NMR. 56 (2): 65–75. doi:10.1007/s10858-013-9740-z. PMID 23686385.
5. Neumann T, Junker HD, Schmidt K, Sekul R (Aug 2007). "SPR-based fragment screening: advantages and applications". Curr. Top. Med. Chem. 7 (16): 1630–42. PMID 17979772.
6. Silvestre HL, Blundell TL, Abell C, Ciulli A (Aug 2013). "Integrated biophysical approach to fragment screening and validation for fragment-based lead discovery". Proc. Natl. Acad. Sci. USA. 110 (32): 12984–9. doi:10.1073/pnas.1304045110. PMID 23872845.
7. Caliandro R, Belviso DB, Aresta BM, de Candia M, Altomare CD (June 2013). "Protein crystallography and fragment-based drug design". Future Med. Chem. 5 (10): 1121–40. doi:10.4155/fmc.13.84. PMID 23795969.
8. Chilingaryan Z, Yin Z, Oakley AJ (Oct 2012). "Fragment-based screening by protein crystallography: successes and pitfalls". Int. J. Mol. Sci. 13 (10): 12857–79. doi:10.3390/ijms131012857. PMID 23202926.
9. de Kloe GE, Bailey D, Leurs R, de Esch IJ (Jul 2009). "Transforming fragments into candidates: small becomes big in medicinal chemistry". Drug Discov. Today. 14 (13-14): 630–46. doi:10.1016/j.drudis.2009.03.009. PMID 19443265.
10. Erlanson DA, McDowell RS, O'Brien T (July 2004). "Fragment-based drug discovery". J. Med. Chem. 47 (14): 3463–82. doi:10.1021/jm040031v. PMID 15214773.

Further reading

• 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_180. PMID 21695633.
• Edward Zartler; Michael Shapiro (2008). Fragment-based drug discovery a practical approach. Wiley.

• Download a example of a Fragment based library here (4,532 compounds, zipped SD-File)