Fragment-based lead discovery

Key Points

  • The concept of a 'target-rich, lead-poor' pipeline in drug discovery, and widespread concern about the attrition rate of chemical compounds in (pre)clinical development, are together fuelling the search for better quality hits and chemical lead series.

  • A particular approach to lead identification for drug discovery, which offers a number of attractive features compared with high-throughput screening, involves the selection, screening and optimization of 'fragments'. Fragments typically have Mr = 120–250 and binding affinities in the range mM–30 μM. However, the weak absolute potency of fragments belies their high efficiency as ligands, because fragments are extremely potent for their size.

  • Generally, fragments are identified using a biophysical screening method, most commonly NMR or protein crystallography supported by a conventional enzyme bioassay. Consequently, information about the structure of the fragment–protein binding interaction is generated as part of the screening.

  • This structural information means that it is possible to incorporate a large element of design in optimizing the fragment into a high-affinity lead, either by growing additional binding groups or joining two fragments together. As a result, fragments can be optimized into nanomolar leads via the synthesis of significantly fewer compounds than in traditional approaches.

  • Furthermore, starting the chemical optimization stage with a low-molecular-mass fragment is likely to produce leads whose Mr is still within the range desired for lead-likeness.

  • This review discusses fragment-based lead discovery, and focuses on the output of this new approach by collating published examples from 25 protein targets. These targets are primarily enzymes and the screening techniques used include X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, in vitro bioassays and mass spectrometry.

Abstract

Fragment-based lead discovery is gaining momentum in both large pharmaceutical companies and biotechnology laboratories as a complementary approach to traditional screening. This is because fragment-based approaches require significantly fewer compounds to be screened and synthesized, and are showing a high success rate in generating chemical series with lead-like properties. Compared with traditional screening hits, the starting fragments have considerably lower molecular mass, and although the binding interactions of these fragments with a target protein are weak, they are structurally understood through X-ray crystallography or NMR, and they exhibit high 'ligand efficiency'. Here, we use examples from 25 different protein targets to describe chemical strategies that exploit this structural knowledge to rapidly develop fragments into high-affinity leads.

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Figure 1: Surface representation of fragment growth against p38 mitogen-activated protein kinase.
Figure 2: Schematic comparison of the usual molecular mass and potency ranges of high-throughput screening hits with fragments as starting points for lead identification and drug discovery.
Figure 3: Schematic representation of a low-quality HTS hit.
Figure 4: Fragment evolution.
Figure 5: Fragment linking.
Figure 6: Fragment self-assembly.
Figure 7: Lead progression via fragment optimization.

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Acknowledgements

H. Jhoti for scientific input, R. Taylor for figure 1 and H. Sore for proof reading.

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Correspondence to David C. Rees.

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The authors are employed by Astex-Technology which uses fragment-based lead discovery.

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DATABASES

EntrezGene

Caspase-3

c-SRC

cyclin-dependent kinase-2

p38 MAP kinase

protein tyrosine phosphatase-1B

tryptase

thymidylate kinase

urokinase

Glossary

RULE OF FIVE

Identifies several key properties that should be considered for compounds with oral delivery in mind. These properties are molecular mass <500 Da, cLogP <5, number of hydrogen-bond donors ≤5 and number of hydrogen-bond acceptors ≤10.

SURFACE PLASMON RESONANCE

(SPR). A phenomenon which occurs when light is reflected off thin metal films to which target molecules are immobilized and addressed by ligands in a mobile phase. If binding occurs to the immobilized target then the local refractive index changes, which leads to the apparent rate constants for the association and dissociation phases of the reaction. The ratio of these values gives the apparent equilibrium constant (affinity).

NUCLEAR OVERHAUSER EFFECTS

(NOEs). Changes in the intensity of NMR signals, which are caused by through-space dipole–dipole coupling. Upper distance constraints obtained from 1H–1H NOEs are used for NMR structure determination of biological macromolecules.

VANCOMYCIN

Vancomycin is an antibiotic that acts by binding to cell-wall precursors that terminate in the sequence D-Ala-D-Ala, thereby inhibiting cell-wall synthesis.

P1′ SITE

The substrate residue that occurs immediately after the scissile amide bond in a protease. It is the key specificity site of matrix metalloproteases like stromelysin.

S1 POCKET

The pocket on a protease occupied by the substrate residue which immediately precedes the scissile amide bond. It is the key specificity pocket of trypsin-like serine proteases such as factor Xa, urokinase, tryptase and thrombin, in which lysine or arginine are the favoured substrate residues.

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Rees, D., Congreve,, M., Murray, C. et al. Fragment-based lead discovery. Nat Rev Drug Discov 3, 660–672 (2004). https://doi.org/10.1038/nrd1467

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