The reason for the low number of successful new CNS drugs is the subject of debate, although it is undoubtedly related to their higher attrition rate during development, particularly from issues related to failures of on-target biological hypotheses. To address this problem, there has been a recent emphasis on research to tackle these issues at an earlier stage in the drug discovery pathway. In particular, there has been increased interest in target discovery both for the identification of novel targets and reducing the subsequent failure from incorrect biological hypotheses through early validation.

Target discovery, which involves the identification and early validation of disease-modifying targets, is an essential first step in the drug discovery process. Furthermore, although the knowledge of the target for a small molecule drug is not required by the FDA for drug development, it is crucial information if the drug discovery process is to be made more efficient and effective. Identifying the targets associated with a small molecule can lead to faster optimization, an early understanding of side-effects and toxicity, and assessment of target engagements and clinically relevant end points.


  • A number of strategies are being pursued in the design of molecules for target identification; the choice of approach depends on whether the compound binds covalently or non-covalently to its target.
  • If a compound does not bind to its target covalently
  • In this strategy an analog is designed that contains a PRG and an alkyne.  The PRG will crosslink to potential target macromolecules.
  • a PRG (e.g., azide 6).
  • The probe 6 then is incubated with a lysate or whole cells.  In the absence of UV light, the PRG is stable, and the probe will bind with its target protein.  Subsequent irradiation of the lysate at a specific wavelength will generate a reactive species that will form a covalent linkage between the probe and its target protein.  The specifically cross-linked proteins will be purified, and their identities will be determined by LC-MS/MS analysis techniques (Haas Lab).
  • Then the alkyne will be used in “click chemistry” to form a triazole, which allows introduction of the biotin fragment. The affinity probe–macromolecule complex 8 now can be isolated (Figure 6).  The advantage of this strategy is that the alkyne will be fairly small compared to biotin, and it is less likely to interfere with binding to the target.  The disadvantage is that a second reaction must be conducted to generate the full affinity probe–macromolecule complex.