Small-molecule macrocycles: Potent and selective Src kinase inhibitors

Macrocyclic compounds have unique properties that allow them to cover regions of chemical space not addressed by other small-molecule structural classes. By performing an in vitro selection screen of a broad untargeted DNA-encoded library of 13,824 synthetic small-molecule macrocycles against 36 biomedically relevant protein targets, including 9 kinases (Akt4, AMPK ERBB4, Mk2, p38a, MKK6, Pim1, Src, VEGFR2) researchers in the laboratory of David Liu have discovered a novel class of highly selective and potent Src kinase inhibitors. Best initial hits included molecules with Src IC50 values of 960nM (cis-All-B1-C5-D7) and 680nM (trans-A10-B1-C5-D6), with trans-A10-B1-C5-D6 having no significant off-target inhibition when tested against a panel of 44 human kinases that included all nine members of the Src kinase family. This specificity is especially intriguing since both of these macrocycles were shown to be ATP-competitive inhibitors.

Chemical structure of screening library and best initial Src inhibitor hits

Selectivity of macrocycles cis-A11-B1-C5-D7 and trans-A10-B1-C5-D6 among Src-related kinases, including all nine Src-family kinases

Future Directions
This research has revealed promising compounds for the further development of selective and potent molecules that can modulate the function of cellular kinases. The work is ongoing in the laboratory where the researchers have synthesized derivatives of the above compounds that have IC50 potencies in the single-digit nM range and that display several other exciting biochemical and therapeutic properties.


Executive Summary

  • Selective inhibitors of protein kinases represent an important therapeutic class for the development of targeted cancer therapy
  • The high degree of structural homology among and within kinase families poses a challenge for the development of selective small molecule inhibitors; the unique features of macrocycles offer the potential to address this challenge
  • A selection screen identified a class of selective macrocyclic kinase inhibitors, with initial hits having submicromolar Src kinase IC50 values.
  • In ongoing unpublished studies the researchers have identified derivatives with single-digit nanomolar IC50 values and other therapeutically important properties.

Given the central role of protein kinases in cellular signal transduction cascades, pharmaceutical companies are intensively pursuing the discovery and development of targeted cancer therapeutic agents that act by selective kinase inhibition. As of 2011 the FDA has approved at least nine small-molecule kinase inhibitors targeting a range of cancers (e.g. imatinib/Gleevec), and dozens more are in development. However, the high sequence conservation around the ATP-binding pocket across the hundreds of kinases in the human kinome suggests that the development of an arsenal of specific kinase inhibitors will require molecules that interact outside the ATP-binding pocket. An additional challenge is the development of agents capable of inhibiting kinases that harbor mutations observed in many drug-resistant cancers.

Intellectual Property Status: Patent(s) Pending