Targeting M-Ras and Raf kinases by dual allosteric inhibitors.

Abstract

We report on a computational design of novel druglike small molecules that could allosterically bind both M-Ras and B/C-Raf kinases. The Ras kinases participate in cellular signal transmission leading to cell growth. Mutations can make Ras kinases continually activated, leading to cancer. Ras proteins activate the Raf kinases, which stimulate MAPK pathways involved in the cell cycle. Many drugs are MAPK inhibitors. However, bypass signaling frequently develops leading to drug resistance. B-Raf kinase inhibitors effectively inhibit the ERK kinase within MAPK in B-Raf-mutant cancers. However, they can also stimulate the C-Raf activation in Ras-mutated cancers. Cancers with Ras mutations can switch their signaling from B-Raf to C-Raf, leading to cancer progression. M-Ras is a non-classical Ras variant, which can compensate for mutated classical Ras kinases (H/K/N), leading to bypass signaling. Thus, M-Ras is a suitable target for small-molecule inhibitors. Most inhibitors bind to the kinases’ catalytic sites, which are similar in various kinases and, thus, difficult to target specifically. Allosteric sites differ in kinases, allowing for selective binding. We analyzed the M-Ras and B/C-Raf allosteric binding sites using the Deep View program. New putative small-molecule inhibitors were designed by systematic alterations of known inhibitors. The druglike properties of the designed molecules were found by the DataWarrior and Molinspiration programs. The molecules with optimal druglike properties and no implied toxicities were docked to M-Ras and B/C-Raf in ArgusLab. Their binding energies were calculated. Two designed molecules were found to bind allosterically to both B/C-Raf and M-Ras with greater binding energies and improved druglike properties than the known single-kinase inhibitors. This study, together with previous experimental findings, suggests that the molecules designed here may be successful allosteric B/C-Raf and M-Ras inhibitors with improved therapeutic results in cancers with mutated Ras or Raf.