Drug‐Ribosome Interaction Energies at Site‐E Reveal a Reversed Pattern with Respect to Site‐A, While Showing a Mismatch of Crystal vs. Solution Conformations

Abstract

AbstractAlthough ribosome is a much hunted target in cancer research, scanty success was achieved with small‐molecule modulators, either because of general toxicity or weak interactions with nucleotides and proteins. On the latter ground, the strength of interactions has been quantitatively evaluated here through MD and QM‐MM simulations in explicit water with the only models of yeast ribosome‐modulator complexes at site‐E for which static structural data were available. It turned out that site‐E is shaped per se by powerful electrostatic forces toward a Mg++ ion, which only allow adaptation of modulators to the site, by mainly sticking to the same Mg++ion. This is in contrast with site‐A, which is known from previous studies to be shaped by a network of H‐bonds with the modulator. From these studies lines of guidance begin to emerge as to tailoring ribosome modulators for better performance as antitumor agents.