Method for identifying Smk box riboswitch modulating compounds

Abstract

The invention is directed, inter alia, to a method for identifying a compound that modulates a gene expression of an mRNA molecule containing a SMK box riboswitch that contains a SAM binding pocket, wherein the mRNA molecule is produced by a lactic acid bacteria, the method comprising: (i) generating a database of structural coordinates that includes atomic positions of the SMK box riboswitch and distances of these atomic positions to atomic positions of a first compound complexed to the SMK box riboswitch; (ii) identifying key interactions between the SMK box riboswitch and the first compound from the database of structural coordinates; and (iii) devising a derivative compound of the first compound by use of a computer modeling program, wherein the derivative compound possesses structural modifications, relative to the first compound, that results in an improved modulating interaction between at least one location of the SAM binding pocket and derivative compound.

Dependencies are inferred from the claim text.