Modulators of rna riboswitches
AssigneeMemorial Sloan Kettering Cancer Center
InventorsDinshaw Patel, Alexander Serganov, Lili Huang
Life of this patent
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Abstract
Provided is a computer model generated from a data array, computer readable storage media encoded with the model, and computers comprising the model, wherein the model is derived from atomic structure coordinates of a FMN riboswitch or a lysine riboswitch. Further provided is a pharmacophore having a spatial arrangement of atoms defined by the binding pocket identified in the model, along with a compound defined by the pharmacophore. Also further provided are methods for rational drug design based on the atomic structure data, and compounds identified by the rational drug design process.
Claims28
A computer model of an FMN riboswitch generated from a data array comprising the atomic structure coordinates of an FMN riboswitch as set forth in any one of Tables 6-14, or a composite thereof.
A method for identifying a compound that interacts with a FMN riboswitch, utilizing a 3-D molecular model of a riboswitch as shown in any one of Tables 6-14, or a composite thereof, comprising:
- (a) using the model in a method of rational drug design to identify candidate compounds that can bind a FMN riboswitch;
- and
- (b) assaying the binding of a candidate compound identified in step (a) using a purified FMN riboswitch to thereby determine a binding characteristic, or lack thereof, of the compound.
A method for identifying a compound that interacts with a FMN riboswitch, utilizing the crystal structure of a FMN riboswitch, comprising the steps of:
- (a) modeling the FMN riboswitch with a test compound;
- and
- (b) determining if the test compound interacts with the FMN riboswitch.
A computer model of a lysine riboswitch generated from a data array comprising the atomic structure coordinates of a lysine riboswitch as set forth in any one of Tables 15-26, or a composite thereof.
A method for identifying a compound that interacts with a lysine riboswitch, utilizing a 3-D molecular model of a lysine riboswitch as shown in any one of Tables 15-26, or a composite thereof, comprising:
- (a) using the model in a method of rational drug design to identify candidate compounds that can bind a lysine riboswitch;
- and
- (b) assaying the binding of a candidate compound identified in step (a) using a purified lysine riboswitch to thereby determine a binding characteristic, or lack thereof, of the compound.
A method for identifying a compound that interacts with a lysine riboswitch, utilizing the crystal structure of a lysine riboswitch, comprising the steps of:
- (a) modeling the lysine riboswitch with a test compound;
- and
- (b) determining if the test compound interacts with the lysine riboswitch.
Dependencies are inferred from the claim text.