Patent DE-10123597-A1 (DE)
Title: Novel crystal useful for identifying a potential inhibitor of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, comprises 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase protein with or without zinc
Inventor: BACHER ADALBERT
IPC: C12N9/88
Filed: 2001-05-15
Abstract: A crystal (I) comprising 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase protein (P) with or without zinc, is new.  Independent claims are also included for the following:  (1) a method of growing a crystal comprising (P) and zinc by vapor diffusion using a reservoir solution containing 01. M 4-(2-hydroxyethyl)-1-piperazine-ethanesulfonic acid (HEPES) (pH 7.5) and 2 M ammonium formate; (2) a data storage device having atomic coordinates of the three-dimensional structure of (P) or of the three-dimensional structure of (P) in complex with a compound (C) selected from 4-diphosphocytidyl-2C-methyl-D-erythritol, 4-diphosphocytidyl-2C- methyl-D-erythritol 2-phosphate, cytidine, cytidine monophoshate, cytidine diphosphate, 2C-methyl-D-erythritol 2,4-cyclodiphosphate or a combination of cytidine monophosphate and 2C-methyl-D-erythritol 2,4-cyclodiphosphate, with or without zinc stored in it; (3) a computer-assisted method (M1) for identifying potential inhibitors of (P) using a programmed computer comprising a processor, a data storage system, a data input device, and a data output device, involves:  (a) inputting into the programmed computer through the input device data comprising atomic coordinates of a subset of the atoms of a complex of (P) with (C) with or without zinc, to generate a criteria data set; (b) comparing using the processor, the criteria data set to a computer data base of low-molecular weight organic chemical structures stored in the data storage system, and selecting from the data base, using computer methods, a chemical structure having a portion that is structurally complementary to the criteria data set pertaining to (P) and/or structurally similar to the criteria data set pertaining to a compound of the group and being free of steric interference with (P), or constructing, using computer methods, a model of a chemical structure having a portion that is structurally complementary to the criteria data set pertaining to (P) and/or structurally similar to the criteria data set pertaining to a compound of the group and being free of steric interference with (P); (4) identifying (M2) a candidate inhibitor capable of binding to and inhibiting the enzymatic activity of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, involves: (a) introducing into a computer information derived from atomic coordinates defining a conformation of the active site of (P) or a complex of (P) with (C), with or without zinc, based on three-dimensional structure determination, where the program utilizes or displays on the computer screen the structures of the conformation; (b) generating a three-dimensional representation of at least one of the three pockets of the active site of (P) and/or (C) by the computer program on a computer screen; (c) superimposing a model of a candidate inhibitor on the representation of at least one pocket of the active site and/or (C) of the group; (d) assessing the possibility of bonding and the absence of steric interference of the candidate inhibitor with the active site of (P); (e) incorporating the candidate compound in an activity assay of the synthase; and (f) determining whether the candidate compound inhibits enzymatic activity of (P); and (5) a compound (II) having a chemical structure obtained or obtainable by (M1), (M2) or using (I), is an inhibitor of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase.