title: Synthesis and evaluation of new substrate analogues of streptomyces R61 DD-peptidase: dissection of a specific ligand.
abstract: Good substrates of the Streptomyces R61 dd-peptidase, such as glycyl-L-alpha-amino-epsilon-pimelyl-D-alanyl-D-alanine, 1 (Anderson, J. W.; Pratt, R. F. Biochemistry 2000, 39, 12200-12209), contain the glycyl-L-alpha-amino-epsilon-pimelyl side chain. A number of thia variants of this structure have been synthesized by means of a disconnection strategy whereby the appropriate thiols were reacted with either acryloyl-D-alanyl-D-alanine or haloalkanoyl-D-alanyl-D-alanines. Kinetics studies of the hydrolysis of these compounds by the R61 DD-peptidase showed that the presence of the N-terminal glycylammonium ion and the pimelyl-alpha-carboxylate are very important for efficient catalysis. The results of deletion of the C-terminal D-alanine indicate a promising direction toward new inhibitors. Shorter (one methylene less) and longer (one methylene more) analogues of 1 are also poor substrates. Molecular modeling and dynamics studies suggest that the higher mobility of the active site residues and the modified substrates in enzyme-substrate complexes may be the dominant factor in this loss of reactivity. The general conclusion is that essentially all of the structural elements of the side chain of 1 are required to produce a good substrate. This result has important implications for the design of inhibitors of DD-peptidases.
authors.affiliation: Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459, USA.
authors.forename: Rajesh
authors.initials: R
authors.lastname: Nagarajan
authors.forename: R F
authors.initials: RF
authors.lastname: Pratt
mesh_terms: D002384:Catalysis; D015195:Drug Design; D008024:Ligands; D008958:Models, Molecular; D015394:Molecular Structure; D009842:Oligopeptides / Q000138:chemical synthesis*; D046929:Serine-Type D-Ala-D-Ala Carboxypeptidase; D013302:Streptomyces / Q000201:enzymology*; D013329:Structure-Activity Relationship; D013379:Substrate Specificity
chemical_list: D008024:Ligands; D009842:Oligopeptides; C493614:glycyl-L-alpha-amino-epsilon-pimelyl-D-alanyl-D-alanine; D046929:Serine-Type D-Ala-D-Ala Carboxypeptidase