Geometry of binding of the N alpha-tosylated piperidides of m-amidino-, p-amidino- and p-guanidino phenylalanine to thrombin and trypsin. X-ray crystal structures of their trypsin complexes and modeling of their thrombin complexes.
The X-ray crystal structures of the complexes formed with bovine trypsin and the N alpha-tosylated piperidides of m-amidino-, p-amidino- and p-guanidino-D,L-phenylalanine (3-TAPAP, 4-TAPAP and 4-TGPAP) were determined with data to 1.8 A resolution. The L-stereoisomer of 3-TAPAP binds as a compact entity into the active site of trypsin, with the amidino and the carbonyl groups of the central amidinophenylalanyl residue hydrogen-bonded to Gly216 of trypsin. According to modeling and energy minimization, 3-TAPAP fits perfectly in this conformation to the more restrictive thrombin active site also (Bajusz et al. (1978) Int. J. Pept. Prot. Res. 12, 217-221); the piperidine moiety extends into the cage-like S2 subsite of thrombin, but leaves room for additional substituents which might help to improve binding and pharmacological properties. In contrast, 4-TAPAP and 4-TGPAP bind only weakly and in an extended conformation to trypsin; their considerably enhanced affinities for thrombin would suggest a more compact binding to thrombin.
Turk
D
D
Max-Planck-Institut für Biochemie, Martinsried, Germany.
Stürzebecher
J
J
Bode
W
W
D000578:Amidines / Q000737:chemistry / Q000378:metabolism*; D000818:Animals; D001665:Binding Sites; D002417:Cattle; D006146:Guanidines / Q000737:chemistry / Q000378:metabolism*; D008958:Models, Molecular; D015394:Molecular Structure; D010880:Piperidines / Q000737:chemistry / Q000378:metabolism*; D013237:Stereoisomerism; D013917:Thrombin / Q000378:metabolism*; D014357:Trypsin / Q000378:metabolism*; D014961:X-Ray Diffraction
D000578:Amidines; D006146:Guanidines; D010880:Piperidines; C070568:N(alpha)-(4-toluenesulfonyl)-4-guanidinophenylalanylpiperidine; C070567:N(alpha)-(4-toluenesulfonyl)-4-amidinophenylalanylpiperidine; C070566:N(alpha)-(4-toluenesulfonyl)-3-amidinophenylalanylpiperidine; D014357:Trypsin; D013917:Thrombin