Design and synthesis of substrate analogue inhibitors of peptide deformylase

Series of substrates derivatives of peptide deformylase were systematically synthesized and studied for their capacities to undergo hydrolysis. Data a nalysis indicated the requirement for a hydrophobic first side chain and fo r at least two main chain carbonyl groups in the substrate. For instance, F o-Met-OCH3 and Fo-Nle-OCH3 were the minimal substrates of peptide deformyla se obtained in this study, while positively charged Fo-Nle-ArgNH(2) was the most efficient substrate (k(cat)/K-m = 4.5 x 10(5) M-1 . s(-1)). On the ba sis of this knowledge, 3-mercapto-2-benzylpropanoylglycine (thiorphan), a k nown inhibitor of thermolysin, could be predicted and further shown to inhi bit the deformylation reaction. The inhibition by this compound was competi tive and proved to depend on the hydrophobicity at the P-1' position. Spect roscopic evidence that the sulfur group of thiorphan binds next to the acti ve site metal ion on the enzyme could be obtained. Consequently, a small th iopseudopeptide derived from Fo-Nle-OCH3 was designed and synthesized. This compound behaved as a competitive inhibitor of peptide deformylase with K- I = 52 +/- 5 mu M. Introduction of a positive charge to this thiopeptide vi a addition of an arginine at P-2' improved the inhibition constant up to 2. 5 +/- 0.5 mu M, a value 4 orders of magnitude smaller than that of the star ting inhibitors. Evidence that this inhibitor, imino [(5-methoxy-5-oxo-4-[[ 2-(sulfanylmethyl)hexanoyl] amino]pentyl)amino]methanamine, binds inside th e active site cavity of peptide deformylase, while keeping intact the 3D fo ld of the protein, was provided by NMR. A fingerprint of the interaction of the inhibitor with the residues of the enzyme was obtained.