Scanning alanine mutagenesis and de-peptidization of a Candida albicans myristoyl-CoA:Protein N-myristoyltransferase octapeptide substrate reveals three elements critical for molecular recognition

Abstract

Candida albicans produces a single myristoyl-CoA: protein N- myristoyltransferase (Nmt) that is essential for its viability. An ADP- ribosylation factor (Arf) is included among the few cellular protein substrates of this enzyme. An octapeptide (GLYASKLS-NH2) derived from a N- terminal Arf sequence was used as the starting point to identify elements critical for recognition by the acyltransferases's peptide-binding site. In vitro kinetic studies, employing purified Nmt and a panel of peptides with single Ala substitutions at each position of GLYASKLS-NH2, established that its Gly1, Ser5, and Lys6 residues play predominant roles in binding. ALYASKLS-NH2 was found to be an inhibitor competitive for peptide (K(i) = 15.3 ± 6.4 μM) and noncompetitive for myristoyl-CoA (K(i) = 31.2 ± 0.7 μM). A survey of 26 derivatives of this inhibitor, representing (i) a complete alanine scan, (ii) progressive C-terminal truncations, and (iii) manipulation of the physical-chemical properties of its residues 1, 5, and 6, confirmed the important stereochemical requirements for the N-terminal amine, the β-hydroxyl of Ser5, and the ε-amino group of Lys6. Remarkably, replacement of the the N-terminal tetrapeptide of ALYASKLS-NH2 with an 11- aminoundecanoyl group produced a competitive inhibitor, 11-aminoundecanoyl- SKLS-NH2, that was 38-fold more potent (K(i) = 0.40 ± 0.03 μM) than the starting octapeptide. Removing the primary amine (undecanoyl-SKLS-NH2), or replacing it with a methyl group (dodecanoyl-SKLS-NH2), resulted in 26- and 34-fold increases in IC50, confirming the important contribution of the amine to recognition. Removal of Leu-Ser from the C terminus (11- aminoundecanoyl-SK-NH2) yielded a competitive dipeptide inhibitor with a K(i) (11.7 ± 0.4 μM) equivalent to that of the starting octapeptide, ALYASKLS-NH2. Substitution of Set with homoserine, cis-4-hydroxyproline, or tyrosine reduces potency by 3-70-fold, emphasizing the requirement for proper presentation of the hydroxyl group in the dipeptide inhibitor. Substituting D- for L-Lys decreases its inhibitory activity >100-fold, while deletion of the ε-amino group (Nle) or masking its charge (ε-N-acetyl-lysine) produces 4-7-fold attenuations. L-His, but not its D-isomer, can fully substitute for L-Lys, producing a competitive dipeptide inhibitor with similar potency (K(i) = 11.9 ± 1.0 μm). 11-Aminoundecanoyl-SK-NH2 and 11-aminoundecanoyl-SH- NH2 establish that a simple alkyl backbone can maintain an appropriate distance between three elements critical for recognition by the fungal enzyme's peptide-binding site: a simple ω-terminal amino group, a β- hydroxyl, and an ε-amino group or an imidazole. These compounds contain one peptide bond and two chiral centers, suggesting that it may be feasible to incorporate these elements of recognition, or functionally equivalent mimics, into a fully de-peptidized Nmt inhibitor.