Proton Dissociation Energies of Zinc-Coordinated Hydroxamic Acids and Their Relative Affinities for Zinc:  Insight into Design of Inhibitors of Zinc-Containing Proteinases

Abstract

Hydroxamic acids, known as iron chelators, have recently been widely used as a key functional group of potential therapeutics targeting at zinc proteinases such as matrix metalloproteinases involved in cancers and at other drug targets associated with cardiovascular diseases, AIDS, and Alzheimer's disease. However, the protonation states of zinc-coordinated hydroxamic acids in proteins and relative affinities of hydroxamic acids for Zn 2+ are still unclear due to the intricacy of the hydroxamic acid structures. Here, we report a comprehensive ab initio study of stable configurations and tautomers of neutral and deprotonated, Zn 2+coordinated acetohydroxamic acid and its N-methyl analogue in the gas-phase employing the B3LYP/6-311+G(2d,2p) method. The results suggest that both zinc-coordinated acetohydroxamic and N-methylacetohydroxamic acids exist in the oxygen-deprotonated Z-keto form with their two oxygen atoms coordinating to zinc in proteins in which the acidic amino acid side chains serve as a proton acceptor. This conclusion is consistent with a survey of experimentally determined protein 3D structures complexed with zinc-coordinated hydroxamic acids documented in the Protein Data Bank. The results also suggest that the zinc affinity of N-methylacetohydroxamic acid is 11 kcal/mol higher than that of acetohydroxamic acid and is up to 43 kcal/ mol higher than those of common zinc ligands in proteins. It thus cautions the use of N-methylacetohydroxamic acid as a functional group in rational design of inhibitors for zinc proteinases, since it may interact with other zinc proteins due to its high affinity for zinc.

A Combination of Docking, QM/MM Methods, and MD Simulation for Binding Affinity Estimation of Metalloprotein Ligands

“…The average C=0, C-N and N-O bond lengths for the bound state obtained here (1.284, 1.308 and 1.364 Å) are closer to deprotonated Zncoordinated hydroxamate (1.294, 1.317 and 1.378 Å) than to neutral hydroxamate with respective distances of 1.279, 1.337 and 1.416 Å. 78 The distance between Glu402 oxygen and oxygen of the reverse hydroxamate (2.70 Å) in MMP-9 and hydroxamate oxygen in MMP-779 and MMP-880 , 81 (2.6-2.8 Å) complex are in close agreement with the distance found in Step 2 (2.604 Å). These facts suggest that bound hydroxamate structure is, in the presence of proton-accepting Glu402, closer to deprotonated state than to neutral form.…”

Metal active site elasticity linked to activation of homocysteine in methionine synthases

“…However, the Cys 2 HisZnHcy site of MetE is not necessarily less efficient for activating Hcy than the Cys 3 ZnHcy site in MetH, because of the aromatic character of histidine, which has finely tunable electron-donating capabilities. Theoretical calculations predict that zinc-bound histidine has more anionic than neutral character, especially in the presence of negatively charged, electron-donating second shell ligands (32)(33)(34). Intriguingly, MetE may have a slightly more negative net charge on the zinc in the transition state if the geometry were more trigonal-bipyramidal than tetrahedral and glutamate were recruited back into the first shell.…”

Serotype-selective, small-molecule inhibitors of the zinc endopeptidase of botulinum neurotoxin serotype A

“…1) with a hydroxamate group as a better zinc ligand 34 was made. A high-pressure-liquid-chromatography-based (HPLC-based) assay showed that 2 is indeed more active in inhibiting the endopeptidase than 1.…”

“…Hydroxamates are known as promiscuous zinc coordinates 34 as exemplified by matrix metalloprotease inhibitors. [49][50][51][52] Therefore, one concern of hydroxamates as inhibitors of the endopeptidase is potential toxicity.…”