Catalytic Zinc Complexes for Phosphate Diester Hydrolysis

Abstract

Creating efficient artificial catalysts that can compete with biocatalysis has been an enduring challenge which has yet to be met. Reported herein is the synthesis and characterization of a series of zinc complexes designed to catalyze the hydrolysis of phosphate diesters. By introducing a hydrated aldehyde into the ligand we achieve turnover for DNA-like substrates which, combined with ligand methylation, increases reactivity by two orders of magnitude. In contrast to current orthodoxy and mechanistic explanations, we propose a mechanism where the nucleophile is not coordinated to the metal ion, but involves a tautomer with a more effective Lewis acid and more reactive nucleophile. This data suggests a new strategy for creating more efficient metal ion based catalysts, and highlights a possible mode of action for metalloenzymes.Substantial efforts have been made to create metal ion complexes that are effective catalysts for phosphate ester hydrolysis.[1] These compounds provide insight into how biological catalysts might function, and hold the promise of creating novel therapeutics or laboratory agents for manipulating nucleic acids.[2] The challenges of sufficient activity to function usefully under biological conditions and achieving turnover remain. Herein we report how incorporating a hydrated aldehyde as a nucleophile can enhance reactivity and lead to turnover. Our mechanistic explanation provides a new strategy for designing metal ion complexes with nuclease activity.In developing artificial metal ion complexes to cleave RNA, the 2'OH group provides an intramolecular nucleophile which can be exploited.[3] For DNA, this is not possible, and the most effective strategies to date have used metal-ioncoordinated nucleophiles to enhance the attack at phosphorus. Chin and co-workers established that the effectiveness of this nucleophile can depend strongly on ligand structure.[4] If this nucleophile is part of the ligand structure, then its efficiency can be enhanced through careful design, and substantial rate enhancements achieved compared to that a metal-bound hydroxide. However, the flaw in this strategy is that the product is a phosphorylated ligand which is very stable, and so the complexes are not catalytic.A potential solution to this problem is suggested by the hydrolysis of model compounds also containing keto or aldehyde groups.[5] Bender and Silver showed that benzoate ester hydrolysis can be accelerated 10 5 -fold by the presence of an ortho aldehyde group. This hydrate form of the aldehyde provides an effective nucleophile, thus producing a product which can readily decompose to reform the carbonyl. [6] Similar effects have been reported for phosphate ester cleavage. [7] To create a catalytic system, Menger and Whitesell incorporated aldehydes into micellar head groups, and these aggregates showed both enhanced activity and turnover. [8] Interestingly, recent work with sulfatases and phosphonohydrolases has shown that a formyl glycine residue in the active site is believed to act as a nu...

Enantioselective Hydrolysis of Amino Acid Esters Promoted by Bis(β-cyclodextrin) Copper Complexes

“…Over the years, significant efforts have been dedicated to the biomimetic study of metalloenzymes to understand their structures and functions and design analogues to mimic the native enzymes’ structures and functions 3 . In the past few decades, synthetic compounds with functions resembling those of, for example, hydrolases, oxidases, and reductases have been reported 4 5 6 7 8 . Remarkable progress has been made in mimicking the functions of the enzymes that mediate electron transfer with respective to the catalytic efficiency 9 10 .…”

“…Remarkable progress has been made in mimicking the functions of the enzymes that mediate electron transfer with respective to the catalytic efficiency 9 10 . However, studies of hydrolase mimetics have lagged far behind, regarding to either catalytic efficiency or selectivity 5 7 8 11 . Specifically, in biomimetic chemistry, the rational design of enantioselective hydrolase mimics remains challenging.…”

Nuclease Activity of Diaza-Crown Ether Complexes of Cerium(III) with Different Functional Groups as Side Arms

“…Artificial nucleases, as cleavage agents of nucleic acids, synthesised chemically, have received considerable interest because of their potential applications in the fields of molecular biology and drug development or in elucidating the mechanisms of the corresponding restriction enzymes and nucleases [1][2][3][4][5][6]. Compared with natural enzymes, artificial nucleases have simpler molecular structures and exhibit higher stability and a lesser dependence on reaction conditions as catalysts in the hydrolysis of phosphodiesters or nucleic acids [7,8]. It is known that the choice of metal ions as catalytic centres is a crucial factor in the design and synthesis of metal complexes as artificial metallonucleases.…”