SPEED LIMITS FOR ARTIFICIAL RIBONUCLEASES

Bulge-Forming miRNases Cleave Oncogenic miRNAs at the Central Loop Region in a Sequence-Specific Manner

The selective degradation of disease-associated microRNA is promising for the development of new therapeutic approaches. In this study, we engineered a series of bulge-loop-forming oligonucleotides conjugated with catalytic peptide [(LeuArg)₂Gly]₂ (BC-miRNases) capable of recognizing and destroying oncogenic miR-17 and miR-21. The principle behind the design of BC-miRNase is the cleavage of miRNA at a three-nucleotide bulge loop that forms in the central loop region, which is essential for the biological competence of miRNA. A thorough study of mono- and bis-BC-miRNases (containing one or two catalytic peptides, respectively) revealed that: (i) the sequence of miRNA bulge loops and neighbouring motifs are of fundamental importance for efficient miRNA cleavage (i.e., motifs containing repeating pyrimidine-A bonds are more susceptible to cleavage); (ii) the incorporation of the second catalytic peptide in the same molecular scaffold increases the potency of BC-miRNase, providing a complete degradation of miR-17 within 72 h; (iii) the synergetic co-operation of BC-miRNases with RNase H accelerates the rate of miRNA catalytic cleavage by both the conjugate and the enzyme. Such synergy allows the rapid destruction of constantly emerging miRNA to maintain sufficient knockdown and achieve a desired therapeutic effect.

Strict conformational demands of RNA cleavage in bulge-loops created by peptidyl-oligonucleotide conjugates

Potent knockdown of pathogenic RNA in vivo is an urgent health need unmet by both small-molecule and biologic drugs. ‘Smart’ supramolecular assembly of catalysts offers precise recognition and potent destruction of targeted RNA, hitherto not found in nature. Peptidyl-oligonucleotide ribonucleases are here chemically engineered to create and attack bulge-loop regions upon hybridization to target RNA. Catalytic peptide was incorporated either via a centrally modified nucleotide (Type 1) or through an abasic sugar residue (Type 2) within the RNA-recognition motif to reveal striking differences in biological performance and strict structural demands of ribonuclease activity. None of the Type 1 conjugates were catalytically active, whereas all Type 2 conjugates cleaved RNA target in a sequence-specific manner, with up to 90% cleavage from 5-nt bulge-loops (BC5-α and BC5L-β anomers) through multiple cuts, including in folds nearby. Molecular dynamics simulations provided structural explanation of accessibility of the RNA cleavage sites to the peptide with adoption of an ‘in-line’ attack conformation for catalysis. Hybridization assays and enzymatic probing with RNases illuminated how RNA binding specificity and dissociation after cleavage can be balanced to permit turnover of the catalytic reaction. This is an essential requirement for inactivation of multiple copies of disease-associated RNA and therapeutic efficacy.

Unraveling mechanisms of the uncoordinated nucleophiles: theoretical elucidations of the cleavage of bis(p-nitrophenyl) phosphate mediated by zinc-complexes with apical nucleophiles

A theoretical approach was used to investigate the hydrolytic cleavage mechanisms of the bis(p-nitrophenyl) phosphate (BNPP⁻) catalyzed by Zn(ii)-complexes featuring uncoordinated nucleophiles. Ligand-based and alternative solvent-based nucleophilic attack reaction models are proposed. The pK_a values of the Zn(ii)-bound water molecules or ligands in the [Zn(LⁿH)(η-H₂O)(H₂O)]²⁺ (n = 1, 2 and 3) complexes, as well as the dimerization tendency of the mononuclear Zn(ii)-complexes, were found to significantly influence the reaction mechanisms. The Zn(ii)-L³ complexes were found to be more favorable for the hydrolytic cleavage of the BNPP⁻via a ligand-based nucleophilic attack pathway. This was due to the lower pK_a value for the deprotonation of the oxime ligand, the hard dimerization of the mononuclear Zn(ii)-L³ species, and the presence of an uncoordinated nucleophile. The origins of the uncoordinated reactions were systematically elucidated. The theoretical results reported here are in good agreement with experimental observations and more importantly, help to elucidate the factors that influence intermolecular nucleophilic attack reactions with coordinated/uncoordinated nucleophiles.

A theoretical approach was used to investigate the hydrolytic cleavage mechanisms of the bis(p-nitrophenyl) phosphate (BNPP⁻) catalyzed by Zn(ii)-complexes featuring uncoordinated nucleophiles.

Mechanistic Studies of Homo- and Heterodinuclear Zinc Phosphoesterase Mimics: What Has Been Learned?

Phosphoesterases hydrolyze the phosphorus oxygen bond of phosphomono-, di- or triesters and are involved in various important biological processes. Carboxylate and/or hydroxido-bridged dizinc(II) sites are a widespread structural motif in this enzyme class. Much effort has been invested to unravel the mechanistic features that provide the enormous rate accelerations observed for enzymatic phosphate ester hydrolysis and much has been learned by using simple low-molecular-weight model systems for the biological dizinc(II) sites. This review summarizes the knowledge and mechanistic understanding of phosphoesterases that has been gained from biomimetic dizinc(II) complexes, showing the power as well as the limitations of model studies.

Influence of conjugation and other structural changes on the activity of Cu²⁺ based PNAzymes

We have previously shown that PNA-neocuproine conjugates can act as artificial RNA restriction enzymes. In the present study we have additionally conjugated the PNA with different entities, such as oligoethers, peptides etc. and also constructed systems where the PNA is designed to clamp the target RNA forming a triplex. Some conjugations are detrimental for the activity while most are silent which means that conjugation can be done to alter physical properties without losing activity. Conjugation with a single oligoether close to the neocuproine does enhance the rate almost twofold compared to the system without the oligoether. The systems designed to clamp the RNA target by forming a triplex retain the activity if the added oligoT sequence is 5 PNA units or shorter and extends the arsenal of artificial RNA restriction enzymes. Changing the direction of a closing base pair, where the target RNA forms a bulge, from a GC to a CG pair enhances the rate of cleavage somewhat without compromising the selectivity, leading to the so far most efficient artificial nuclease reported.

Near-infrared luminescence and RNA cleavage ability of lanthanide Schiff base complexes derived from N,N'-bis(3-methoxysalicylidene)ethylene-1,2-diamine ligands

A complete series of lanthanide Schiff base salen-type complexes were prepared with trivalent lanthanide ions (Ln³⁺) and the N,N'-bis-(3-methoxysalicylidene)ethylene-1,2-diamine ligand (Ln³⁺=La³⁺, Ce³⁺, Pr³⁺, Nd³⁺, Sm³⁺, Eu³⁺, Gd³⁺, Tb³⁺, Dy³⁺, Ho³⁺, Er³⁺, Tm³⁺, Yb³⁺, Lu³⁺). Three unique crystal structures of La³⁺ and Pr³⁺N,N'-bis-(3-methoxysalicylidene)ethylene-1,2-diamine complexes, with the La³⁺ complex prepared in two different synthetic approaches, are reported, namely a dimeric [La(H₂L)(NO₃)₃]₂ (H₂L=N,N'-bis-(3-methoxysalicylidene)ethylene-1,2-diamine) complex, an asymmetric two-centered [La₂(H₂L)₂(NO₃)₆] complex and a discrete mononuclear [Pr(H₂L)(NO₃)₂(H₂O)₂] complex. For Nd³⁺ and Sm³⁺, an isotypic mononuclear [Nd(H₂L)(NO₃)₃] and 1D polymeric [Sm(H₂L)(NO₃)₃(MeOH)]_n structure was obtained, respectively. The whole series of complexes was tested for their ability to cleave the 20-mer RNA oligonucleotide 5'-AGC-GAU-AAG-AUU-CAU-AUA-UC-3'. Additionally three complexes (Ln³⁺=Nd³⁺, Sm³⁺, Ho³⁺) were tested for the cleavage of the 12-mer RNA oligonucleotide 5'-GCA-CCC-UGU-CAG-3'. A detailed luminescence study was additionally carried out and revealed that the Eu³⁺ complex emitted bright red light upon excitation at both 285.8nm and 394.4nm. The Nd³⁺, Er³⁺, and Yb³⁺ complexes showed strong emission in the near-infrared region after excitation at 380nm.

Hydrolytic Metallo-Nanozymes: From Micelles and Vesicles to Gold Nanoparticles

Although the term nanozymes was coined by us in 2004 to highlight the enzyme-like properties of gold nanoparticles passivated with a monolayer of Zn(II)-complexes in the cleavage of phosphate diesters, systems resembling those metallo-nanoparticles, like micelles and vesicles, have been the subject of investigation since the mid-eighties of the last century. This paper reviews what has been done in the field and compares the different nanosystems highlighting the source of catalysis and frequent misconceptions found in the literature.

Tri- and tetra-substituted cyclen based lanthanide(III) ion complexes as ribonuclease mimics: a study into the effect of log Ka, hydration and hydrophobicity on phosphodiester hydrolysis of the RNA-model 2-hydroxypropyl-4-nitrophenyl phosphate (HPNP)

A series of tetra-substituted 'pseudo' dipeptide ligands of cyclen (1,4,7,10,-tetraazacyclododecane) and a tri-substituted 3'-pyridine ligand of cyclen, and the corresponding lanthanide(III) complexes were synthesised and characterised as metallo-ribonuclease mimics. All complexes were shown to promote hydrolysis of the phosphodiester bond of 2-hydroxypropyl-4-nitrophenyl phosphate (HPNP, τ1/2 = 5.87 × 10(3) h), a well known RNA mimic. The La(III) and Eu(III) tri-substituted 3'-pyridine lanthanide(III) complexes being the most efficient in promoting such hydrolysis at pH 7.4 and at 37 °C; with τ1/2 = 1.67 h for La(III) and 1.74 h for Eu(III). The series was developed to provide the opportunity to investigate the consequences of altering the lanthanide(III) ion, coordination ability and hydrophobicity of a metallo-cavity on the rate of hydrolysis using the model phosphodiester, HPNP, at 37 °C. To further provide information on the role that the log Ka of the metal bound water plays in phosphodiester hydrolysis the protonation constants and the metal ion stability constants of both a tri and tetra-substituted 3'pyridine complex were determined. Our results highlighted several key features for the design of lanthanide(III) ribonucelase mimics; the presence of two metal bound water molecules are vital for pH dependent rate constants for Eu(III) complexes, optimal pH activity approximating physiological pH (∼7.4) may be achieved if the log Ka values for both MLOH and ML(OH)2 species occur in this region, small changes to hydrophobicity within the metallo cavity influence the rate of hydrolysis greatly and an amide adjacent to the metal ion capable of forming hydrogen bonds with the substrate is required for achieving fast hydrolysis.

Role of para-substitution in controlling phosphatase activity of dinuclear NiII complexes of Mannich-base ligands: experimental and DFT studies

Five dinuclear Ni^II complexes synthesized by Mannich reaction portray remarkable phosphatase activity where the tert-butyl complex exhibits the maximum reactivity.

Macrocyclic metal complexes for metalloenzyme mimicry and sensor development

Examples of proteins that incorporate one or more metal ions within their structure are found within a broad range of classes, including oxidases, oxidoreductases, reductases, proteases, proton transport proteins, electron transfer/transport proteins, storage proteins, lyases, rusticyanins, metallochaperones, sporulation proteins, hydrolases, endopeptidases, luminescent proteins, iron transport proteins, oxygen storage/transport proteins, calcium binding proteins, and monooxygenases. The metal coordination environment therein is often generated from residues inherent to the protein, small exogenous molecules (e.g., aqua ligands) and/or macrocyclic porphyrin units found, for example, in hemoglobin, myoglobin, cytochrome C, cytochrome C oxidase, and vitamin B12. Thus, there continues to be considerable interest in employing macrocyclic metal complexes to construct low-molecular weight models for metallobiosites that mirror essential features of the coordination environment of a bound metal ion without inclusion of the surrounding protein framework. Herein, we review and appraise our research exploring the application of the metal complexes formed by two macrocyclic ligands, 1,4,7-triazacyclononane (tacn) and 1,4,7,10-tetraazacyclododecane (cyclen), and their derivatives in biological inorganic chemistry. Taking advantage of the kinetic inertness and thermodynamic stability of their metal complexes, these macrocyclic scaffolds have been employed in the development of models that aid the understanding of metal ion-binding natural systems, and complexes with potential applications in biomolecule sensing, diagnosis, and therapy. In particular, the focus has been on "coordinatively unsaturated" metal complexes that incorporate a kinetically inert and stable metal-ligand moiety, but which also contain one or more weakly bound ligands, allowing for the reversible binding of guest molecules via the formation and dissociation of coordinate bonds. With regards to mimicking metallobiosites, examples are presented from our work on tacn-based complexes developed as simplified structural models for multimetallic enzyme sites. In particular, structural comparisons are made between multinuclear copper(II) complexes formed by such ligands and multicopper enzymes featuring type-2 and type-3 copper centers, such as ascorbate oxidase (AO) and laccase (Lc). Likewise, with the aid of relevant examples, we highlight the importance of cooperativity between either multiple metal centers or a metal center and a proximal auxiliary unit appended to the macrocyclic ligand in achieving efficient phosphate ester cleavage. Finally, the critical importance of the Zn(II)-imido and Zn(II)-phosphate interactions in Zn-cyclen-based systems for delivering highly sensitive electrochemical and fluorescent chemosensors is also showcased. The Account additionally highlights some of the factors that limit the performance of these synthetic nucleases and the practical application of the biosensors, and then identifies some avenues for the development of more effective macrocyclic constructs in the future.

Peptidyl-oligonucleotide conjugates demonstrate efficient cleavage of RNA in a sequence-specific manner

Described here is a new class of peptidyl-oligonucleotide conjugates (POCs) which show efficient cleavage of a target RNA in a sequence-specific manner. Through phosphoramidate attachment of a 17-mer TΨC-targeting oligonucleotide to amphiphilic peptide sequences containing leucine, arginine, and glycine, zero-linker conjugates are created which exhibit targeted phosphodiester cleavage under physiological conditions. tRNA(Phe) from brewer's yeast was used as a model target sequence in order to probe different structural variants of POCs in terms of selective TΨC-arm directed cleavage. Almost quantitative (97-100%) sequence-specific tRNA cleavage is observed for several POCs over a 24 h period with a reaction half-life of less than 1 h. Nontargeted cleavage of tRNA(Phe) or HIV-1 RNA is absent. Structure-activity relationships reveal that removal of the peptide's central glycine residue significantly decreases tRNA cleavage activity; however, this can be entirely restored through replacement of the peptide's C-terminal carboxylic acid group with the carboxamide functionality. Truncation of the catalytic peptide also has a detrimental effect on POC activity. Based on the encouraging results presented, POCs could be further developed with the aim of creating useful tools for molecular biology or novel therapeutics targeting specific messenger, miRNA, and genomic viral RNA sequences.

Enhancing Phosphate Diester Cleavage by a Zinc Complex through Controlling Nucleophile Coordination

Metal-ion complexes are the most effective artificial catalysts capable of cleaving phosphate diesters under mild aqueous conditions. A central strategy for making these complexes highly reactive has been to use ligand-based alcohols that are coordinated to the ion, providing an ionised nucleophile under neutral conditions but at the expense of deactivating it. We have created a highly reactive Zn complex that is 350-fold more reactive than an alcohol analogue by preventing the nucleophile binding to the metal ion. This strategy successfully delivers the benefits of efficient nucleophile delivery without strongly deactivating the metal ion Lewis acidity nor the oxyanion nucleophilicity. Varying the leaving group reveals that the transition state of the reaction is much further advanced than the reaction with hydroxide.

Catalytic zinc complexes for phosphate diester hydrolysis

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.

Metal-promoted synthesis, characterization, crystal structure and RNA cleavage ability of 2,6-diacetylpyridine bis(2-aminobenzoylhydrazone) lanthanide complexes

New 2,6-diacetylpyridine bis(2-aminobenzoylhydrazone) lanthanide complexes were formed in the metal-induced one-step [1+2] condensation reaction between 2,6-diacetylpyridine and 2-aminobenzoylhydrazide in the presence of lanthanide (La(3+), Pr(3+), Nd(3+), Sm(3+), Eu(3+), Gd(3+), Tb(3+), Dy(3+), Ho(3+), Er(3+), Tm(3+) or Yb(3+)) nitrates as template agents. The analytical and spectral characterizations of all the compounds were correlated with the single crystal X-ray structural determination of Eu(3+), Gd(3+), Tb(3+), Dy(3+) and Er(3+) nitrate complexes. The Eu(3+), Gd(3+), Tb(3+)and Dy(3+) complexes of pentadentate 2,6-diacetylpyridine bis(2-aminobenzoylhydrazone) with the N3O2 set of donor atoms display a high and relatively rare coordination number of 11, whereas the Er(3+) ion complex is 9-coordinated, which is consistent with the lanthanide contraction phenomenon. The scission of 21-mer RNA was assessed for Eu(3+), Gd(3+) and Tb(3+) nitrate complexes. Lanthanide complexes not covalently attached to the oligonucleotide are able to cleave RNA at the target site in a sequence-selective or non-selective manner depending on the presence of protecting 12-mer 2'OMe RNA.

Trifunctional metal ion-catalyzed solvolysis: Cu(II)-promoted methanolysis of N,N-bis(2-picolyl) benzamides involves unusual Lewis acid activation of substrate, delivery of coordinated nucleophile, powerful assistance of the leaving group departure

The methanolyses of Cu(II) complexes of a series of N,N-bis(2-picolyl) benzamides (4a-g) bearing substituents X on the aromatic ring were studied under (s)(s)pH-controlled conditions at 25 °C. The active form of the complexes at neutral (s)(s)pH has a stoichiometry of 4:Cu(II):((-)OCH(3))(HOCH(3)) and decomposes unimolecularly with a rate constant k(x). A Hammett plot of log(k(x)) vs σ(x) values has a ρ(x) of 0.80 ± 0.05. Solvent deuterium kinetic isotope effects of 1.12 and 1.20 were determined for decomposition of the 4-nitro and 4-methoxy derivatives, 4b:Cu(II):((-)OCH(3))(HOCH(3)) and 4g:Cu(II):((-)OCH(3))(HOCH(3)), in the plateau region of the (s)(s)pH/log(k(x)) profiles in both CH(3)OH and CH(3)OD. Activation parameters for decomposition of these complexes are ΔH(++) = 19.1 and 21.3 kcal mol(-1) respectively and ΔS(++) = -5.1 and -2 cal K(-1) mol(-1). Density functional theory (DFT) calculations for the reactions of the Cu(II):((-)OCH(3))(HOCH(3)) complexes of 4a,b and g (4a, X = 3,5-dinitro) were conducted to probe the relative transition state energies and geometries of the different states. The experimental and computational data support a mechanism where the metal ion is coordinated to the N,N-bis(2-picolyl) amide unit and positioned so that it permits delivery of a coordinated Cu(II):((-)OCH(3)) nucleophile to the C═O in the rate-limiting transition state (TS) of the reaction. This proceeds to a tetrahedral intermediate INT, occupying a shallow minimum on the free energy surface with the Cu(II) coordinated to both the methoxide and the amidic N. Breakdown of INT is a virtually barrierless process, involving a Cu(II)-assisted departure of the bis(2-picolyl)amide anion. The analysis of the data points to a trifunctional role for the metal ion in the solvolysis mechanism where it activates intramolecular nucleophilic attack on the C═O group by coordination to an amidic N in the first step of the reaction and subsequently assists leaving group departure in the second step. The catalysis is very large; compared with the second order rate constant for methoxide attack on 4b, the computed reaction of CH3O(-) and 4b:Cu(II):(HOCH(3))(2) is accelerated by roughly 2.0 × 10(16) times.

Solvent induced cooperativity of Zn(II) complexes cleaving a phosphate diester RNA analog in methanol

The kinetics of cyclization of 2-hydroxypropyl p-nitrophenyl phosphate (1) promoted by two mononuclear Zn(II) catalytic complexes of bis(2-pyridylmethyl)benzylamine (4) and bis(2-methyl 6-pyridylmethyl)benzylamine (5) in methanol were studied under (s)(s)pH-controlled conditions (where (s)(s)pH refers to [H(+)] activity in methanol). Potentiometric titrations of the ligands in the absence and presence of Zn(2+) and a non-reactive model for 1 (2-hydroxylpropyl isopropyl phosphate (HPIPP, 6)) indicate that the phosphate is bound tightly to the 4:Zn(II) and 5:Zn(II) complexes as L:Zn(II):6(-), and that each of these undergoes an additional ionization to produce L:Zn(II):6(-):((-)OCH(3)) or a bound deprotonated form of the phosphate, L:Zn(II):6(2-). Kinetic studies as a function of [L:Zn(II)] indicate that the rate is linear in [L:Zn(II)] at concentrations well above those required for complete binding of the substrate. Plots of the second order rate constants (defined as the gradient of the rate constant vs. [complex] plot) vs. (s)(s)pH in methanol are bell-shaped with rate maxima of 23 dm mol(-1) s(-1) and 146 dm mol(-1) s(-1) for 4:Zn(II) and 5:Zn(II), respectively, at their (s)(s)pH maxima of 10.5 and 10. A mechanism is proposed that involves binding of one molecule of complex to the phosphate to yield a poorly reactive 1 : 1 complex, which associates with a second molecule of complex to produce a transient cooperative 2 : 1 complex within which the cyclization of 1 is rapid. The observations support an effect of the reduced polarity solvent that encourages the cooperative association of phosphate and two independent mononuclear complexes to give a reactive entity.

The Utility of 2,2′-Bipyrimidine in Lanthanide Chemistry: From Materials Synthesis to Structural and Physical Properties

This paper reviews the recent investigations undertaken on the use of 2,2′-bipyrimidine (bpm) as a ligand for designing molecular complexes as well as polymeric lanthanide materials. A special emphasis is put on the ability of this polydentate neutral ligand to yield compounds of various dimensionalities, to act as a connector between these large ions, and influence their emissive and magnetic properties. This ligand can adopt a terminal or a bridging coordination mode with lanthanide ions, thus generating a wealth of frameworks of various topologies with the 4f elements. The main focus of this review is to show the originality brought by bpm in lanthanide structural chemistry and solid-state photophysics and magnetism.