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1.
Molecules ; 29(9)2024 May 03.
Artículo en Inglés | MEDLINE | ID: mdl-38731616

RESUMEN

PNAzymes are a group of artificial enzymes which show promising results in selective and efficient cleavage of RNA targets. In the present study, we introduce a series of metal chelating groups based on N,N-bis(2-picolyl) groups (parent, 6-methyl and 6-amino substituted) as the active sites of novel PNAzymes. An improved synthetic route for the 6-amino analogues is described. The catalytic activity of the chelating groups for cleaving phosphodiesters were assessed with the model substrate 2-hydroxypropyl p-nitrophenyl phosphate (HPNPP), confirming that the zinc complexes have the reactivity order of parent < 2-methyl < 2-amino. The three ligands were conjugated to a PNA oligomer to form three PNAzymes which showed the same order of reactivity and some sensitivity to the size of the RNA bulge designed into the catalyst-substrate complex. This work demonstrates that the kinetic activity observed for the model substrate HPNPP could be translated onto the PNAzymes, but that more reactive Zn complexes are required for such PNAzymes to be viable therapeutic agents.


Asunto(s)
Zinc , Zinc/química , Ácidos Nucleicos de Péptidos/química , Quelantes/química , ARN/química , ARN/metabolismo , Catálisis , Aminas/química , Cinética , Organofosfatos
2.
Chem Res Toxicol ; 36(12): 1921-1929, 2023 12 18.
Artículo en Inglés | MEDLINE | ID: mdl-37983188

RESUMEN

Human exposure to DNA alkylating agents is poorly characterized, partly because only a limited range of specific alkyl DNA adducts have been quantified. The human DNA repair protein, O6-methylguanine O6-methyltransferase (MGMT), irreversibly transfers the alkyl group from DNA O6-alkylguanines (O6-alkGs) to an acceptor cysteine, allowing the simultaneous detection of multiple O6-alkG modifications in DNA by mass spectrometric analysis of the MGMT active site peptide (ASP). Recombinant MGMT was incubated with oligodeoxyribonucleotides (ODNs) containing different O6-alkGs, Temozolomide-methylated calf thymus DNA (Me-CT-DNA), or human colorectal DNA of known O6-MethylG (O6-MeG) levels. It was digested with trypsin, and ASPs were detected and quantified by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry. ASPs containing S-methyl, S-ethyl, S-propyl, S-hydroxyethyl, S-carboxymethyl, S-benzyl, and S-pyridyloxobutyl cysteine groups were detected by incubating MGMT with ODNs containing the corresponding O6-alkGs. The LOQ of ASPs containing S-methylcysteine detected after MGMT incubation with Me-CT-DNA was <0.05 pmol O6-MeG per mg CT-DNA. Incubation of MGMT with human colorectal DNA produced ASPs containing S-methylcysteine at levels that correlated with those of O6-MeG determined previously by HPLC-radioimmunoassay (r2 = 0.74; p = 0.014). O6-CMG, a putative O6-hydroxyethylG adduct, and other potential unidentified MGMT substrates were also detected in human DNA samples. This novel approach to the identification and quantitation of O6-alkGs in human DNA has revealed the existence of a human DNA alkyl adductome that remains to be fully characterized. The methodology establishes a platform for characterizing the human DNA O6-alkG adductome and, given the mutagenic potential of O6-alkGs, can provide mechanistic information about cancer pathogenesis.


Asunto(s)
Neoplasias Colorrectales , O(6)-Metilguanina-ADN Metiltransferasa , Humanos , Dominio Catalítico , Cisteína , ADN/química , Reparación del ADN , Espectrometría de Masas , O(6)-Metilguanina-ADN Metiltransferasa/genética , Oligodesoxirribonucleótidos/química , Péptidos
3.
Chemistry ; 26(14): 3065-3073, 2020 Mar 09.
Artículo en Inglés | MEDLINE | ID: mdl-31774202

RESUMEN

The hydrophobic central cavity of a water-soluble M8 L12 cubic coordination cage can accommodate a range of phospho-diester and phospho-triester guests such as the insecticide "dichlorvos" (2,2-dichlorovinyl dimethyl phosphate) and the chemical warfare agent analogue di(isopropyl) chlorophosphate. The accumulation of hydroxide ions around the cationic cage surface due to ion-pairing in solution generates a high local pH around the cage, resulting in catalysed hydrolysis of the phospho-triester guests. A series of control experiments unexpectedly demonstrates that-in marked contrast to previous cases-it is not necessary for the phospho-triester substrates to be bound inside the cavity for catalysed hydrolysis to occur. This suggests that catalysis can occur on the exterior surface of the cage as well as the interior surface, with the exterior-binding catalysis pathway dominating here because of the small binding constants for these phospho-triester substrates in the cage cavity. These observations suggest that cationic but hydrophobic surfaces could act as quite general catalysts in water by bringing substrates into contact with the surface (via the hydrophobic effect) where there is also a high local concentration of anions (due to ion pairing/electrostatic effects).

4.
Langmuir ; 36(46): 13843-13852, 2020 Nov 24.
Artículo en Inglés | MEDLINE | ID: mdl-33172276

RESUMEN

Polyelectrolyte adhesives, either poly[2-(dimethylamino)ethyl methacrylate] or poly(methacrylic acid), functionalized with a surface-active calix[4]resorcinarene were grafted onto silicon wafers. Adhesion studies on these grafted-to brushes using polyelectrolyte hydrogels of opposite charge showed that it is the calix[4]resorcinarene, rather than adsorption of polyelectrolyte monomers, that adheres the brush to the silicon substrate. The adhesion measured was similar to that measured using polymers grafted from the surface, and was stronger than a control layer of poly(vinyl acetate) under the same test conditions. The limiting factor was determined to be adhesive failure at the hydrogel-brush interface, rather than the brush-silicon interface. Therefore, the adhesion has not been adversely affected by changing from a grafted-from to a grafted-to brush, demonstrating the possibility of a one-pot approach to creating switchable adhesives.

5.
J Org Chem ; 85(10): 6489-6497, 2020 05 15.
Artículo en Inglés | MEDLINE | ID: mdl-32309943

RESUMEN

Phosphate and sulfate esters have important roles in regulating cellular processes. However, while there has been substantial experimental and computational investigation of the mechanisms and the transition states involved in phosphate ester hydrolysis, there is far less work on sulfate ester hydrolysis. Here, we report a detailed computational study of the alkaline hydrolysis of diaryl sulfate diesters, using different DFT functionals as well as mixed implicit/explicit solvation with varying numbers of explicit water molecules. We consider the impact of the computational model on computed linear free-energy relationships (LFER) and the nature of the transition states (TS) involved. We obtain good qualitative agreement with experimental LFER data when using a pure implicit solvent model and excellent agreement with experimental kinetic isotope effects for all models used. Our calculations suggest that sulfate diester hydrolysis proceeds through loose transition states, with minimal bond formation to the nucleophile and bond cleavage to the leaving group already initiated. Comparison to prior work indicates that these TS are similar in nature to those for the alkaline hydrolysis of neutral arylsulfonate monoesters or charged phosphate diesters and fluorophosphates. Obtaining more detailed insights into the transition states involved assists in understanding the selectivity of enzymes that hydrolyze these reactions.

6.
J Am Chem Soc ; 141(44): 17847-17853, 2019 11 06.
Artículo en Inglés | MEDLINE | ID: mdl-31642667

RESUMEN

A molecular signal displayed on the external surface of one population of vesicles was used to trigger a catalytic process on the inside of a second population of vesicles. The key recognition event is the transfer of a protein (NeutrAvidin) bound to vesicles displaying desthiobiotin to vesicles displaying biotin. The desthiobiotin-protein complex was used to anchor a synthetic transducer in the outer leaflet of the vesicles, and when the protein was displaced, the transducer translocated across the bilayer to expose a catalytic headgroup to the internal vesicle solution. As a result, an ester substrate encapsulated on the inside of this second population of vesicles was hydrolyzed to give a fluorescence output signal. The protein has four binding sites, which leads to multivalent interactions with membrane-anchored ligands and very high binding affinities. Thus, biotin, which has a dissociation constant 3 orders of magnitude higher than desthiobiotin, did not displace the protein from the membrane-anchored transducer, and membrane-anchored biotin displayed on the surface of a second population of vesicles was required to generate an effective input signal.


Asunto(s)
Células Artificiales/química , Avidina/química , Liposomas/química , Transducción de Señal , Biotina/análogos & derivados , Biotina/química , Membrana Dobles de Lípidos/química , Fosfatidilcolinas/química , Fosfatidiletanolaminas/química
7.
Acc Chem Res ; 51(9): 2073-2082, 2018 09 18.
Artículo en Inglés | MEDLINE | ID: mdl-30085644

RESUMEN

We describe here a family of coordination cages with interesting structural, guest-binding, and catalytic properties. Flexible bridging ligands containing two bidentate pyrazolylpyridine termini assemble with transition-metal dications to afford coordination cages containing a metal ion at each vertex, a bridging ligand spanning each edge, and a 2:3 metal:ligand ratio. This stoichiometry is expressed in structures ranging from M4L6 tetrahedra to M16L24 tetracapped truncated tetrahedra, which are stabilized by the formation of π-stacked arrays between electron-rich and electron-poor ligand segments that form around the cage periphery. In some cases concentration- and/or temperature-dependent equilibria between multiple cage structures occur, arising from a balance between entropy, which favors the formation of a larger number of smaller assemblies, and enthalpy, which maximizes both interligand aromatic stacking and solvophobic effects in the larger assembles. The cages are hollow and can accommodate guests-often anions or solvent molecules-in the central cavity. For one cage family, M8L12 species with an approximately cubic structure and a ca. 400 Å3 cavity, the guest binding properties have been studied extensively. This cage can accommodate a wide range of neutral organic guests, with binding in water being driven principally by the hydrophobic effect, which leads to binding constants of up to 108 M-1. The accumulation of a large amount of empirical data on guest binding in the M8L12 cage in water provided the basis for a predictive tool for in silico screening of potential guests using the molecular docking program GOLD; this methodology has allowed the identification of numerous new guests with accurately predicted binding constants and provides a transformative new approach to exploring the host/guest chemistry of cages. Binding of benzisoxazole inside the M8L12 cage results in substantial rate enhancements-by a factor of up to 2 × 105-of the Kemp elimination, in which benzisoxazole reacts to give 2-cyanophenolate. Catalysis arises because the 16+ cage cation accumulates anions around the surface by ion pairing, leading to a high effective concentration of hydroxide ions surrounding the guest even when the bulk pH is modest. Thus, the catalysis relies on the operation of two orthogonal interactions that bring the reaction partners together: hydrophobic guest binding in the cavity, which is lined with CH groups from the ligands, and ion pairing around the highly cationic cage surface. A consequence of this is that under some conditions the product of the cage-catalyzed Kemp elimination (the 2-cyanophenolate anion) itself accumulates around the cage surface and deprotonates another benzisoxazole guest, perpetuating the reaction in an autocatalytic manner. Thus, different anions accumulating around the cage can act as partners for reaction with a cavity-bound guest, opening up the possibility that the M8L12 cage can act as a general catalyst for reactions of electrophilic guests with surface-bound anions.

8.
J Am Chem Soc ; 140(8): 2821-2828, 2018 02 28.
Artículo en Inglés | MEDLINE | ID: mdl-29412665

RESUMEN

The Kemp elimination (reaction of benzisoxazole with base to give 2-cyanophenolate) is catalyzed in the cavity of a cubic M8L12 coordination cage because of a combination of (i) benzisoxazole binding in the cage cavity driven by the hydrophobic effect, and (ii) accumulation of hydroxide ions around the 16+ cage surface driven by ion-pairing. Here we show how reaction of the cavity-bound guest is modified by the presence of other anions which can also accumulate around the cage surface and displace hydroxide, inhibiting catalysis of the cage-based reaction. Addition of chloride or fluoride inhibits the reaction with hydroxide to the extent that a new autocatalytic pathway becomes apparent, resulting in a sigmoidal reaction profile. In this pathway the product 2-cyanophenolate itself accumulates around the cationic cage surface, acting as the base for the next reaction cycle. The affinity of different anions for the cage surface is therefore 2-cyanophenolate (generating autocatalysis) > chloride > fluoride (which both inhibit the reaction with hydroxide but cannot deprotonate the benzisoxazole guest) > hydroxide (default reaction pathway). The presence of this autocatalytic pathway demonstrates that a reaction of a cavity-bound guest can be induced with different anions around the cage surface in a controllable way; this was confirmed by adding different phenolates to the reaction, which accelerate the Kemp elimination to different extents depending on their basicity. This represents a significant step toward the goal of using the cage as a catalyst for bimolecular reactions between a cavity-bound guest and anions accumulated around the surface.

9.
Chemistry ; 24(7): 1554-1560, 2018 Feb 01.
Artículo en Inglés | MEDLINE | ID: mdl-29083066

RESUMEN

The cavity of an M8 L12 cubic coordination cage can accommodate a cluster of ten water molecules in which the average number of hydrogen bonds per water molecule is 0.5 H-bonds less than it would be in the bulk solution. The presence of these "hydrogen-bond frustrated" or "high-energy" water molecules in the cavity results in the hydrophobic effect associated with guest binding being predominantly enthalpy-based, as these water molecules can improve their hydrogen-bonding environment on release. This contrasts with the classical form of the hydrophobic effect in which the favourable entropy change associated with release of ordered molecules from hydrophobic surfaces dominates. For several guests Van't Hoff plots showed that the free energy of binding in water is primarily enthalpy driven. For five homologous pairs of guests related by the presence or absence of a CH2 group, the incremental changes to ΔH and TΔS for guest binding-that is, ΔΔH and TΔΔS, the difference in contributions arising from the CH2 group-are consistently 5(±1) kJ mol-1 for ΔΔH and 0(±1) kJ mol-1 for TΔΔS. This systematic dominance of ΔH in the binding of hydrophobic guests is consistent with the view that guest binding is dominated by release of "high energy" water molecules into a more favourable solvation environment, as has been demonstrated recently for some members of the cucurbituril family.

10.
Org Biomol Chem ; 16(12): 2060-2073, 2018 03 28.
Artículo en Inglés | MEDLINE | ID: mdl-29508879

RESUMEN

ß-Phosphoglucomutase (ß-PGM) has served as an important model system for understanding biological phosphoryl transfer. This enzyme catalyzes the isomerization of ß-glucose-1-phosphate to ß-glucose-6-phosphate in a two-step process proceeding via a bisphosphate intermediate. The conventionally accepted mechanism is that both steps are concerted processes involving acid-base catalysis from a nearby aspartate (D10) side chain. This argument is supported by the observation that mutation of D10 leaves the enzyme with no detectable activity. However, computational studies have suggested that a substrate-assisted mechanism is viable for many phosphotransferases. Therefore, we carried out empirical valence bond (EVB) simulations to address the plausibility of this mechanistic alternative, including its role in the abolished catalytic activity of the D10S, D10C and D10N point mutants of ß-PGM. In addition, we considered both of these mechanisms when performing EVB calculations of the catalysis of the wild type (WT), H20A, H20Q, T16P, K76A, D170A and E169A/D170A protein variants. Our calculated activation free energies confirm that D10 is likely to serve as the general base/acid for the reaction catalyzed by the WT enzyme and all its variants, in which D10 is not chemically altered. Our calculations also suggest that D10 plays a dual role in structural organization and maintaining electrostatic balance in the active site. The correct positioning of this residue in a catalytically competent conformation is provided by a functionally important conformational change in this enzyme and by the extensive network of H-bonding interactions that appear to be exquisitely preorganized for the transition state stabilization.


Asunto(s)
Simulación por Computador , Proteínas Mutantes/genética , Fosfoglucomutasa/genética , Animales , Catálisis , Dominio Catalítico , Humanos , Enlace de Hidrógeno , Transferasas Intramoleculares/metabolismo , Conformación Proteica , Electricidad Estática , Especificidad por Sustrato , Termodinámica
11.
Biochemistry ; 56(30): 3923-3933, 2017 08 01.
Artículo en Inglés | MEDLINE | ID: mdl-28678475

RESUMEN

Catalytically promiscuous enzymes are an attractive frontier for biochemistry, because enzyme promiscuities not only plausibly explain enzyme evolution through the mechanism of gene duplication but also could provide an efficient route to changing the catalytic function of proteins by mimicking this evolutionary process. PP1γ is an effectively promiscuous phosphatase for the hydrolysis of both monoanionic and dianionic phosphate ester-based substrates. In addition to its native phosphate monoester substrate, PP1γ catalyzes the hydrolysis of aryl methylphosphonates, fluorophosphate esters, phosphorothioate esters, and phosphodiesters, with second-order rate accelerations that fall within the narrow range of 1011-1013. In contrast to the different transition states in the uncatalyzed hydrolysis reactions of these substrates, PP1γ catalyzes their hydrolysis through similar transition states. PP1γ does not catalyze the hydrolysis of a sulfate ester, which is unexpected. The PP1γ active site is tolerant of variations in the geometry of bound ligands, which permit the effective catalysis even of substrates whose steric requirements may result in perturbations to the positioning of the transferring group, both in the initial enzyme-substrate complex and in the transition state. The conservative mutation of arginine 221 to lysine results in a mutant that is a more effective catalyst toward monoanionic substrates. The surprising conversion of substrate preference lends support to the notion that mutations following gene duplication can result in an altered enzyme with different catalytic capabilities and preferences and may provide a pathway for the evolution of new enzymes.


Asunto(s)
Modelos Moleculares , Proteína Fosfatasa 1/metabolismo , Sustitución de Aminoácidos , Arginina/química , Unión Competitiva , Biocatálisis , Dominio Catalítico , Inhibidores Enzimáticos/farmacología , Estabilidad de Enzimas , Evolución Molecular , Humanos , Enlace de Hidrógeno , Hidrólisis , Ligandos , Lisina/química , Conformación Molecular , Mutagénesis Sitio-Dirigida , Mutación , Nitrofenoles/química , Nitrofenoles/metabolismo , Organofosfonatos/química , Organofosfonatos/metabolismo , Compuestos Organofosforados/química , Compuestos Organofosforados/metabolismo , Compuestos Organotiofosforados/química , Compuestos Organotiofosforados/metabolismo , Proteína Fosfatasa 1/antagonistas & inhibidores , Proteína Fosfatasa 1/química , Proteína Fosfatasa 1/genética , Proteínas Recombinantes/química , Proteínas Recombinantes/metabolismo , Especificidad por Sustrato
12.
J Am Chem Soc ; 139(18): 6461-6466, 2017 05 10.
Artículo en Inglés | MEDLINE | ID: mdl-28462993

RESUMEN

Membrane signaling proteins transduce information across lipid bilayer membranes in response to extra-cellular binding of chemical messengers. The design of chemical systems that initiate transmembrane signal transduction through molecular binding events is a critical step toward preparing responsive synthetic vesicles. Here we report a vesicle-based signaling system controlled by a metal cation binding event. Competition between binding of copper ions to a membrane-embedded synthetic transducer and to an extra-vesicle messenger (EDTA) is used to control translocation of the transducer across the lipid bilayer. The translocation process is coupled to activation of a catalyst that turns over encapsulated substrates on the inside of the vesicle to generate an amplified fluorescence output signal. External EDTA and copper ions can be used to reversibly switch catalysis inside the vesicles on and off in a controlled manner.


Asunto(s)
Cobre/metabolismo , Cobre/farmacología , Membrana Dobles de Lípidos/metabolismo , Transducción de Señal/efectos de los fármacos , Cobre/química , Ácido Edético/farmacología , Fluorescencia , Concentración de Iones de Hidrógeno , Iones/química , Iones/metabolismo , Membrana Dobles de Lípidos/química , Conformación Molecular
13.
J Am Chem Soc ; 139(44): 15768-15773, 2017 11 08.
Artículo en Inglés | MEDLINE | ID: mdl-28876061

RESUMEN

The on-demand delivery of drug molecules from nanoscale carriers with spatiotemporal control is a key challenge in modern medicine. Here we show that lipid bilayer vesicles (liposomes) can be triggered to release an encapsulated molecular cargo in response to an external control signal by employing an artificial transmembrane signal transduction mechanism. A synthetic signal transducer embedded in the lipid bilayer membrane acts as a switchable catalyst, catalyzing the formation of surfactant molecules inside the vesicle in response to a change in external pH. The surfactant permeabilizes the lipid bilayer membrane to facilitate release of an encapsulated hydrophilic cargo. In the absence of the pH control signal, the catalyst is inactive, and the cargo remains encapsulated within the vesicle.


Asunto(s)
Biomimética , Permeabilidad de la Membrana Celular , Sistemas de Liberación de Medicamentos/métodos , Membrana Dobles de Lípidos/metabolismo , Transducción de Señal , Concentración de Iones de Hidrógeno , Interacciones Hidrofóbicas e Hidrofílicas , Liposomas , Tensoactivos/metabolismo
14.
Org Biomol Chem ; 15(35): 7308-7316, 2017 Sep 13.
Artículo en Inglés | MEDLINE | ID: mdl-28819656

RESUMEN

Phosphoryl transfer reactions can proceed through several plausible mechanisms, and the potential for both solvent and substrate-assisted pathways (involving proton transfer to the phosphoryl oxygens) complicates both experimental and computational interpretations. To avoid this problem, we have used electronic structure calculations to probe the mechanisms of the reactions of pyridinio-N-phosphonates with pyridine. These compounds avoid the additional complexity introduced by proton transfer between the nucleophile and the leaving group, while also serving as a valuable model for biological P-N cleavage. Through a comparative study of a range of substrates of varying basicity, we demonstrate a unified concerted mechanism for the phosphoryl transfer reactions of these model compounds, proceeding through a dissociative transition state. Finally, a comparison of these transition states with previously characterized transition states for related compounds provides a more complete model for non-enzymatic phosphoryl transfer, which is a critical stepping stone to being able to fully understand phosphoryl transfer in biology.


Asunto(s)
Organofosfonatos/química , Fosfatos/química , Piridinas/química , Teoría Cuántica , Estructura Molecular , Fosfatos/metabolismo , Fosforilación , Protones
15.
J Am Chem Soc ; 138(33): 10664-73, 2016 08 24.
Artículo en Inglés | MEDLINE | ID: mdl-27471914

RESUMEN

Despite the numerous experimental and theoretical studies on phosphate monoester hydrolysis, significant questions remain concerning the mechanistic details of these biologically critical reactions. In the present work we construct a linear free energy relationship for phosphate monoester hydrolysis to explore the effect of modulating leaving group pKa on the competition between solvent- and substrate-assisted pathways for the hydrolysis of these compounds. Through detailed comparative electronic-structure studies of methyl phosphate and a series of substituted aryl phosphate monoesters, we demonstrate that the preferred mechanism is dependent on the nature of the leaving group. For good leaving groups, a strong preference is observed for a more dissociative solvent-assisted pathway. However, the energy difference between the two pathways gradually reduces as the leaving group pKa increases and creates mechanistic ambiguity for reactions involving relatively poor alkoxy leaving groups. Our calculations show that the transition-state structures vary smoothly across the range of pKas studied and that the pathways remain discrete mechanistic alternatives. Therefore, while not impossible, a biological catalyst would have to surmount a significantly higher activation barrier to facilitate a substrate-assisted pathway than for the solvent-assisted pathway when phosphate is bonded to good leaving groups. For poor leaving groups, this intrinsic preference disappears.

16.
Soft Matter ; 12(22): 5022-8, 2016 Jun 14.
Artículo en Inglés | MEDLINE | ID: mdl-27160067

RESUMEN

For environmentally-switchable adhesive systems to be reused repeatedly, the adhesive strength must not deteriorate after each adhesion cycle. An important criterion to achieve this goal is that the integrity of the interface must be retained after each adhesion cycle. Furthermore, in order to have practical benefits, reversing the adhesion must be a relatively rapid process. Here, a double-network hydrogel of poly(methacrylic acid) and poly[oligo(ethylene glycol)methyl ether methacrylate] is shown to undergo adhesive failure during pH-switchable adhesion with a grafted (brush) layer of polycationic poly[2-(diethyl amino)ethyl methacrylate], and can be reused at least seven times. The surfaces are attached at pH 6 and detached at pH 1. A single-network hydrogel of poly(methacrylic acid), also exhibits pH-switchable adhesion with poly[2-(diethyl amino)ethyl methacrylate] but cohesive failure leads to an accumulation of the hydrogel on the brush surface and the hydrogel can only be reused at different parts of that surface. Even without an environmental stimulus (i.e. attaching and detaching at pH 6), the double-network hydrogel can be used up to three times at the same point on the brush surface. The single-network hydrogel cannot be reused under such circumstances. Finally, the time taken for the reuse of the double-network hydrogel is relatively rapid, taking no more than an hour to reverse the adhesion.

17.
J Am Chem Soc ; 137(3): 1081-93, 2015 Jan 28.
Artículo en Inglés | MEDLINE | ID: mdl-25423607

RESUMEN

Understanding phosphoryl and sulfuryl transfer is central to many biochemical processes. However, despite decades of experimental and computational studies, a consensus concerning the precise mechanistic details of these reactions has yet to be reached. In this work we perform a detailed comparative theoretical study of the hydrolysis of p-nitrophenyl phosphate, methyl phosphate and p-nitrophenyl sulfate, all of which have served as key model systems for understanding phosphoryl and sulfuryl transfer reactions, respectively. We demonstrate the existence of energetically similar but mechanistically distinct possibilities for phosphate monoester hydrolysis. The calculated kinetic isotope effects for p-nitrophenyl phosphate provide a means to discriminate between substrate- and solvent-assisted pathways of phosphate monoester hydrolysis, and show that the solvent-assisted pathway dominates in solution. This preferred mechanism for p-nitrophenyl phosphate hydrolysis is difficult to find computationally due to the limitations of compressing multiple bonding changes onto a 2-dimensional energy surface. This problem is compounded by the need to include implicit solvation to at least microsolvate the system and stabilize the highly charged species. In contrast, methyl phosphate hydrolysis shows a preference for a substrate-assisted mechanism. For p-nitrophenyl sulfate hydrolysis there is only one viable reaction pathway, which is similar to the solvent-assisted pathway for phosphate hydrolysis, and the substrate-assisted pathway is not accessible. Overall, our results provide a unifying mechanistic framework that is consistent with the experimentally measured kinetic isotope effects and reconciles the discrepancies between theoretical and experimental models for these biochemically ubiquitous classes of reaction.


Asunto(s)
Organofosfatos/química , Teoría Cuántica , Hidrólisis , Modelos Moleculares
18.
Chemistry ; 21(19): 7053-6, 2015 May 04.
Artículo en Inglés | MEDLINE | ID: mdl-25787696

RESUMEN

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.

19.
J Org Chem ; 79(7): 2816-28, 2014 Apr 04.
Artículo en Inglés | MEDLINE | ID: mdl-24279349

RESUMEN

Sulfonate ester hydrolysis has been the subject of recent debate, with experimental evidence interpreted in terms of both stepwise and concerted mechanisms. In particular, a recent study of the alkaline hydrolysis of a series of benzene arylsulfonates (Babtie et al., Org. Biomol. Chem. 10, 2012, 8095) presented a nonlinear Brønsted plot, which was explained in terms of a change from a stepwise mechanism involving a pentavalent intermediate for poorer leaving groups to a fully concerted mechanism for good leaving groups and supported by a theoretical study. In the present work, we have performed a detailed computational study of the hydrolysis of these compounds and find no computational evidence for a thermodynamically stable intermediate for any of these compounds. Additionally, we have extended the experimental data to include pyridine-3-yl benzene sulfonate and its N-oxide and N-methylpyridinium derivatives. Inclusion of these compounds converts the Brønsted plot to a moderately scattered but linear correlation and gives a very good Hammett correlation. These data suggest a concerted pathway for this reaction that proceeds via an early transition state with little bond cleavage to the leaving group, highlighting the care that needs to be taken with the interpretation of experimental and especially theoretical data.


Asunto(s)
Alcaloides/química , Bencenosulfonatos/química , Óxidos N-Cíclicos/química , Mesilatos/química , Piridinas/química , Compuestos de Piridinio/química , Ésteres , Hidrólisis , Cinética , Modelos Teóricos , Estructura Molecular
20.
Angew Chem Int Ed Engl ; 53(31): 8246-50, 2014 Jul 28.
Artículo en Inglés | MEDLINE | ID: mdl-24919567

RESUMEN

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.


Asunto(s)
Fosfatos/química , Zinc/química , Catálisis , Cristalografía por Rayos X , Ésteres/química , Hidrólisis , Metilación
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