Nucleophilic displacements upon phenyl esters in which the direct relation between basicity of the leaving group and rate is determined by ground state conformations. Question of concerted catalysis in the hydrolysis of hexachlorophene esters

1974 ◽  
Vol 96 (14) ◽  
pp. 4500-4507 ◽  
Author(s):  
Thomas C. Bruice ◽  
Isao Oka
Keyword(s):  
Ground State ◽  
Direct Relation ◽  
Leaving Group ◽  
Hydrolysis Of

Effect of Medium on Reactivity for Alkaline Hydrolysis of p-Nitrophenyl Acetate and S-p-Nitrophenyl Thioacetate in DMSO-H2O Mixtures of Varying Compositions: Ground State and Transition State Contributions

2021 ◽  
Author(s):  
Ik-Hwan Um ◽  
Seungjae Kim
Keyword(s):  
Transition State ◽  
Alkaline Hydrolysis ◽  
Ground State ◽  
Rate Constants ◽  
Kinetic Data ◽  
Reaction Medium ◽  
Stepwise Mechanism ◽  
Rate Determining Step ◽  
Leaving Group ◽  
Hydrolysis Of

Second-order rate constants (kN) for reactions of p-nitrophenyl acetate (1) and S-p-nitrophenyl thioacetate (2) with OH‒ have been measured spectrophotometrically in DMSO-H2O mixtures of varying compositions at 25.0 ± 0.1 oC. The kN value increases from 11.6 to 32,800 M‒1s‒1 for the reactions of 1 and from 5.90 to 190,000 M‒1s‒1 for those of 2 as the reaction medium changes from H2O to 80 mol % DMSO, indicating that the effect of medium on reactivity is more remarkable for the reactions of 2 than for those of 1. Although 2 possesses a better leaving group than 1, the former is less reactive than the latter by a factor of 2 in H2O. This implies that expulsion of the leaving group is not advanced in the rate-determining transition state (TS), i.e., the reactions of 1 and 2 with OH‒ proceed through a stepwise mechanism, in which expulsion of the leaving group from the addition intermediate occurs after the rate-determining step (RDS). Addition of DMSO to H2O would destabilize OH‒ through electronic repulsion between the anion and the negative-dipole end in DMSO. However, destabilization of OH‒ in the ground state (GS) is not solely responsible for the remarkably enhanced reactivity upon addition of DMSO to the medium. The effect of medium on reactivity has been dissected into the GS and TS contributions through combination of the kinetic data with the transfer enthalpies (ΔΔHtr) from H2O to DMSO-H2O mixtures for OH‒ ion.

scholarly journals Pseudomonas putida MPE, a manganese-dependent endonuclease of the binuclear metallophosphoesterase superfamily, incises single-strand DNA in two orientations to yield a mixture of 3′-PO4 and 3′-OH termini

2020 ◽  
Author(s):  
Shreya Ghosh ◽  
Anam Ejaz ◽  
Lucas Repeta ◽  
Stewart Shuman
Keyword(s):  
Pseudomonas Putida ◽  
Bound Water ◽  
Acid Catalyst ◽  
Nuclease Activity ◽  
Single Strand ◽  
Dna Endonuclease ◽  
Dependent Endonuclease ◽  
Leaving Group ◽  
Phosphodiester Hydrolysis ◽  
Hydrolysis Of

Abstract Pseudomonas putida MPE exemplifies a novel clade of manganese-dependent single-strand DNA endonuclease within the binuclear metallophosphoesterase superfamily. MPE is encoded within a widely conserved DNA repair operon. Via structure-guided mutagenesis, we identify His113 and His81 as essential for DNA nuclease activity, albeit inessential for hydrolysis of bis-p-nitrophenylphosphate. We propose that His113 contacts the scissile phosphodiester and serves as a general acid catalyst to expel the OH leaving group of the product strand. We find that MPE cleaves the 3′ and 5′ single-strands of tailed duplex DNAs and that MPE can sense and incise duplexes at sites of short mismatch bulges and opposite a nick. We show that MPE is an ambidextrous phosphodiesterase capable of hydrolyzing the ssDNA backbone in either orientation to generate a mixture of 3′-OH and 3′-PO4 cleavage products. The directionality of phosphodiester hydrolysis is dictated by the orientation of the water nucleophile vis-à-vis the OH leaving group, which must be near apical for the reaction to proceed. We propose that the MPE active site and metal-bound water nucleophile are invariant and the enzyme can bind the ssDNA productively in opposite orientations.

scholarly journals A Degradation Product from Hydrolysate of Imipenem with Imis Broad-Spectrum Inhibits Metallo-β-Lactamases

2020 ◽  
Vol 13 (10) ◽  
Author(s):  
Ying Ge ◽  
Li-Wei Xu ◽  
Jian-Bin Zhen ◽  
Cheng Chen ◽  
Miao Lv ◽  
...  
Keyword(s):  
Broad Spectrum ◽  
Degradation Product ◽  
Substrate Inhibition ◽  
Resistant Bacteria ◽  
Drug Resistant ◽  
Antibiotic Resistant Bacteria ◽  
Antibiotic Resistant ◽  
Leaving Group ◽  
Ic50 Values ◽  
Hydrolysis Of

Background: Infections caused by metallo-β-lactamases (MβLs)-producing antibiotic-resistant bacteria pose a severe threat to public health. The synergistic use of current antibiotics in combination with MβL inhibitors is a promising therapeutic mode against these antibiotic-resistant bacteria. Objectives: The study aimed to probe the inhibition of MβLs and obtain the active component, P1, in the degradation product after imipenem was hydrolyzed by ImiS. Methods: The hydrolysis of two carbapenems with MβL ImiS was monitored by UV-Vis in real-time, and the degradation product from the leaving group produced after imipenem was hydrolyzed (but not for faropenem) was purified by HPLC to give one component, P1. Results: Kinetic assays revealed that P1 exhibited a broad-spectrum inhibition against VIM-2, NDM-1, ImiS, and L1, from three sub-classes of MβLs, with IC50 values of 8 - 32, 13.8 - 29.3, and 14.2 - 19.2 µM, using imipenem, cefazolin, and nitrocefin as substrates, respectively. Also, P1 showed synergistic antibacterial efficacy against drug-resistant Escherichia coli producing VIM-2, NDM-1, ImiS, and L1, in combination with antibiotics, restoring 16 to 32-fold and 32 to 128-fold efficacies of imipenem and cefazolin, respectively. Spectroscopic and Ellman's reagent analyses suggested that P1, a mercaptoethyl-form imidamide, is a mechanism-based inhibitor, while faropenem has no substrate inhibition, due to the lack of a leaving group. Conclusions: This work reveals that the hydrolysate of imipenem, a carbapenem with a good leaving group, can be used in screening for broad-spectrum inhibitors of MβLs.

Effet de groupe partant dans l'hydrolyse d'orthoesters cycliques: changement de conformère réactif dans l'hydrolyse des diéthoxy-2,2 tétrahydropyrannes

1983 ◽  
Vol 61 (12) ◽  
pp. 2651-2656 ◽  
Author(s):  
Gérard Lamaty ◽  
Philippe Lorente ◽  
Claude Moreau
Keyword(s):  
Leaving Group ◽  
Two Temperatures ◽  
Hydrolysis Of

The rates of hydrolysis of 6-substituted 2,2-diethoxy 3,4-dihydro benzo-1-pyrans (X = MeO, Me, H and Cl) were determined at two temperatures in water/dioxane 2:1 by volume. The observed change of sign of the Hammett ρ constants [Formula: see text] is characteristic of a phenolate leaving group, i.e. of the rate-determining cleavage of the endocyclic C—O bond in the systems here studied; these results clearly indicate a change in the nature of the reactive conformer in hydrolysis of 2,2-diethoxy tetrahydropyrans.

scholarly journals Common-type acylphosphatase: steady-state kinetics and leaving-group dependence

1997 ◽  
Vol 327 (1) ◽  
pp. 177-184 ◽  
Author(s):  
Paolo PAOLI ◽  
Paolo CIRRI ◽  
Lucia CAMICI ◽  
Giampaolo MANAO ◽  
Gianni CAPPUGI ◽  
...  
Keyword(s):  
Inorganic Phosphate ◽  
Strong Dependence ◽  
Common Type ◽  
Enzyme Active Site ◽  
Enzyme Substrate ◽  
Linear Relationships ◽  
Steady State Kinetics ◽  
Spontaneous Hydrolysis ◽  
Leaving Group ◽  
Hydrolysis Of

A number of acyl phosphates differing in the structure of the acyl moiety (as well as in the leaving-group pKa of the acids produced in hydrolysis) have been synthesized. The Km and Vmax values for the bovine common-type acylphosphatase isoenzyme have been measured at 25 °C and pH 5.3. The values of kcat differ widely in relation to the different structures of the tested acyl phosphates: linear relationships between log kcat and the leaving group pKa, as well as between log kcat/Km and the leaving-group pKa, were observed. On the other hand, the Km values of the different substrates are very close to each other, suggesting that the phosphate moiety of the substrate is the main chemical group interacting with the enzyme active site in the formation of the enzyme–substrate Michaelis complex. The enzyme does not catalyse transphosphorylation between substrate and concentrated nucleophilic acceptors (glycerol and methanol); nor does it catalyse H218O–inorganic phosphate oxygen exchange. It seems that no phosphoenzyme intermediate is formed in the catalytic pathway. Furthermore, during the enzymic hydrolysis of benzoyl phosphate in the presence of 18O-labelled water, only inorganic phosphate (and not benzoate) incorporates 18O, suggesting that no acyl enzyme is formed transiently. All these findings, as well as the strong dependence of kcat upon the leaving group pKa, suggest that neither a nucleophilic enzyme group nor general acid catalysis are involved in the catalytic pathway. The enzyme is competitively inhibited by Pi, but it is not inhibited by the carboxylate ions produced during substrate hydrolysis, suggesting that the last step of the catalytic process is the release of Pi. The activation energy values for the catalysed and spontaneous hydrolysis of benzoyl phosphate have been determined.

Effect of modification of the electrophilic center on the α effect

2005 ◽  
Vol 83 (9) ◽  
pp. 1365-1371 ◽  
Author(s):  
Ik-Hwan Um ◽  
Ji-Youn Lee ◽  
Sun-Young Bae ◽  
Erwin Buncel
Keyword(s):  
Ground State ◽  
Strong Dependence ◽  
Solvation Energy ◽  
The Other ◽  
Substrate Structure ◽  
Leaving Group ◽  
The Common ◽  
The Difference ◽  
The Impact

We report on a nucleophilic study of esters R-C(=X)-Y-Ar in which the electrophilic center has been modified by replacing O by S in the leaving group or carbonyl center: 4-nitrophenyl acetate (1), S-4-nitrophenyl thioacetate (2), 4-nitrophenyl benzoate (3), and O-4-nitrophenyl thionobenzoate (4). The studies include O– and S– nucleophiles as well as α nucleophiles in H2O at 25.0 ± 0.1 °C. The sulfur nucleophile (4-chlorothiophenoxide, 4-ClPhS–) exhibits significant enhanced reactivity for the reactions with thiol and thione esters 2 and 4 compared with their oxygen analogues 1 and 3. On the contrary, the common nucleophile OH– is much less reactive towards 2 and 4 compared with 1 and 3. The effect of changing both the electrophilic center and the nucleofugic center on the reactivity of the other oxygen nucleophiles is not so significant: 4-chlorophenoxide (4-ClPhO–) is four to six times more reactive in the reactions with thiol and thione esters 2 and 4 compared with their oxygen analogues 1 and 3. The α effects exhibited by butan-2,3-dione monoximate (Ox–) and HOO– are strongly dependent on the nature of the electrophilic center of the substrates, indicating that the difference in the ground-state solvation energy cannot be fully responsible for the α effect. Our results clearly emphasize the strong dependence of the α effect on the substrate structure, notably, the nature of the electrophilic center. The impact of change in the nucleofuge (1→2) and the electrophilic center (3→4) on reactivity indicates that α nucleophiles will need to be “purpose built” for decontamination and nucleophilic degradation of specific biocides.Key words: α effect, nucleophilicity, nucleofuge effect, electrophilicity, polarizability.

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