Bond Hydrolysis Reaction Research Articles

A 1,3,4-thiadiazole functionalized Schiff base based fluorescence enhancement and colorimetric probe for detection of Cu (II) ion and its potential applications

A fluorescence enhancement probe XS-1 based on coumarin, 1,3,4-thiadiazole and Schiff base cores was synthesized for detection of Cu2+ via the CN bond hydrolysis reaction. Furthermore, Cu2+ ion induced ‘turn-on’ fluorescence emission was preserved in the presence of other competing ions which clearly suggests the high selectivity and anti-interference. In addition, remarkable changes of solution color from light pink to bright yellow and fluorescence color from colorless to bright green realized the visual detection of Cu2+ by naked eyes. The excellent characters and low detection limit (0.17 μM) enabled its application of Cu2+ detection in actual water samples and organisms/living cells. Systematic investigations were also conducted to demonstrate the behavior of XS-1 to Cu2+ ion by the help of 1H NMR titration, HRMS titration and DFT calculations.

Xylonolactonase from Caulobacter crescentus Is a Mononuclear Nonheme Iron Hydrolase

Caulobacter crescentus xylonolactonase (Cc XylC, EC 3.1.1.68) catalyzes an intramolecular ester bond hydrolysis over a nonenzymatic acid/base catalysis. Cc XylC is a member of the SMP30 protein family, whose members have previously been reported to be active in the presence of bivalent metal ions, such as Ca2+, Zn2+, and Mg2+. By native mass spectrometry, we studied the binding of several bivalent metal ions to Cc XylC and observed that it binds only one of them, namely, the Fe2+ cation, specifically and with a high affinity (Kd = 0.5 μM), pointing out that Cc XylC is a mononuclear iron protein. We propose that bivalent metal cations also promote the reaction nonenzymatically by stabilizing a short-lived bicyclic intermediate on the lactone isomerization reaction. An analysis of the reaction kinetics showed that Cc XylC complexed with Fe2+ can speed up the hydrolysis of d-xylono-1,4-lactone by 100-fold and that of d-glucono-1,5-lactone by 10-fold as compared to the nonenzymatic reaction. To our knowledge, this is the first discovery of a nonheme mononuclear iron-binding enzyme that catalyzes an ester bond hydrolysis reaction.

Developing a 3D Physical Model of HIV Protease to Explore Drug Resistance to Tipranavir and Darunavir

HIV infections affect over 38 million people worldwide and cause approximately one million deaths every year. Despite advances in antiretroviral therapies and disease prevention strategies, drug resistance remains a major challenge in HIV treatment. HIV protease plays a key role in viral replication by facilitating the peptide bond hydrolysis reactions necessary for the development of functional viral particles. Diverse inhibitors have been developed to target the active site and substrate envelope of HIV protease. While these drugs have been effective at inactivating the enzyme, mutations at the active site give rise to HIV resistance strains which are insensitive to protease inhibitors. The goal of this project was to create 3D printed models of HIV protease to illustrate the mechanisms of action of two inhibitors, Tipranavir and Darunavir, and the mutations involved in the development of resistance to these drugs. Database searches and sequence alignments were performed to identify conserved amino acids and structural features important in the catalytic mechanism of HIV proteases. Details of the protein structure and its interaction with Tipranavir and Darunavir were obtained by analyzing the Protein Databank Files: 6DIF, 6DGX, 6OPS, and 6DH6. To construct the physical models, the structure files were imported into Jmol and modified into a format suitable for 3D printing using scripts created by undergraduate researchers. The 3D models feature the overall structure of HIV protease, and its inhibitor molecules, Tipranavir and Darunavir. An active site box was constructed to illustrate the biochemical interactions between the enzyme and the inhibitors. The physical models also highlight key amino acids such as Asp25, Ile50, Val82, and Val84, which are critical for catalytic activity and the development of drug resistance. Magnetic pieces were created to show the effects of mutations in inhibitor binding and enzyme activity. A Jmol tutorial was designed to complement the 3D models and assess students’ learning of the structure and function of HIV protease.Support or Funding InformationThis project is funded in part by NSF‐IUSE #1725940 for the CREST Project.

Dinuclear Lanthanide(III)-m-ODO2A-dimer Macrocyclic Complexes: Solution Speciation, DFT Calculations, Luminescence Properties, and Promoted Nitrophenyl-Phosphate Hydrolysis Rates.

Potentiometric speciation studies, mass spectrometry, and DFT calculations helped to predict the various structural possibilities of the dinuclear trivalent lanthanide ion (LnIII , Ln=La, Eu, Tb, Yb, Y) complexes of a novel macrocyclic ligand, m-ODO2A-dimer (H4 L), to correlate with their luminescence properties and the promoted BNPP and HPNP phosphodiester bond hydrolysis reaction rates. The stability constants of the dinuclear Ln2 (m-ODO2A-dimer) complexes and various hydrolytic species confirmed by mass spectrometry were determined. DFT calculations revealed that the Y2 LH-1 and the Y2 LH-2 species tended to form structures with the respective closed- and open-form conformations. Luminescence lifetime data for the heterodimetallic TbEuL system confirmed the fluorescence resonance energy transfer from the TbIII to EuIII ion. The internuclear distance RTbEu values were estimated to be in the range of 9.4-11.3 Å (pH 6.7-10.6), which were comparable to those of the DFT calculated open-form conformations. Multiple linear regression analysis of the kobs data was performed using the equation: kobs,corr. =kobs -kobs,OH =kLn2LHM->1 [Ln2 LH-1 ]+kLn2LH-2 [Ln2 LH-2 ] for the observed Ln2 L-promoted BNPP/HPNP hydrolysis reactions in solution pH from 7 to 10.5 (Ln=Eu, Yb). The results showed that the second-order rate constants for the Eu2 LH-2 and Yb2 LH-2 species were about 50-400 times more reactive than the structural analogous Zn2 (m-12 N3 O-dimer) system.

Naphthalimide derived fluorescent probes with turn-on response for Au3+ and the application for biological visualization

The 4−N,N-dimethyl-1,8-naphthalimide based fluorescent probes have been explored for selective detection of Au3+. Both probes show a pronounced fluorescence enhancement response to Au3+. Hydroxy is introduced as ligand of Au3+ for Probe 1 and the newly designed Probe 2 contains an alkyne moiety to recognize Au3+ through an irreversible C≡C bond hydrolysis reaction. Probe 1 exhibits higher performance such as faster response, lower detection limit of 0.050μM and the better responsive effect in 99.5% water system compared with most of probes published. The Probe 2 displays high stability to pH, suitable water solubility, wider linear range (0–100μM) to Au3+, and live-cells imaging with low cytotoxicity.

A high performance Schiff-base fluorescent probe for monitoring Au3+ in zebrafish based on BODIPY

We designed and synthesized a mono-Schiff-base fluorescent probe (Probe 1) based on a boron-dipyrromethene (BODIPY) dye. By investigating the recognition of Au3+ through an irreversible C=N bond hydrolysis reaction, Probe 1 exhibited higher properties such as acting as a “naked eye” probe, stability to pH, fast-response of 90s, a lower detection limit of 60nM, stronger antijamming capability, and better live-cells imaging with low cytotoxicity compared with other probes. Even in relatively high temperatures, Probe 1 maintained its own excellent characteristic. More importantly, this is the first time that one chemosensor could be successfully applied to Au3+ imaging in zebrafish, which demonstrated the performance that Probe 1 exhibited wonderful organism permeability.

Discrete and Polymeric Cu(II) Complexes Derived from in Situ Generated Pyridyl-Functionalized Bis(amido)phosphate Ligands, [PO2(NHPy)2]−

New examples of Cu(II) complexes containing in situ generated bis(amido)phosphate ligands, [PO2(NHPy)2]−, have been synthesized [(L1)−, where Py = 2-pyridyl, and (L2)−, where Py = 4-pyridyl). These anionic ligands were obtained by the P–N bond hydrolysis reaction of the corresponding phosphonium salts or phosphoric triamides in the presence of Lewis acidic Cu(II) ions in polar solvents. A discrete mononuclear complex {Cu[PO2(NH2Py)2]2} (3) was obtained for the in situ ligand featuring 2-pyridyl substituents, whereas a 1D coordination polymer {[Cu(PO2(NH4Py)2)2(H2O)2]·2DMF·2H2O}∞ (4) was obtained for the ligand containing 4-pyridyl functionalities. The structural analyses show that in 3 the ligand (L1)− is bonded to the metal ion in a chelating tridentate N,N,O coordination and the coordinated P–O group is oriented in a syn fashion with respect to the pyridylamino groups. However, in 4 the ligand (L2)− is bonded in a bridging fashion to two Cu(II) ions via its pyridyl nitrogen donors. The two phosphorus-bo...

A BODIPY-based reactive probe for the detection of Au(III) species and its application to cell imaging.

A BODIPY-based fluorescent probe bearing a pyridyl hydrazone motif responds selectively to Au(III) ions through an irreversible C=N bond hydrolysis reaction.

Promotion of phosphoester hydrolysis by MoO2Cl2L (L = bipyridine derivatives, H2O, no ligand), MoO2(CH3)2L (L = bipyridine derivatives) and related inorganic–organic hybrids in aqueous media

The compounds MoO2Cl2L (L = 2,2′-bipyridine (bipy) (1); 4,4′-di-tert-butyl-2,2′-bipyridine (di-tBu-bipy) (2)), [MoO2Cl2(H2O)2]·(diglyme)2 (3), MoO2Cl2 (4), MoO2(CH3)2L (L = bipy (5); di-tBu-bipy (6)), [MoO3(bipy)]n (7), {[MoO3(bipy)][MoO3(H2O)]}n (8), [Mo8O22(OH)4(di-tBu-bipy)4] (9) and MoO3 (10) were tested as phosphoester bond hydrolysis promoters in aqueous media. Sodium para-nitrophenylphosphate (pNPP) was used as a model substrate for the phosphoester bond hydrolysis reaction, which was performed at 55 °C, using D2O as solvent and 100 or 10 mol% of the chosen promoter. The progression of all the reactions was monitored by 1H NMR spectroscopy. All studied systems promote phosphoester bond hydrolysis. The best performance was obtained with MoO2Cl2L compounds (1–4) and with the inorganic–organic hybrid {[MoO3(bipy)][MoO3(H2O)]}n (8). The studied compounds originate either homogeneous or solid/liquid biphasic systems. For the biphasic systems (1, 2, 5–9), the solid phase was recovered at the end of the reaction and characterized by FT-IR spectroscopy.

Zn(ii) coordination polymer of an in situ generated 4-pyridyl (4Py) attached bis(amido)phosphate ligand, [PO2(NH4Py)2]− showing preferential water uptake over aliphatic alcohols

Two polymorphic 2D-coordination polymers of composition [ZnL(HCO2)]∞ were synthesized from an in situ generated ligand [PO2(NH(4)Py)2](-) (L(-)). The ligand L(-) was generated by a facile metal-assisted P-N bond hydrolysis reaction from the corresponding phosphonium salt 1, [P(NH(4)Py)4]Cl, or from the neutral phosphoric triamide 2, [PO(NH(4)Py)3]. The de-solvated sample of the polymer [ZnL(HCO2)]∞ features polar micropores and shows a type I isotherm for CO2 sorption whereas a type II behaviour was observed for N2. The vapour sorption isotherm of the de-solvated sample of [ZnL(HCO2)]∞ shows preferential adsorption of water vapour over aliphatic alcohols.

Vibrational study on the solvates formed during interactions of amide with alkaline earth metal ions

We present in this paper very interesting vibrational data for formamide (FA) complexes with Mg and Ca ions. The νCO and νCN modes of FA are shifted to lower (45cm−1) and higher (30cm−1) wavenumbers, respectively, in the presence of Mg(II), whereas both modes are upshifted (∼15cm−1) as Ca(II) is present. The shifts observed for the system containing Mg(II) indicate that the HC−ON+H2 form is majority due to the coordination through the O atom. On the other hand, the HCONH2 form is dominant because of the coordination to Ca(II) via both O and N atoms. Such differences may be explained based on the ionic radii of Mg and Ca, which lead to the formation of FA complexes with coordination numbers equal to 6 and 8, respectively. The results here presented may help us for a better understanding about amide bond hydrolysis reactions catalyzed by metal ions, since the ionic and molecular FA forms have been recognized as active and inactive intermediates, respectively, in the hydrolysis mechanisms proposed so far.

Dynamics in the Active Site of β-Secretase: A Network Analysis of Atomistic Simulations

The aspartic protease β-secretase (BACE) catalyzes the hydrolysis of the amyloid precursor protein (APP) which leads to amyloid-β aggregation and, ultimately, the perilous Alzheimer's disease. The conformational dynamics and free energy surfaces of BACE at three steps of the catalytic cycle are studied here by explicit solvent molecular dynamics simulations (multiple runs for a total of 2.2 μs). The overall plasticity of BACE is essentially identical for the three states of the substrate: the octapeptide reactant, gem-diol intermediate, and cleavage products. In contrast, the network of hydrogen bonds in the active site is more stable in the complex of BACE with the gem-diol intermediate than the other two states of the substrate. The spontaneous release of the C-terminal (P1'-P4') fragment of the product follows a single-exponential time dependence with a time constant of 50 ns and does not require the opening of the flap. The fast dissociation of the C-terminal fragment is consistent with the transmembrane location and orientation of APP and its further processing by γ-secretase. On the other hand, the N-terminal (P4-P1) fragment of the product does not exit the BACE active site within the simulation time scale of 80 ns. A unified network analysis of the complexes of BACE with the three states of the substrate provides an estimation of the activation free energy associated with the structural rearrangements that involve only noncovalent interactions. The estimated rearrangement barriers are not negligible (up to 3 kcal/mol) but are significantly smaller than the barrier of the peptide bond hydrolysis reaction.

Selective peptide bond hydrolysis of cysteine peptides in the presence of Ni(II) ions

Recently, we described a sequence-specific R1-(Ser/Thr) peptide bond hydrolysis reaction in peptides of a general sequence R1–(Ser/Thr)–Xaa–His–Zaa–R, which occurs in the presence of Ni(II) ions [A. Krężel, E. Kopera, A. M. Protas, A. Wysłouch-Cieszyńska, J. Poznański, W. Bal, J. Am. Chem. Soc. 132 (2010) 3355–3366]. In this study we explored the possibility of substituting the Ser/Thr and the His residues, necessary for the reaction to occur according to the Ni(II)-assisted acyl shift reaction mechanism, with Cys residues. We tested this concept by synthesizing three homologous peptides: R1-Ser-Arg-Cys-Trp-R2, R1-Cys-Arg-His-Trp-R2, and R1-Cys-Arg-Cys-Trp-R2, and the R1-Ser-Arg-His-Trp-R2 peptide as comparator (R1 and R2 were CH3CO-Gly-Ala and Lys-Phe-Leu-NH2, respectively). We studied their hydrolysis in the presence of Ni(II) ions, under anaerobic conditions and in the presence of TCEP as a thiol group antioxidant. We measured hydrolysis rates using HPLC and identified products of reaction using electrospray mass spectrometry. Potentiometry and UV–vis spectroscopy were used to assess Ni(II) complexation. We demonstrated that Ni(II) is not compatible with the Cys substitution of the Ser/Thr acyl acceptor residue, but the substitution of the Ni(II) binding His residue with a Cys yields a peptide susceptible to Ni(II)-related hydrolysis. The relatively high activity of the R1-Ser-Arg-Cys-Trp-R2 peptide at pH 7.0 suggests that this peptide and its Cys-containing analogs might be useful in practical applications of Ni(II)-dependent peptide bond hydrolysis.

HIV protease inhibitors and nuclear lamin processing: Getting the right bells and whistles

One of the most notable successes of rational pharmaceutical design has been the development of drugs that inhibit the protease cleaving the polyproteins of the HIV into their structural and catalytic protein components (1, 2). Several of these inhibitors are currently used as components of “highly active antiretroviral therapy” for treating HIV infection and AIDS (2, 3). Given the similar chemistry involved in all peptide bond hydrolysis reactions, as well as the different sequence contexts of the polyprotein cleavage sites, the ability of these drugs to specifically target the HIV protease and not the hundreds of other proteases required for human health—digestive enzymes, enzymes of the coagulation pathway, enzymes of the complement cascade, proteases involved in protein maturation and transport—is truly remarkable. However, in a recent issue of PNAS, Coffinier et al. (4) demonstrate that these drugs do inhibit at least one unrelated protease and that this inhibition could conceivably account for some of the side effects of these pharmaceuticals. They show that HIV protease inhibitors, including lopinavir, a first-line widely used member of the saquinavir family, can also inhibit ZMPSTE24, a distinct protease involved in the conversion of farnesylprelamin A to lamin A, a key structural component of the nuclear lamina (Fig. 1). In recent years, genetic defects in the conversion of farnesylprelamin A to lamin A in humans have been shown to cause severe progeroid disorders (e.g., restrictive dermopathy, Hutchinson–Gilford progeria syndrome) (6–8). These findings suggest that the inhibition of prelamin A processing by HIV protease inhibitors may result in some of the same disease phenotypes observed in the genetic prelamin A-processing disorders.

The merits of bipartite transition-state mimics for inhibition of uracil DNA glycosylase

The glycosidic bond hydrolysis reaction of the enzyme uracil DNA glycosylase (UDG) occurs by a two-step mechanism involving complete bond breakage to the uracil anion leaving group in the first step, formation of a discrete glycosyl cation-uracil anion intermediate, followed by water attack in a second transition-state leading to the enzyme-bound products of uracil and abasic DNA. We have synthesized and determined the binding affinities of unimolecular mimics of the substrate and first transition-state (TS1) in which the uracil base is covalently attached to the sugar, and in addition, bimolecular mimics of the second addition transition state (TS2) in which the base and sugar are detached. We find that the bipartite mimics of TS2 are superior to the TS1 mimics. These results indicate that bipartite TS2 inhibitors could be useful for inhibition of glycosylases that proceed by stepwise reaction mechanisms.

The partitioning of phosphoramide mustard and its aziridinium ions among alkylation and P-N bond hydrolysis reactions.

NMR (1H and 31P) and HPLC techniques were used to study the partitioning of phosphoramide mustard (PM) and its aziridinium ions among alkylation and P-N bond hydrolysis reactions as a function of the concentration and strength of added nucleophiles at 37 degrees C and pH 7.4. With water as the nucleophile, bisalkylation accounted for only 10-13% of the product distribution given by PM. The remainder of the products resulted from P-N bond hydrolysis reactions. With 50 mM thiosulfate or 55-110 mM glutathione (GSH), bisalkylation by a strong nucleophile increased to 55-76%. The rest of the PM was lost to either HOH alkylation or P-N bond hydrolysis reactions. Strong experimental and theoretical evidence was obtained to support the hypothesis that the P-N bond scission observed at neutral pH does not occur in the parent PM to produce nornitrogen mustard; rather it is an aziridinium ion derived from PM which undergoes P-N bond hydrolysis to give chloroethylaziridine. In every buffer studied (bis-Tris, lutidine, triethanolamine, and Tris), the decomposition of PM (with and without GSH) gave rise to 31P NMR signals which could not be attributed to products of HOH or GSH alkylation or P-N bond hydrolysis. The intensities of these unidentified signals were dependent on the concentration of buffer.

The albite-water system: Part IV. Diffusion modeling of leached and hydrogen-enriched layers

Measured H and Na concentration depth profiles in albite samples dissolved at 300°C at various pH conditions (Hellmann et al., 1997-Part III) are indicative of the complex nature of diffusion within leached/H-enriched layers. A qualitative comparison between the measured profiles and profiles based on various diffusion models reveals that the inward diffusion of H species and the outward diffusion of Na are not independent, but rather are interrelated by- an interdiffusion process that can be modeled with a single interdiffusion coefficient ~D. The coefficient ~D varies as a function of the concentration of either H or Na and is thus dependent on depth. The proposed interdiffusion model is based on rates of Na diffusion that are up to several orders of magnitude faster than H diffusion ( D Na/ D H ≫ 1), this being in accord with direct diffusion measurements from the glass dissolution literature. Modeling results reveal that the rate of H diffusion is one of the most important parameters in determining the depths of leached/ H-enriched layers. Based on a qualitative comparison between the measured profiles and the interdiffusion model, a lower limit of D H ≥ 10 −13cm 2s −1 can be estimated for leached/H-enriched layers created at acid pH (3.3-3.4) and 300°C. Depending on the estimated value of D Na/ D H, this corresponds to D Na ≫ 10 −13cm 2s −1. The use of a structural factor with ~D imparts an even greater concentration dependence on the interdiffusion coefficient. Increasing the value of the structural factor has the effect of greatly increasing the depth of leaching/H enrichment for any given set of constant DH and D Na/ D H values. Irreversible chemical reactions which result in the uptake of H species, such as framework bond hydrolysis reactions, are also potentially important in correctly modeling diffusion of leached/ H-enriched layers. Increasing the rate of reaction acts as a damping factor on steady-state diffusion profiles. Chemical reactions within leached/ H-enriched layers potentially necessitate the addition of a chemical reaction term to the applied diffusion model in order to avoid an underestimation of diffusion rates.