Steady-state Kinetic Data Research Articles

Fast Reaction of the Prussian Blue Based Nanozyme "Artificial Peroxidase" with the Substrates: Pre-Steady-State Kinetic Approach.

This letter introduces the pre-steady-state kinetic approach, which is traditional for evaluation of elementary constants in molecular (enzyme) catalysis, for nanozymes. Apparently, the most active peroxidase-mimicking nanozyme based on catalytically synthesized Prussian Blue nanoparticles has been chosen. The elementary constants (k1) for the nanozymes' reduction by an electron-donor substrate (being the fastest stage according to steady-state kinetic data) have been determined by means of stopped-flow spectroscopy. These constants have been found to be dependent on both the size of the nanozyme and the reducing substrate redox potential. For the smallest nanozymes (32 nm in diameter), log(k1) linearly decays with an increase of the substrate redox potential (cotangent value ≈125 mV). On the contrary, for the largest nanozymes with a diameter above 150 nm, k1 is almost independent of it. Moreover, for the substrate with the lowest redox potential (K4[Fe(CN)6]), the rate constant under discussion (k1) is almost independent of the nanozymes' size. Perhaps, the rate of the intrananozyme electron transfer causing bleaching becomes comparative or even lower than that of the nanoparticle interaction with the fastest substrate. Anyway, the elementary constant of nanozyme reduction with potassium ferrocyanide (k1) reaches the value of 1 × 1010 M-1 s-1, which is 3-4 orders of magnitude faster than for enzymes peroxidases. The obtained results obviously demonstrate that the pre-steady-state kinetic approach is able to discover novel advantages of nanozymes from both fundamental and practical points of view.

Iron-carbon dots embedded in molybdenum single-atom nanoflowers as multifunctional nanozyme for dual-mode detection of hydrogen peroxide and uric acid

Single-atom catalysts (SACs) have attracted extensive attention in the field of catalysis due to their excellent catalytic ability and enhanced atomic utilization, but the multi-mode single-atom nanozymes for biosensors remain a challenging issue. In this work, iron-doped carbon dots (Fe CDs) were loaded onto the edges and pores of Mo SACs with nanoflower morphology; accordingly, a composite material Fe CDs/Mo SACs was prepared successfully, which improves the catalytic performance and develops a fluorescence mode without changing the original morphology. The steady-state kinetic data indicates that the material prepared have better affinity for substrates and faster reaction rates under optimized conditions. The specific kinetic parameters Km and Vmax were calculated as 0.39 mM and 7.502×10−7 M·s−1 respectively. The excellent peroxidase-like activity of Fe CDs/Mo SACs allows H2O2 to decompose into •OH, which in turn oxidizes colorless o-phenylenediamine (OPD) to yellow 2,3-diaminophenazine (DAP). At the same time, the fluorescence signal of Fe CDs/Mo SACs quenches obviously by DAP at 460 nm through internal filtration effect (IFE), while the characteristic fluorescence response of DAP gradually increases at 590 nm. Based on this sensing mechanism, a sensitive and accurate dual-mode (colorimetric and ratiometric fluorescent) sensor was constructed to detect H2O2 and uric acid, and the rate of recovery and linearity were acceptable for the detection of UA in human serum and urine samples. This method provides a new strategy for rapid and sensitive detection of UA, and also broadens the development of SACs in the field of biosensors.

Recent advances in the use of Steady-State Isotopic Transient Kinetic Analysis data in (micro)kinetic modeling for catalyst and process design

Recent advances in the use of Steady-State Isotopic Transient Kinetic Analysis data in (micro)kinetic modeling for catalyst and process design

Saccharomyces cerevisiae apurinic/apyrimidinic endonuclease 1 repairs abasic site-mediated DNA-peptide/protein cross-links

Saccharomyces cerevisiae apurinic/apyrimidinic (AP) endonuclease 1 (yApn1) is a key player of the base excision repair pathway. This multifunctional enzyme is an AP endonuclease, 3′–5′ exonuclease, 3′-phosphodiesterase, and participates in nucleotide incision repair. To the best of our knowledge, the known substrates of yApn1 are small DNA lesions such as AP sites and 3′-phospho-α,β-unsaturated aldehyde (3′-PUA). Here, we wish to report in vitro findings that yApn1 repairs bulky DNA-peptide cross-links (DpCs) and DNA-protein cross-links (DPCs) arising from AP sites and 3′-PUA. We chemically synthesized stable and linkage-defined DpCs and DPCs by oxime ligation and reductive amination, respectively. Our steady-state kinetic data showed that yApn1 repairs a 10-mer peptide-conjugated AP site and 3′-PUA with comparable efficiencies to that of processing the unconjugated lesions. We demonstrated that yApn1 is the predominant enzyme that incises AP-DpC in yeast cell extracts. We also demonstrated that yApn1 incises AP-DPCs in a DPC size-dependent manner, and prior DPC proteolysis by trypsin facilitates the repair. We further found that yApn1 removes 3′-PUA-histone DPCs with moderate efficiencies. Together, our results uncovered a novel role of yApn1 in DPC repair, and support the emerging model that proteolysis is required for efficient DPC repair.

Modeling the stimulation by glutathione of the steady state kinetics of an adenosine triphosphate binding cassette transporter.

We report the steady state ATPase activities of the ATP Binding Cassette (ABC) exporter NaAtm1 in the absence and presence of a transported substrate, oxidized glutathione (GSSG), in detergent, nanodiscs, and proteoliposomes. The steady state kinetic data were fit to the “nonessential activator model” where the basal ATPase rate of the transporter is stimulated by GSSG. The detailed kinetic parameters varied between the different reconstitution conditions, highlighting the importance of the lipid environment for NaAtm1 function. The increased ATPase rates in the presence of GSSG more than compensate for the modest negative cooperativity observed between MgATP and GSSG in lipid environments. These studies highlight the central role of the elusive ternary complex in accelerating the ATPase rate that is at the heart of coupling mechanism between substrate transport and ATP hydrolysis.

Unimolecular and bimolecular formic acid decomposition routes on dispersed Cu nanoparticles

The elementary steps and site requirements in formic acid (HCOOH) dehydrogenation on Cu surfaces remain of keen interest because formate species act as intermediates or spectators in methanol synthesis and water–gas shift reactions. Steady-state and transient kinetic data, isotopic effects, infrared spectra during catalytic and stoichiometric reactions, and theoretical treatments based on density functional theory (DFT) provide evidence for bimolecular reactions, in which saturated bidentate formate (*HCOO*) adlayers, present at 0.25 ML (0.25 *HCOO* per surface Cu atom), react with undissociated species (HCOOH□) bound at interstices within formate adlayers (□) to form H-bonded bimolecular HCOOH□-*HCOO* adducts. The co-existence of vicinal HCOOH□ and *HCOO* moieties is evident from antisymmetric infrared bands for *HCOO* that become stronger as a result of their H-bonding that perturbs the induced dipole moment of *HCOO* upon vibration, consistent with DFT-derived vibrational frequencies and intensities for such perturbed species. The *HCOO* moiety in this complex undergoes C-H activation via a transition state that is preferentially stabilized through H-bonding with the vicinal HCOOH□ relative to its *HCOO* precursor. DFT-derived HCOOH dehydrogenation activation barriers and those determined from the evolution of CO2 from pre-adsorbed *HCOO* species are about 10 kJ mol−1 smaller in the presence of gaseous HCOOH reactants (because of HCOOH□-*HCOO* interactions) than those for the unimolecular decomposition of bound *HCOO* species. Such bimolecular routes are consistent with measured effects of HCOOH, H2, and CO pressures and of H/D isotopic substitution on dehydrogenation turnover rates and represent the predominant channel for the formation of CO2 and H2 during catalytic HCOOH dehydrogenation on Cu nanoparticles. A saturated *HCOO* adlayer that retains binding interstices and the presence of HCOOH(g) enable a sequence of elementary steps unavailable for *HCOO* species, thus circumventing unassisted unimolecular routes that exhibit higher activation barriers.

Characterisation of an exo-(α-1,3)-3,6-anhydro-d-galactosidase produced by the marine bacterium Zobellia galactanivorans DsijT: Insight into enzyme preference for natural carrageenan oligosaccharides and kinetic characterisation on a novel chromogenic substrate

Flavobacteriia are important degraders in the marine carbon cycle, due to their ability to efficiently degrade complex algal polysaccharides. A novel exo-(α-1,3)-3,6-anhydro-D-galactosidase activity was recently discovered from a marine Flavobacteriia (Zobellia galactanivorans DsijT) on red algal carrageenan oligosaccharides. The enzyme activity is encoded by a gene found in the first described carrageenan-specific polysaccharide utilization locus (CarPUL) that codes for a family 129 glycoside hydrolase (GH129). The GH129 family is a CAZy family that is strictly partitioned into two niche-based clades: clade 1 contains human host bacterial enzymes and clade 2 contains marine bacterial enzymes. Clade 2 includes the GH129 exo-(α-1,3)-3,6-anhydro-D-galactosidase from Z. galactanivorans (ZgGH129). Despite the discovery of the unique activity for ZgGH129, finer details on the natural substrate specificity for this enzyme are lacking. Examination of enzyme activity on natural carrageenan oligomers using mass spectrometry demonstrated that ZgGH129 hydrolyses terminal 3,6-anhydro-D-galactose from unsulfated non-reducing end neo-β-carrabiose motifs. Due to the lack of chromogenic substrates to examine exo-(α-1,3)-3,6-anhydro-D-galactosidase activity, a novel substrate was synthesised to facilitate the first kinetic characterisation of an exo-(α-1,3)-3,6-anhydro-D-galactosidase, allowing determination of pH and temperature optimums and Michaelis-Menten steady state kinetic data.

Hybrid Heme Peroxidases from Rice Blast Fungus Magnaporthe oryzae Involved in Defence against Oxidative Stress.

Hybrid B heme peroxidases are recently discovered unique oxidoreductases present solely in the fungal kingdom. We have investigated two typical representatives from Magnaporthe oryzae—one of the most dangerous phytopathogens known as a causal agent of the rice blast disease. First, we focused on native expression of two detected hyBpox paralogs by the means of reverse-transcription quantitative real-time PCR. Our results indicate a 7-fold induction of the MohyBpox1 transcript in a medium with H2O2 and a 3-fold induction in a medium with peroxyacetic acid. For the MohyBpox2 paralog the induction patterns were up to 12-fold and 6.7-fold, respectively. We have successfully expressed the shorter gene, MohyBpox1, heterologously in Pichia pastoris for detailed characterization. Observed biochemical and biophysical properties of the highly purified protein reveal that a typical HyBPOX is significantly different from previously investigated APx-CcP hybrids. This newly discovered secretory peroxidase reveals a Soret maximum at 407 nm, Q bands at 532 and 568 nm, CT band at 625 nm and a purity number of 1.48. Electron paramagnetic resonance (EPR) analysis suggests a mixture of high and low spin species in the ferric state dependent on calcium contents. Steady-state kinetic data reveal the highest peroxidase activity with ABTS, 5-aminosalycilate and efficient oxidation of tyrosine. MoHyBPOX1 as a fusion protein consists of two domains. The longer conserved N-terminal peroxidase domain is connected with a shorter C-terminal domain containing a carbohydrate binding motif of type CBM21. We demonstrate the capacity of MoHyBPOX1 to bind soluble starch efficiently. Potential involvement of hybrid peroxidases in the pathogenicity of M. oryzae is discussed.

Effects of dioxygen pressure on rates of NOx selective catalytic reduction with NH3 on Cu-CHA zeolites

At low temperatures (<523 K), the selective catalytic reduction (SCR) of NO with NH3 on Cu-exchanged zeolites occurs via elementary steps catalyzed by NH3-solvated Cu ions, which are reactive intermediates in a CuII/CuI redox cycle. SCR rates are typically measured under “standard” reaction conditions, in which O2 is the oxidant and present at partial pressures (~10 kPa O2) that cause both single-site CuII reduction and dual-site CuI oxidation to behave as kinetically relevant steps. As a result, “standard” SCR rates (per g) transition from a second-order to a first-order dependence on isolated Cu content (per g) among Cu-CHA zeolites with increasing Cu content and thus spatial density (Si/Al = 15, Cu/Al = 0.08–0.37), as dual-site CuI oxidation steps limit SCR rates to lesser extents. On a given Cu-CHA catalyst, SCR rates (per Cu, 473 K) show a Langmuirian dependence on dioxygen pressure when varied widely (0–60 kPa O2), enabling the isolation of first-order or zero-order kinetic regimes with respect to O2. These kinetic regimes respectively correspond to limiting conditions in which either CuI oxidation or CuII reduction becomes the dominant kinetically relevant step, consistent with in operando X-ray absorption spectra. First-order rate constants (per Cu) increase approximately linearly with Cu density, reflecting the dual-site requirement of O2-assisted CuI-oxidation steps. Zero-order rate constants (per Cu) increase more gradually with Cu density, in part reflecting the increasing fraction of isolated Cu ions that are able to form binuclear intermediates and thus participate in SCR turnovers. Combining steady-state and transient kinetic data with in operando spectra provides a methodology to quantitatively describe the rate dependences of SCR reduction and oxidation processes on Cu-zeolite properties such as Cu ion density as shown here, and others including the zeolite framework topology and its density and distribution of Al atoms.

New standards for collecting and fitting steady state kinetic data.

The Michaelis–Menten equation is usually expressed in terms of kcat and Km values: v = kcat[S]/(Km + [S]). However, it is impossible to interpret Km in the absence of additional information, while the ratio of kcat/Km provides a measure of enzyme specificity and is proportional to enzyme efficiency and proficiency. Moreover, kcat/Km provides a lower limit on the second order rate constant for substrate binding. For these reasons it is better to redefine the Michaelis–Menten equation in terms of kcat and kcat/Km values: v = kSP[S]/(1 + kSP[S]/kcat), where the specificity constant, kSP = kcat/Km. In this short review, the rationale for this assertion is explained and it is shown that more accurate measurements of kcat/Km can be derived directly using the modified form of the Michaelis–Menten equation rather than calculated from the ratio of kcat and Km values measured separately. Even greater accuracy is achieved with fitting the raw data directly by numerical integration of the rate equations rather than using analytically derived equations. The importance of fitting to derive kcat and kcat/Km is illustrated by considering the role of conformational changes in enzyme specificity where kcat and kcat/Km can reflect different steps in the pathway. This highlights the pitfalls in attempting to interpret Km, which is best understood as the ratio of kcat divided by kcat/Km.

Knockout of the peroxiredoxin 5 homologue PFAOP does not affect the artemisinin susceptibility of Plasmodium falciparum

Artemisinins are the current mainstay of malaria chemotherapy. Their exact mode of action is an ongoing matter of debate, and several factors have recently been reported to affect an early stage of artemisinin resistance of the most important human malaria parasite Plasmodium falciparum. Here, we identified a locus on chromosome 7 that affects the artemisinin susceptibility of P. falciparum in a quantitative trait locus analysis of a genetic cross between strains 7G8 and GB4. This locus includes the peroxiredoxin gene PFAOP. However, steady-state kinetic data with recombinant PfAOP do not support a direct interaction between this peroxidase and the endoperoxide artemisinin. Furthermore, neither the overexpression nor the deletion of the encoding gene affected the IC50 values for artemisinin or the oxidants diamide and tert-butyl hydroperoxide. Thus, PfAOP is dispensable for blood stage parasite survival, and the correlation between the artemisinin susceptibility and chromosome 7 is probably based on another gene within the identified locus.

Significance of Individual Residues at the Regulatory Site of Yeast Pyruvate Decarboxylase for Allosteric Substrate Activation

The catalytic activity of the allosteric enzyme pyruvate decarboxylase from yeast is strictly controlled by its own substrate pyruvate via covalent binding at a separate regulatory site. Kinetic studies, chemical modifications, cross-linking, small-angle X-ray scattering, and crystal structure analyses have led to a detailed understanding of the substrate activation mechanism at an atomic level with C221 as the core moiety of the regulatory site. To characterize the individual role of the residues adjacent to C221, we generated variants H92F, H225F, H310F, A287G, S311A, and C221A/C222A. The integrity of the protein structure of the variants was established by small-angle X-ray scattering measurements. The analyses of both steady state and transient kinetic data allowed the identification of the individual roles of the exchanged side chains during allosteric enzyme activation. In each case, the kinetic pattern of activation was modulated but not completely abolished. Despite the crucial role of C221, the covalent binding of pyruvate is not obligate for enzyme activation but is a requirement for a kinetically efficient transition from the inactive to the active state. Moreover, only one of the three histidines guiding the activator molecule to the binding pocket, H310, specifically interacts with C221. H310 stabilizes the thiolate form of C221, ensuring a rapid nucleophilic attack of the thiolate sulfur on C2 of the regulatory pyruvate, thus forming a regulatory dyad. The influence of the other two histidines is less pronounced. Substrate activation is slightly weakened for A287G and significantly retarded for S311A.

Structural and Biochemical Characterization of 6-Hydroxynicotinic Acid 3-Monooxygenase, A Novel Decarboxylative Hydroxylase Involved in Aerobic Nicotinate Degradation.

The genes coding for the enzymes of oxidative degradation of nicotinic acid have recently been identified in several species of aerobic bacteria, namely, Pseudomonas putida KT2440, Bordetella bronchiseptica RB50, and Bacillus niacini. One of the enzymes involved in an early step of this pathway is a flavin-dependent monooxygenase (6-hydroxynicotinic acid 3-monooxygenase; NicC) that catalyzes the decarboxylative hydroxylation of 6-hydroxynicotinic acid (6-HNA) to 2,5-dihydroxypyridine (2,5-DHP), with concomitant oxidation of NADH to NAD+. The nicC genes from B. bronchiseptica RB50 and P. putida have been cloned, and the purified enzymes have been characterized functionally and structurally. Global fits of the steady-state kinetic data show that both enzymes are efficient catalysts, with an apparent kcat/KM6-HNA of 5.0 × 104 M–1 s–1 for B. bronchiseptica NicC. The pH dependence of Vmax/[E]t fits a double-bell model showing an optimum around pH 8 with apparent pKas of 7.24 ± 0.08 and 8.64 ± 0.08, whereas the...

Recent adaptations of fluorescence techniques for the determination of mechanistic parameters of helicases and translocases

Helicases and translocases are nucleic acid (NA)-based molecular motors that use the free energy liberated during the nucleoside triphosphate (NTP, usually ATP) hydrolysis cycle for unidirectional translocation along their NA (DNA, RNA or heteroduplex) substrates. Determination of the kinetic and thermodynamic parameters of their mechanoenzymatic cycle serves as a basis for the exploration of their physiological behavior and various cellular functions. Here we describe how recent adaptations of fluorescence-based solution kinetic methods can be used to determine practically all important mechanistic parameters of NA-based motor proteins. We outline practically useful analysis procedures for equilibrium, steady-state and transient kinetic data. This analysis can be used to quantitatively characterize the enzymatic steps of the NTP hydrolytic cycle, the binding site size, stoichiometry and energetics of protein-NA interactions, the rate and processivity of translocation along and unwinding of NA strands, and the mechanochemical coupling between these processes. The described methods yield insights into the functional role of the enzymes, and also greatly aid the design and interpretation of single-molecule experiments as well as the engineering of enzymatic properties for biotechnological applications.

Mutagenic Bypass of an Oxidized Abasic Lesion-Induced DNA Interstrand Cross-Link Analogue by Human Translesion Synthesis DNA Polymerases.

5'-(2-Phosphoryl-1,4-dioxobutane) (DOB) is an oxidized abasic site that is produced by several antitumor agents and γ-radiolysis. DOB reacts reversibly with a dA opposite the 3'-adjacent nucleotide to form DNA interstrand cross-links (ICLs), genotoxic DNA lesions that can block DNA replication and transcription. Translesion synthesis (TLS) is an important step in several ICL repair pathways to bypass unhooked intermediates generated by endonucleolytic incision. The instability of DOB-ICLs has made it difficult to learn about their TLS-mediated repair capability and mutagenic potential. We recently developed a method for chemically synthesizing oligonucleotides containing a modified DOB-ICL analogue. Herein, we examined the capabilities of several highly relevant eukaryotic TLS DNA polymerases (pols), including human pol η, pol κ, pol ι, pol ν, REV1, and yeast pol ζ, to bypass this DOB-ICL analogue. The prelesion, translesion, and postlesion replication efficiency and fidelity were examined. Pol η showed moderate bypass activity when encountering the DOB-ICL, giving major products one or two nucleotides beyond the cross-linked template nucleotide. In contrast, DNA synthesis by the other pols was stalled at the position before the cross-linked nucleotide. Steady-state kinetic data and liquid chromatography-mass spectrometry sequencing of primer extension products by pol η unambiguously revealed that pol η-mediated bypass is highly error-prone. Together, our study provides the first set of in vitro evidence that the DOB-ICL is a replication-blocking and highly miscoding lesion. Compared to several other TLS pols examined, pol η is likely to contribute to the TLS-mediated repair of the DOB-ICL in vivo.

Pressure and Temperature Effects on the Activity and Structure of the Catalytic Domain of Human MT1-MMP

Membrane type 1-matrix metalloproteinase (MT1-MMP or MMP-14) is a zinc-transmembrane metalloprotease involved in the degradation of extracellular matrix and tumor invasion. While changes in solvation of MT1-MMP have been recently studied, little is known about the structural and energetic changes associated with MT1-MMP while interacting with substrates. Steady-state kinetic and thermodynamic data (including activation energies and activation volumes) were measured over a wide range of temperatures and pressures by means of a stopped-flow fluorescence technique. Complementary temperature- and pressure-dependent Fourier-transform infrared measurements provided corresponding structural information of the protein. MT1-MMP is stable and active over a wide range of temperatures (10–55°C). A small conformational change was detected at 37°C, which is responsible for the change in activity observed at the same temperature. Pressure decreases the enzymatic activity until complete inactivation occurs at 2 kbar. The inactivation is associated with changes in the rate-limiting step of the reaction caused by additional hydration of the active site upon compression and/or minor conformational changes in the active site region. Based on these data, an energy and volume diagram could be established for the various steps of the enzymatic reaction.

Sbi00515, a Protein of Unknown Function from Streptomyces bingchenggensis, Highlights the Functional Versatility of the Acetoacetate Decarboxylase Scaffold.

The acetoacetate decarboxylase-like superfamily (ADCSF) is a group of ~4000 enzymes that, until recently, was thought to be homogeneous in terms of the reaction catalyzed. Bioinformatic analysis shows that the ADCSF consists of up to seven families that differ primarily in their active site architectures. The soil-dwelling bacterium Streptomyces bingchenggensis BCW-1 produces an ADCSF enzyme of unknown function that shares a low level of sequence identity (~20%) with known acetoacetate decarboxylases (ADCs). This enzyme, Sbi00515, belongs to the MppR-like family of the ADCSF because of its similarity to the mannopeptimycin biosynthetic protein MppR from Streptomyces hygroscopicus. Herein, we present steady state kinetic data that show Sbi00515 does not catalyze the decarboxylation of any α- or β-keto acid tested. Rather, we show that Sbi00515 catalyzes the condensation of pyruvate with a number of aldehydes, followed by dehydration of the presumed aldol intermediate. Thus, Sbi00515 is a pyruvate aldolase-dehydratase and not an acetoacetate decarboxylase. We have also determined the X-ray crystal structures of Sbi00515 in complexes with formate and pyruvate. The structures show that the overall fold of Sbi00515 is nearly identical to those of both ADC and MppR. The pyruvate complex is trapped as the Schiff base, providing evidence that the Schiff base chemistry that drives the acetoacetate decarboxylases has been co-opted to perform a new function, and that this core chemistry may be conserved across the superfamily. The structures also suggest possible catalytic roles for several active site residues.

Furan-based benzene mono- and dicarboxylic acid derivatives as multiple inhibitors of the bacterial Mur ligases (MurC-MurF): experimental and computational characterization.

Bacterial resistance to the available antibiotic agents underlines an urgent need for the discovery of novel antibacterial agents. Members of the bacterial Mur ligase family MurC-MurF involved in the intracellular stages of the bacterial peptidoglycan biosynthesis have recently emerged as a collection of attractive targets for novel antibacterial drug design. In this study, we have first extended the knowledge of the class of furan-based benzene-1,3-dicarboxylic acid derivatives by first showing a multiple MurC-MurF ligase inhibition for representatives of the extended series of this class. Steady-state kinetics studies on the MurD enzyme were performed for compound 1, suggesting a competitive inhibition with respect to ATP. To the best of our knowledge, compound 1 represents the first ATP-competitive MurD inhibitor reported to date with concurrent multiple inhibition of all four Mur ligases (MurC-MurF). Subsequent molecular dynamic (MD) simulations coupled with interaction energy calculations were performed for two alternative in silico models of compound 1 in the UMA/D-Glu- and ATP-binding sites of MurD, identifying binding in the ATP-binding site as energetically more favorable in comparison to the UMA/D-Glu-binding site, which was in agreement with steady-state kinetic data. In the final stage, based on the obtained MD data novel furan-based benzene monocarboxylic acid derivatives 8-11, exhibiting multiple Mur ligase (MurC-MurF) inhibition with predominantly superior ligase inhibition over the original series, were discovered and for compound 10 it was shown to possess promising antibacterial activity against S. aureus. These compounds represent novel leads that could by further optimization pave the way to novel antibacterial agents.

Mechanism of N-Acylthiourea-mediated Activation of Human Histone Deacetylase 8 (HDAC8) at Molecular and Cellular Levels

We reported previously that an N-acylthiourea derivative (TM-2-51) serves as a potent and isozyme-selective activator for human histone deacetylase 8 (HDAC8). To probe the molecular mechanism of the enzyme activation, we performed a detailed account of the steady-state kinetics, thermodynamics, molecular modeling, and cell biology studies. The steady-state kinetic data revealed that TM-2-51 binds to HDAC8 at two sites in a positive cooperative manner. Isothermal titration calorimetric and molecular modeling data conformed to the two-site binding model of the enzyme-activator complex. We evaluated the efficacy of TM-2-51 on SH-SY5Y and BE(2)-C neuroblastoma cells, wherein the HDAC8 expression has been correlated with cellular malignancy. Whereas TM-2-51 selectively induced cell growth inhibition and apoptosis in SH-SY5Y cells, it showed no such effects in BE(2)-C cells, and this discriminatory feature appears to be encoded in the p53 genotype of the above cells. Our mechanistic and cellular studies on HDAC8 activation have the potential to provide insight into the development of novel anticancer drugs.

Bridging of a substrate between cyclodextrin and an enzyme's active site pocket triggers a unique mode of inhibition

BackgroundMethionyl-7-amino-4-methylcoumarin (MetAMC) serves as a substrate for the Escherichia coli methionine aminopeptidase (MetAP) catalyzed reaction, and is routinely used for screening compounds to identify potential antibiotic agents. In pursuit of screening the enzyme's inhibitors, we observed that 2-hydroxypropyl-β-cyclodextrin (HP-β-CD), utilized to solubilize hydrophobic inhibitors, inhibited the catalytic activity of the enzyme, and such inhibition was not solely due to sequestration of the substrate by HP-β-CD. MethodsThe mechanistic path for the HP-β-CD mediated inhibition of MetAP was probed by performing a detailed account of steady-state kinetics, ligand binding, X-ray crystallographic, and molecular modeling studies. ResultsX-ray crystallographic data of the β-cyclodextrin–substrate (β-CD–MetAMC) complex reveal that while the AMC moiety of the substrate is confined within the CD cavity, the methionine moiety protrudes outward. The steady-state kinetic data for inhibition of MetAP by HP-β-CD–MetAMC conform to a model mechanism in which the substrate is “bridged” between HP-β-CD and the enzyme's active-site pocket, forming HP-β-CD–MetAMC–MetAP as the catalytically inactive ternary complex. Molecular modeling shows that the scissile bond of HP-β-CD-bound MetAMC substrate does not reach within the proximity of the enzyme's catalytic metal center, and thus the substrate fails to undergo cleavage. ConclusionsThe data presented herein suggests that the bridging of the substrate between the enzyme and HP-β-CD cavities is facilitated by interaction of their surfaces, and the resulting complex inhibits the enzyme activity. General significanceDue to its potential interaction with physiological proteins via sequestered substrates, caution must be exercised in HP-β-CD mediated delivery of drugs under pathophysiological conditions.