On the active site of mononuclear B1 metallo β-lactamases: a computational study

Metallo-β-lactamases (MβLs) are Zn(II)-based bacterial enzymes that hydrolyze β-lactam antibiotics, hampering their beneficial effects. In the most relevant subclass (B1), X-ray crystallography studies on the enzyme from Bacillus Cereus point to either two zinc ions in two metal sites (the so-called ‘3H’ and ‘DCH’ sites) or a single Zn(II) ion in the 3H site, where the ion is coordinated by Asp120, Cys221 and His263 residues. However, spectroscopic studies on the B1 enzyme from B. Cereus in the mono-zinc form suggested the presence of the Zn(II) ion also in the DCH site, where it is bound to an aspartate, a cysteine, a histidine and a water molecule. A structural model of this enzyme in its DCH mononuclear form, so far lacking, is therefore required for inhibitor design and mechanistic studies. By using force field based and mixed quantum–classical (QM/MM) molecular dynamics (MD) simulations of the protein in aqueous solution we constructed such structural model. The geometry and the H-bond network at the catalytic site of this model, in the free form and in complex with two common β-lactam drugs, is compared with experimental and theoretical findings of CphA and the recently solved crystal structure of new B2 MβL from Serratia fonticola (Sfh-I). These are MβLs from the B2 subclass, which features an experimentally well established mono-zinc form, in which the Zn(II) is located in the DCH site. From our simulations the εεδ and δεδ protomers emerge as possible DCH mono-zinc reactive species, giving a novel contribution to the discussion on the MβL reactivity and to the drug design process.     

HPIC–UV–ICP–SFMS study of the interaction of cisplatin with guanosine monophosphate

Interaction of cis-[Pt(NH₃)₂Cl₂] (cisplatin) with 5′-guanosine monophosphate (5′-GMP) has been investigated for the first time by on-line coupling of high performance ion chromatography (HPIC) to inductively coupled plasma sector field mass spectrometry (ICP–SFMS). The time-dependent reaction course of the cisplatin-5′-GMP system was followed after incubation under simulated physiological conditions by monitoring the decrease in the concentration of 5′-GMP and the increase in the concentration of formed adducts, on the basis of speciation analysis. Because of the two-step mechanism an intermediate mono adduct was observed together with the major product, the bis adduct cis-[Pt(NH₃)₂(GMP)₂]^2–. The data obtained correlated well with those from earlier studies employing orthogonal techniques such as capillary electrophoresis (CE). Furthermore, HPIC–ICP–SFMS provided unambiguous stoichiometric information about the major GMP-adduct. For this purpose the platinum-to-phosphorus ratio was determined by simultaneously measuring ³¹P and ¹⁹⁵Pt. To separate significant interferences from ¹⁵N¹⁶O⁺, ¹⁴N¹⁶O¹H⁺, ¹²C¹⁸O¹H⁺, and ¹³C¹⁷O¹H⁺ on ³¹P, high-mass resolution (m/Δm = 4500) proved to be mandatory. The P/Pt signal ratio of 2/1 obtained corresponds to the molar ratio in the bis adduct cis-[Pt(NH₃)₂(GMP)₂]^2–.     

Structures and energetics of darunavir and active site amino acids of native and mutant HIV–1 protease: a computational study

Structural Chemistry - Quantum chemical calculations have been performed at the M06–2X/6–31G(d,p) level of theory to investigate the strength and nature of interactions between the...     

Quantum algebraic–combinatoric study of the conformational properties of n‐alkanes. I

Based on quantum chemical calculation results, four rules were previously derived for the numbers and the sequences of the conformers of free alkane molecules. This paper builds up first an algebra to handle the conformational problem of alkanes. Partitioning the set of all sequences, the whole problem is then subdivided into three independent subcases. With the help of an equivalence relation, the sequences can be classified. According to the quantum chemical rules, certain equivalence classes do not represent conformers. A welldefined subcase of the whole problem is solved.     

A quantum mechanics/molecular mechanics study on the hydrolysis mechanism of New Delhi metallo-β-lactamase-1

New Delhi metallo-β-lactamase-1 (NDM-1) has emerged as a major global threat to human health for its rapid rate of dissemination and ability to make pathogenic microbes resistant to almost all known β-lactam antibiotics. In addition, effective NDM-1 inhibitors have not been identified to date. In spite of the plethora of structural and kinetic data available, the accurate molecular characteristics of and details on the enzymatic reaction of NDM-1 hydrolyzing β-lactam antibiotics remain incompletely understood. In this study, a combined computational approach including molecular docking, molecular dynamics simulations and quantum mechanics/molecular mechanics calculations was performed to characterize the catalytic mechanism of meropenem catalyzed by NDM-1. The quantum mechanics/molecular mechanics results indicate that the ionized D124 is beneficial to the cleavage of the C–N bond within the β-lactam ring. Meanwhile, it is energetically favorable to form an intermediate if no water molecule coordinates to Zn2. Moreover, according to the molecular dynamics results, the conserved residue K211 plays a pivotal role in substrate binding and catalysis, which is quite consistent with previous mutagenesis data. Our study provides detailed insights into the catalytic mechanism of NDM-1 hydrolyzing meropenem β-lactam antibiotics and offers clues for the discovery of new antibiotics against NDM-1 positive strains in clinical studies.     

Quantum chemical study on the thermal rearrangements of HNCRCR''''CO

MINDO/3 molecular orbital theory has been used to study the thermal rearrangements of HNCRCR'CO.The results obtained show that the activation energy of this rearrangement depends on the migrating group R and the group R'.     

On the accuracy of numerical Hartree–Fock energies

It is demonstrated that numerical Hartree–Fock (HF) energies reported in the literature in some cases have errors in the milliHartree range. The main cause of these errors is due to the use of too small a value for the practical infinity parameter in the finite difference method for generating the results. By systematically investigating the convergence with respect to the computational parameters, HF energies accurate to at least 1 microHartree are generated for 42 diatomic systems containing first and second row elements, encompassing both cationic, neutral and anionic systems.     

Quantum chemical study on the one-carbon unit transfer of imidazolinium

One-carbon unit transfer reaction of folate cofactor model compound, 1-acetyl-2-methyl-imidazolinium, with 1,2-diaminobenzene has been studied theoretically with ONIOM method. The result shows that there are two pathways to complete this reaction because the imidazolinium ring has two breaking patterns. Both the two pathways have six steps. They are combination of two reactants, proton migration, break of five-membered ring, formation of benzimidazole derivate, another proton migration, and formation of final products. In each of the above pathways, the two proton migration steps have higher energy, which illuminate that the reaction is catalyzed by general acid-base. This fact agrees with the experimental results of enzymatic one-carbon unit transfer at oxidation level of formate.     

Quantum chemical study on the mechanism of the consecutive addition of HCN to aminoacetonitrile

MINDO/3 method has been used to study the mechanism of the consecutive addition ofHCN to aminoacetonitrile.The results obtained for the first three steps show that the reaction isexothermic,and step I is the rate determining step.     

Circular dichroism active artificial phospholipids for the study of molecular membrane dynamics focused on lipid—lipid interaction

Artificial phospholipid with an azobenzene chromophore in a close proximity to the asymmetric carbon of the choline skeleton was prepared. The artificial phospholipid was miscible with the natural phospholipid and provides CD information sensitive to the membrane motion.     

Quantum cluster size and solvent polarity effects on the geometries and Mössbauer properties of the active site model for ribonucleotide reductase intermediate X: a density functional theory study

In studying the properties of metalloproteins using ab initio quantum mechanical methods, one has to focus on the calculations on the active site. The bulk protein and solvent environment is often neglected, or is treated as a continuum dielectric medium with a certain dielectric constant. The size of the quantum cluster of the active site chosen for calculations can vary by including only the first-shell ligands which are directly bound to the metal centers, or including also the second-shell residues which are adjacent to and normally have H-bonding interactions with the first-shell ligands, or by including also further hydrogen bonding residues. It is not well understood how the size of the quantum cluster and the value of the dielectric constant chosen for the calculations will influence the calculated properties. In this paper, we have studied three models (A, B, and C) of different sizes for the active site of the ribonucleotide reductase intermediate X, using density functional theory (DFT) OPBE functional with broken-symmetry methodology. Each model is studied in gas-phase and in the conductor-like screening (COSMO) solvation model with different dielectric constants ε = 4, 10, 20, and 80, respectively. All the calculated Fe-ligand geometries, Heisenberg J coupling constants, and the Mössbauer isomer shifts, quadrupole splittings, and the ⁵⁷Fe, ¹H, and ¹⁷O hyperfine tensors are compared. We find that the calculated isomer shifts are very stable. They are virtually unchanged with respect to the size of the cluster and the dielectric constant of the environment. On the other hand, certain Fe-ligand distances are sensitive to both the size of the cluster and the value of ε. ε = 4, which is normally used for the protein environment, appears too small when studying the diiron active site geometry with only the first-shell ligands as seen by comparisons with larger models.     

Thermochemical study of the reactions of acid–base interaction in an aqueous solution of α-aminobutyric acid

The heat effects of the interaction between a solution of α-aminobutyric acid and solutions of HNO₃ and KОН are measured by means of calorimetry in different ranges of рН at 298.15 K and values of ionic strength of 0.25, 0.5, and 0.75 (KNO₃). The heat effects of the stepwise dissociation of the amino acid are determined. Standard thermodynamic characteristics (Δ_r H ⁰, Δ_r G ⁰, and Δ_r S ⁰) of the reactions of acid–base interaction in aqueous solutions of α-aminobutyric acid are calculated. The connection between the thermodynamic characteristics of the dissociation of the amino acid and the structure of this compound is considered.     

l-Proline-derived ligands to mimic the ‘2-His-1-carboxylate’ triad of the non-haem iron oxidase active site

Non-haem iron(II) oxidases (NHIOs) catalyse a variety of oxidative transformations in biology. The iron-binding environment of the NHIO active site typically incorporates a ‘2-His-1-carboxylate’ facial triad of amino acid side-chains, a motif that has emerged as a defining feature of the enzyme family. Towards the goal of biomimetic, iron-mediated C–H activation we have synthesized a series of peptidomimetic ligands from l-proline. By coupling l-proline to 2,6-bis(bromomethyl)pyridine, 2-(bromomethyl)-6-((tert-butyldimethylsilyloxy)methyl)pyridine and picolinic acid, we have generated several new ligand architectures designed to complex with iron(II) and mimic the NHIO active site. The resulting iron complexes promote modest levels of alkene dihydroxylation and allylic oxidation using hydrogen peroxide as oxidant.     

Bridged aromatic alkenes for the study of carbocation-π interaction

Toward the goal of gaining further insight into carbocation-π interactions, bridged-ring aromatic alkene model systems are being investigated in which one isomer will permit π complexation of an intramolecular tertiary carbocation with a benzene ring, but the other isomer will not. The syntheses of three sets of such isomers, having, respectively, benzobicyclo[3.2.1]octene, benzobicyclo[2.2.1]heptene, and benzobicyclo[4.2.1]nonene structures, are described.     

Quantum chemical study of σ-dimerization reaction of 1-silacycloprop-2-enes

The PBE/TZ2P method was used to study a concerted σ-dimerization reaction of 1-silacycloprop-2-enes having substituents with different electron effects. The corresponding reaction channels were founds in all the cases, that indicated a general character of this reaction. The reaction barriers varied from moderately high to extremely low. The suggestions made earlier on a possibility for this process to take place in the course of the reaction of silylenes with alkynes at elevated temperature were quantitatively confirmed for the first time. The influence of substituents on the barrier heights and exothermicity of σ-dimerization of 1-silacycloprop-2-enes was studied. The σ-dimerization reaction of 1-silacycloprop-2-enes is one of a few examples of metathesis of s-bonds in the absence of transition metal complexes.     

Theoretical study on the size consistency of the second and third order energies of the multireference perturbation theory

The size consistency of the second and third order energies of the multireference perturbation theory(Chen F, Davidson E, Iwata S. Int J Quant Chem, 2002, 86: 256) is investigated theoretically with a su-per-molecular model composed of N-hydrogen molecules separated by a large distance. It is found that the two perturbation series corresponding to two Hamiltonian partitions are not size consistent at the second and third order. However, two size consistent forms are suggested for two Hamiltonian parti-tions at the second order, if some approximations to the denominators of the original second order energies are assumed.     

Mössbauer studies of the iron-sulfur cluster-free hydrogenase: the electronic state of the mononuclear Fe active site

The iron-sulfur cluster-free hydrogenase (Hmd) from methanogenic archaea harbors an iron-containing, light-sensitive cofactor of still unknown structure as prosthetic group. The enzyme is reversibly inhibited by CO and cyanide and is EPR silent. We report here on M?ssbauer spectra of the (57)Fe-labeled enzyme and of the isolated cofactor. The spectrum of the holoenzyme measured at 80 K revealed a doublet peak with an isomer shift delta = 0.06 mm.s(-)(1) and a quadrupole splitting of DeltaE(Q) = 0.65 mm.s(-)(1) (at pH 8.0). The signal intensity corresponded to the enzyme concentration assuming 1 Fe per mol active site. Upon addition of CO or cyanide to the enzyme, the isomer shift decreased to -0.03 mm.s(-)(1) and -0.00(1) mm.s(-)(1), and the quadrupole splitting increased to 1.38 mm.s(-)(1) and 1.75 mm.s(-)(1), respectively. The three spectra could be perfectly simulated assuming the presence of only one type of iron in Hmd. The low isomer shift is characteristic for Fe in a low oxidation state (0, +1, +2). When the spectra of the holoenzyme and of the CO- or cyanide-inhibited enzyme were measured at 4 K in a magnetic field of 4 and 7 T, the spectra obtained could be simulated assuming the presence of only the external magnetic field, which excludes that the iron in the active site of Hmd is Fe(I), high-spin Fe(0), or high-spin Fe(II). M?ssbauer spectra of the isolated Hmd cofactor are also reported.     

Insight into the cation-π interaction at the metal binding site of the copper metallochaperone CusF

The periplasmic Cu(+)/Ag(+) chaperone CusF features a novel cation-π interaction between a Cu(+)/Ag(+) ion and Trp44 at the metal binding site. The nature and strength of the Cu(+)/Ag(+)-Trp44 interactions were investigated using computational methodologies. Quantum-mechanical (QM) calculations showed that the Cu(+) and Ag(+) interactions with Trp44 are of similar strength (~14 kcal/mol) and bond order. Quantum-mechanical/molecular-mechanical (QM/MM) calculations showed that Cu(+) binds in a distorted tetrahedral coordination environment in the Trp44Met mutant, which lacks the cation-π interaction. Molecular dynamics (MD) simulations of CusF in the apo and Cu(+)-bound states emphasized the importance of the Cu(+)-Trp44 interaction in protecting Cu(+) from water oxidation. The protein structure does not change over the time scale of hundreds of nanoseconds in the metal-bound state. The metal recognition site exhibits small motions in the apo state but remains largely preorganized toward metal binding. Trp44 remains oriented to form the cation-π interaction in the apo state and faces an energetic penalty to move away from the metal ion. Cu(+) binding quenches the protein's internal motions in regions linked to binding CusB, suggesting that protein motions play an essential role in Cu(+) transfer to CusB.     

Molecular mechanics study on conformation of perylene-quinonoid photosensitizers

Using molecular mechanics method,values of the heat of formation (HF) of different conformations,of perylenequinonoid photosensitizes hypocrellin A (HA) and hypocrellin B (HB) were calculated and the variance of HF after phenolic protons' dissociation were calculated as well The following was found:(i) The HF values of lour conformational isomers of HA and HB are similar to each other,so the four isomcrs can transform to each other room temperature,(ii) There exists the difference between the ability of dissociation of phenolic protons of HA and that of HB,the former is higher than the latter (iii) There exist two intramolecular hydrogen bonds in HA and HB The bond energy is approximately 8 kJ/mol and the energy of conformation Ⅰ is lower than that of conformationⅡ The bond energy of HA is lower than that of HB.(iv) There exists a low energy snot when phenolic hydroxyl bond twists 180° from the position where hydrogen bond is formed,which suggests that this kind of conformation probably exists,(v) Th