Mechanistic insights into the inhibition mechanism of cysteine cathepsins by chalcone-based inhibitors—a QM cluster model approach

Structural Chemistry - Cathepsins are the most abundant cysteine proteases involved in many physiological processes. The imbalance between the natural cysteine protease inhibitors and cathepsins...     

QM/MM studies of monozinc β-lactamase CphA suggest that the crystal structure of an enzyme-intermediate complex represents a minor pathway

QM/MM studies of the hydrolysis of a β-lactam antibiotic molecule (biapenem) catalyzed by a monozinc β-lactamase (CphA) have revealed the complete reaction mechanism and shown that an experimentally determined enzyme-intermediate complex is a stable intermediate or product in a minor pathway.     

Structures of the Peptide–Water Complexes Studied by the Hybrid Quantum Mechanical—Molecular Mechanical (QM/MM) Technique

Applications of a new approach to the hybrid quantum mechanical and molecular mechanical (QM/MM) theory based on the effective fragment potential technique to calculations of the structures of the peptide—water complexes are described. Our approach assumes that the MM subsystem is viewed as a flexible composition of effective fragments, while fragment–fragment interactions are replaced by MM force fields. In this work, the QM subsystem is composed of water molecules and the MM part refers to peptides. Different isomers of the hydrogen-bonded complex of the dipeptide N-acetyl-L-alanine N-methylamide (AAMA) with four water molecules are considered, and the results of QM/MM calculations are compared to experimental data and to the results of the density functional theory (DFT) treatment. The properties of water chains inside polypeptide tubes, modeling proton wires inside ionic channels, are described.     

An efficient implementation of a QM�CMM method in SIESTA

We present the major features of a new implementation of a QM?CMM method that uses the DFT code Siesta to treat the quantum mechanical subsystem and the AMBER force field to deal with the classical part. The computation of the electrostatic interaction has been completely revamped to treat periodic boundary conditions exactly, using a real-space grid that encompasses the whole system. Additionally, we present a new parallelization of the Siesta grid operations that provides near-perfect load balancing for all the relevant operations and achieves a much better scalability, which is important for efficient massive QM?CMM calculations in which the grid can potentially be very large.     

Is the DPT tautomerization of the long A·G Watson–Crick DNA base mispair a source of the adenine and guanine mutagenic tautomers? A QM and QTAIM response to the biologically important question

Herein, we first address the question posed in the title by establishing the tautomerization trajectory via the double proton transfer of the adenine·guanine (A·G) DNA base mispair formed by the canonical tautomers of the A and G bases into the A*·G* DNA base mispair, involving mutagenic tautomers, with the use of the quantum‐mechanical calculations and quantum theory of atoms in molecules (QTAIM). It was detected that the A·G ? A*·G* tautomerization proceeds through the asynchronous concerted mechanism. It was revealed that the A·G base mispair is stabilized by the N6H···O6 (5.68) and N1H···N1 (6.51) hydrogen bonds (H‐bonds) and the N2H···HC2 dihydrogen bond (DH‐bond) (0.68 kcal·mol^?1), whereas the A*·G* base mispair—by the O6H···N6 (10.88), N1H···N1 (7.01) and C2H···N2 H‐bonds (0.42 kcal·mol^?1). The N2H···HC2 DH‐bond smoothly and without bifurcation transforms into the C2H···N2 H‐bond at the IRC = ?10.07 Bohr in the course of the A·G ? A*·G* tautomerization. Using the sweeps of the energies of the intermolecular H‐bonds, it was observed that the N6H···O6 H‐bond is anticooperative to the two others—N1H···N1 and N2H···HC2 in the A·G base mispair, while the latters are significantly cooperative, mutually strengthening each other. In opposite, all three O6H···N6, N1H···N1, and C2H···N2 H‐bonds are cooperative in the A*·G* base mispair. All in all, we established the dynamical instability of the А*·G* base mispair with a short lifetime (4.83·10^?14 s), enabling it not to be deemed feasible source of the A* and G* mutagenic tautomers of the DNA bases. The small lifetime of the А*·G* base mispair is predetermined by the negative value of the Gibbs free energy for the A*·G* → A·G transition. Moreover, all of the six low‐frequency intermolecular vibrations cannot develop during this lifetime that additionally confirms the aforementioned results. Thus, the A*·G* base mispair cannot be considered as a source of the mutagenic tautomers of the DNA bases, as the A·G base mispair dissociates during DNA replication exceptionally into the A and G monomers in the canonical tautomeric form. © 2013 Wiley Periodicals, Inc.     

What is the active species of cytochrome P450 during camphor hydroxylation? QM/MM studies of different electronic states of compound I and of reduced and oxidized iron-oxo intermediates

We have investigated C-H hydroxylation of camphor by Compound I (Cpd I) of cytochrome P450cam in different electronic states and by its one-electron reduced and oxidized forms, using QM/MM calculations in the native protein/solvent environment. Cpd I species with five unpaired electrons (pentaradicaloids) are ca. 12 kcal/mol higher in energy than the ground state Cpd I species with three unpaired electrons (triradicaloids). The H-abstraction transition states of pentaradicaloids lie ca. 21 (9) kcal/mol above the triradicaloid (pentaradicaloid) reactants. Hydroxylation via pentaradicaloids is thus facile provided that they can react before relaxing to the ground-state triradicaloids. Excited states of Cpd I with an Fe(V)-oxo moiety lie more than 20 kcal/mol above the triradicaloid ground state in single-point gas-phase calculations, but these electronic configurations are not stable upon including the point-charge protein environment which causes SCF convergence to the triradicaloid ground state. One-electron reduced species (Cpd II) show sluggish reactivity compared with Cpd I in agreement with experimental model studies. One-electron oxidized species are more reactive than Cpd I but seem too high in energy to be accessible. The barriers to hydrogen abstraction for the various forms of Cpd I are generally not affected much by the chosen protonation states of the Asp297 and His355 residues near the propionate side chains of the heme or by the appearance of radical character at Asp297, His355, or the propionates.     

What is so special about Arg 55 in the catalysis of cyclophilin A? insights from hybrid QM/MM simulations

Potential of mean force (PMF) simulations with a hybrid QM/MM potential function were used to analyze the catalytic mechanism of human cyclophilin A (CypA). PMF calculations were performed for proline isomerization of peptides in solution, the wild-type CypA, and several CypA mutants. With an approximate density functional theory, the self-consistent-charge density functional tight binding (SCC-DFTB) as the QM level, and CHARMM 22 force field as MM, satisfactory energetics compared to available experiments were obtained. Calculations for the Arg55Ala and zero-charge-Arg55 mutants clearly indicated that Arg 55 significantly stabilizes the isomerization transition state through electrostatic interactions. However, the decrease in the average distance (thus the increase in interaction) between Arg 55 and the substrate amide N in going from the stable states to the transition state is mainly due to the pyramidalization of the amide N rather than motions associated with Arg 55. Although the nanosecond simulations cannot exclude the existence of sub-millisecond collective motions proposed on the basis of recent elegant NMR relaxation and line-shape analyses, the energetics obtained for the various enzyme systems here indicate that the contribution from motions of active site residues to catalysis is expected to be small. Instead, the present simulations support that the structural stability rather than mobility of the preorganized active site is more important. Through hydrogen-bonding interactions among the substrate, Arg 55, Gln 63, and Asn 102, the active site of the wild-type enzyme is structurally very stable and puts Arg 55 in a favorable position to perform its catalytic role in the transition state. This is further illustrated with the somewhat unexpected prediction that Arg55Lys is largely catalytically inactive, because Lys does not have the unique bifurcating construct of the guanidino group in Arg and thus the active site of Arg55Lys cannot accommodate Lys in a position capable of providing electrostatic stabilization of the isomerization transition state. Among all the enzyme systems studied, the wild-type CypA is the only one that selects the syn/exo transition state, while the syn/endo conformation is also present in the mutants, which is another reason for their higher barriers. Finally, the present analysis indicated that the population of near-attack-conformations (NAC) is not relevant to catalysis in CypA.     

Construction of the Skeleton of Phthalascidin, Mechanism of the Formation of the Key Tricyclic Lactam Intermediate

Phthalascidin is a structurally simplified version of Et-743, which is a potent anti-tumor marine natural product isolated from Ecteinascidia turbinata. Its antiproliferative activity is greater than that of the agents taxol, camptothecin, adriamycin, mitomycin C, cisplatin, bleomycin, and etoposide by 1-3 orders of magnitude. An elegant synthesis of Et-743 and phthalascidin has been reported by E. J. Corey and co-workers1,2. As part of our continuing program, we have also engaged in dev…     

Toward identification of the compound I reactive intermediate in cytochrome P450 chemistry: a QM/MM study of its EPR and Mössbauer parameters

Quantum mechanical/molecular mechanical (QM/MM) methods have been used in conjunction with density functional theory (DFT) and correlated ab initio methods to predict the electron paramagnetic resonance (EPR) and Mossbauer (MB) properties of Compound I in P450(cam). For calibration purposes, a small Fe(IV)-oxo complex [Fe(O)(NH(3))(4)(H(2)O)](2+) was studied. The (3)A(2) and (5)A(1) states (in C(4)(v)() symmetry) are found to be within 0.1-0.2 eV. The large zero-field splitting (ZFS) of the (FeO)(2+) unit in the (3)A(2) state arises from spin-orbit coupling with the low-lying quintet and singlet states. The intrinsic g-anisotropy is very small. The spectroscopic properties of the model complex [Fe(O)(TMC)(CH(3)CN)](2+) (TMC = 1,4,8,11-tetramethyl-1,4,8,11-tetraazacyclotetradecane) are well reproduced by theory. In the model complexes [Fe(O)(TMP)(X)](+) (TMP = tetramesitylporphyrin, X = nothing or H(2)O) the computations again account for the observed spectroscopic properties and predict that the coupling of the (5)A(1) state of the (FeO)(2+) unit to the porphyrin radical leads to a low-lying sextet/quartet manifold approximately 12 kcal/mol above the quartet ground state. The calculations on cytochrome P450(cam), with and without the simulation of the protein environment by point charges, predict a small antiferromagnetic coupling (J approximately -13 to -16 cm(-)(1); H(HDvV) = - 2JS(A)S(B)) and a large ZFS > 15 cm(-)(1) (with E/D approximately 1/3) which will compete with the exchange coupling. This leads to three Kramers doublets of mixed multiplicity which are all populated at room temperature and may therefore contribute to the observed reactivity. The MB and ligand hyperfine couplings ((14)N, (1)H) are fairly sensitive to the protein environment which controls the spin density distribution between the porphyrin ring and the axial cysteinate ligand.     

Synthesis of two peptides of α-bungarotoxin and the participation of the amino acid residue Trp-28 of the neurotoxin in the antigenicity of the molecule

Using the method of solid-phase peptide synthesis, two peptides have been synthesized, one of which corresponds to the central ring structure of -bungarotoxin (-BTX), while the second has in position 28 a Gly residue in place of the Trp in the first peptide, and their interrelationship with antitoxin antibodies has been investigated. It has been shown that the amino acid residue Trp-28 of -BTX, which is the contact residue in binding with the acetylcholine receptor, also participates directly in binding with the active centers of antibodies to -BTX.Translated from Khimiya Prirodnykh Soedinenii, No. 4, pp. 628–631, July–August, 1997.     

Studies of the dissociation and the protonation of TB-chlorosulphophenol

The dissociation constant of each step for TB-chlorosulphophenol has been determined by potentiometric method, and the thermodynamic constants, △G°, △H° and △S°, of the dissociation process have been calculated. The protonation constants were measured by the spectrophotometric method. The pH values of various forms of anions of the chromogenic reagent at their concentrations were also calculated.     

Determination of the equilibrium melting point of the β-form of polypropylene

The melting behavior of the -form of isotactic polypropylene (-iPP) was investigated as a function of crystallization time and temperature. Calcium suberate, a selective -nucleating agent was used to produce samples that consist entirely of -form i-PP. The experimental melting points were recorded at different crystallization times and were extrapolated to the start of the crystallization process in order to eliminate the effect of lamellar thickening. Using the non-linear Hoffman—Weeks approach to correlate these extrapolated experimental melting temperatures with the corresponding crystallization temperatures, an equilibrium melting point of 209°C was obtained for -iPP. The equilibrium melting point estimated through the non-linear Hoffman—Weeks analysis is about 30°C higher than that (T _m ⁰=177°C) obtained on the basis of the linear extrapolation. These results are consistent with earlier claims that a linear extrapolation of T _m–T _c data leads to an underestimation of the equilibrium melting point. The results obtained for -iPP exemplify the importance of accounting for both the isothermal lamellar thickening effects and the non-linearity in the T _m–T _c correlation, when the determination of an equilibrium melting point is carried out using a procedure based on the predictions of the Lauritzen—Hoffman secondary nucleation theory.This revised version was published online in November 2005 with corrections to the Cover Date.     

The applicability of the “straight-line method” of asmus in the determination of the composition of polynuclear complexes

The straight-line method of Asmus was originally developed for the determination of n in mononuclear complexes of the general form AB_n (n≧ 1). In the present investigation it is demonstrated that the method also can be used for determining the value of n in polynuclear complexes of the form A[_mB_n (m > 1). The method as suggested by Asmus, is, however, not capable of distinguishing between mono- and polynuclear species. It is further shown, that the straight-line method can be applied for the determination of the value of m.     

The effect of the primary structure of the polypeptide catalyst on the enantioselectivity of the Juliá-Colonna asymmetric epoxidation of enones

Epoxidation of chalcone (1), using basic hydrogen peroxide, catalysed by polypeptides with defined primary structures demonstrates that the residues in the chain near to the N-terminus determine the stereochemical outcome of the reaction.     

Addition of γ-silyloxyallyltins on ethyl glyoxylate: evaluation of the influence of the experimental conditions on the stereochemical course of the reaction

Ethyl glyoxylate was reacted with α-substituted γ-(t-butyldimethylsilyloxy)-allyltributyltin in order to obtain selectively each diastereomer of ethyl 3-(t-butyldimethylsilyloxy)-2-hydroxyhex-4-enoate and subsequently the corresponding diols. Diastereomers syn-E, anti-E and anti-Z were obtained in good yields with good to high selectivities and the obtained results were rationalized by consideration of cyclic or open transition states in agreement with the experimental conditions and with the structure of the starting reagents.     

The kinetics of the polymorphic transition of the α-form of 2,4,6,8,10,12-hexanitrohexaazaisowurtzitane

The α → γ polymorphic transition in hexanitrohexaazaisowurtzitane was studied by optical microscopy, calorimetry, IR spectroscopy, thermogravimetry, and X-ray diffraction. The thermal effect of the transition was determined. The kinetics of the process is complex because of the relation between structural rearrangement and transition with the removal of water stabilizing the structure of the α polymorph. Depending on the morphological characteristics of the initial sample, the polymorphic transition can follow a frontal-heterogeneous mechanism (single crystal → polycrystalline aggregate) or a quasi-homogeneous mechanism (single crystal → single crystal).     

Application of the Mössbauer spectroscopy to the study of the oxidation state of azaferrocene derivatives

Azaferrocene has two active sites of iron and nitrogen atoms. Drastic change of the oxidation state in iodine oxidation of azaferrocene is observed by introducing the methyl substituents into the pyrrole ring, while all the N-methylates show a similar electronic state. It was revealed that an introduction of methyl substituent to the pyrrole ring promotes the oxidation of nitrogen atom in pyrrole ring more than the central iron atom.