A QM/MM study of the binding of RAPTA ligands to cathepsin B

We have carried out quantum mechanical (QM) and QM/MM (combined QM and molecular mechanics) calculations, as well as molecular dynamics (MD) simulations to study the binding of a series of six RAPTA (Ru(II)-arene-1,3,5-triaza-7-phosphatricyclo-[3.3.1.1] decane) complexes with different arene substituents to cathepsin B. The recently developed QM/MM-PBSA approach (QM/MM combined with Poisson–Boltzmann solvent-accessible surface area solvation) has been used to estimate binding affinities. The QM calculations reproduce the antitumour activities of the complexes with a correlation coefficient (r ²) of 0.35–0.86 after a conformational search. The QM/MM-PBSA method gave a better correlation (r ² = 0.59) when the protein was fixed to the crystal structure, but more reasonable ligand structures and absolute binding energies were obtained if the protein was allowed to relax, indicating that the ligands are strained when the protein is kept fixed. In addition, the best correlation (r ² = 0.80) was obtained when only the QM energies were used, which suggests that the MM and continuum solvation energies are not accurate enough to predict the binding of a charged metal complex to a charged protein. Taking into account the protein flexibility by means of MD simulations slightly improves the correlation (r ² = 0.91), but the absolute energies are still too large and the results are sensitive to the details in the calculations, illustrating that it is hard to obtain stable predictions when full flexible protein is included in the calculations.     

Binding free energies in the SAMPL6 octa-acid host–guest challenge calculated with MM and QM methods

We have estimated free energies for the binding of eight carboxylate ligands to two variants of the octa-acid deep-cavity host in the SAMPL6 blind-test challenge (with or without endo methyl groups on the four upper-rim benzoate groups, OAM and OAH, respectively). We employed free-energy perturbation (FEP) for relative binding energies at the molecular mechanics (MM) and the combined quantum mechanical (QM) and MM (QM/MM) levels, the latter obtained with the reference-potential approach with QM/MM sampling for the MM → QM/MM FEP. The semiempirical QM method PM6-DH+ was employed for the ligand in the latter calculations. Moreover, binding free energies were also estimated from QM/MM optimised structures, combined with COSMO-RS estimates of the solvation energy and thermostatistical corrections from MM frequencies. They were performed at the PM6-DH+ level of theory with the full host and guest molecule in the QM system (and also four water molecules in the geometry optimisations) for 10–20 snapshots from molecular dynamics simulations of the complex. Finally, the structure with the lowest free energy was recalculated using the dispersion-corrected density-functional theory method TPSS-D3, for both the structure and the energy. The two FEP approaches gave similar results (PM6-DH+/MM slightly better for OAM), which were among the five submissions with the best performance in the challenge and gave the best results without any fit to data from the SAMPL5 challenge, with mean absolute deviations (MAD) of 2.4–5.2 kJ/mol and a correlation coefficient (R²) of 0.77–0.93. This is the first time QM/MM approaches give binding free energies that are competitive to those obtained with MM for the octa-acid host. The QM/MM-optimised structures gave somewhat worse performance (MAD?=?3–8 kJ/mol and R²?=?0.1–0.9), but the results were improved compared to previous studies of this system with similar methods.     

Blind prediction of SAMPL4 cucurbit[7]uril binding affinities with the mining minima method

Accurate methods for predicting protein–ligand binding affinities are of central interest to computer-aided drug design for hit identification and lead optimization. Here, we used the mining minima (M2) method to predict cucurbit[7]uril binding affinities from the SAMPL4 blind prediction challenge. We tested two different energy models, an empirical classical force field, CHARMm with VCharge charges, and the Poisson–Boltzmann surface area solvation model; and a semiempirical quantum mechanical (QM) Hamiltonian, PM6-DH+, coupled with the COSMO solvation model and a surface area term for nonpolar solvation free energy. Binding affinities based on the classical force field correlated strongly with the experiments with a correlation coefficient (R²) of 0.74. On the other hand, binding affinities based on the QM energy model correlated poorly with experiments (R² = 0.24), due largely to two major outliers. As we used extensive conformational search methods, these results point to possible inaccuracies in the PM6-DH+ energy model or the COSMO solvation model. Furthermore, the different binding free energy components, solute energy, solvation free energy, and configurational entropy showed significant deviations between the classical M2 and quantum M2 calculations. Comparison of different classical M2 free energy components to experiments show that the change in the total energy, i.e. the solute energy plus the solvation free energy, is the key driving force for binding, with a reasonable correlation to experiment (R² = 0.56); however, accounting for configurational entropy further improves the correlation.     

Reactions of Hf, Ta, and W with O2 and CO: Metal carbide and metal oxide cation bond energies

The reactions of Hf⁺, Ta⁺, and W⁺ with O₂ and CO are studied as a function of translational energy in a guided ion beam tandem mass spectrometer. All three reactions with O₂ form diatomic metal oxide cations in exothermic reactions that occur at the collision rate. In the CO systems, formation of both diatomic metal oxide and metal carbide cations is observed to be endothermic. The energy-dependent cross sections in the latter systems are interpreted to give 0 K bond energies (in eV) of D₀(HfC⁺) = 3.19 ± 0.03, D₀(TaC⁺) = 3.79 ± 0.04, D₀(WC⁺) = 4.76 ± 0.09, D₀(HfO⁺) = 6.91 ± 0.11, D₀(TaO⁺) = 7.10 ± 0.12, and D₀(WO⁺) = 6.77 ± 0.07. The present experimental values for TaO⁺ and WC⁺ agree well with literature thermochemistry, those for HfO⁺ and WO⁺ refine the available literature bond energies, and those for HfC⁺ and TaC⁺ are the first measurements available. The nature of the bonding in MO⁺ and MC⁺ is discussed and compared for these three metal ions and analyzed using theoretical calculations at a B3LYP/HW+/6-311+G(3df) level of theory. Bond energies for all MO⁺ and MC⁺ species are calculated using geometries calculated at this level and single point energies determined at B3LYP, CCSD, CCSD(T), QCISD, and QCISD(T) levels of theory with the same basis set. Reasonable agreement between the theoretical and experimental bond energies for the three metal oxide and three metal carbide cations is found. Potential energy surfaces for reaction of the metal cations with CO are also calculated at the B3LYP level of theory and reveal additional information about the reaction mechanisms.     

Nonfitting protein–ligand interaction scoring function based on first‐principles theoretical chemistry methods: Development and application on kinase inhibitors

Targeted therapy is currently a hot topic in the fields of cancer research and drug design. An important requirement for this approach is the development of potent and selective inhibitors for the identified target protein. However, current ways to estimate inhibitor efficacy rely on empirical protein–ligand interaction scoring functions which, suffering from their heavy parameterizations, often lead to a low accuracy. In this work, we develop a nonfitting scoring function, which consists of three terms: (1) gas‐phase protein‐ligand binding enthalpy obtained by the eXtended ONIOM hybrid method based on an integration of density functional theory (DFT) methods (XYG3 and ωB97X‐D) and the semiempirical PM6 method, (2) solvation free energy based on DFT‐SMD solvation model, and (3) entropy effect estimated by using DFT frequency analysis. The new scoring function is tested on a cyclin‐dependent kinase 2 (CDK2) inhibitor database including 76 CDK2 protein inhibitors and a p21‐activated kinase 1 (PAK1) inhibitor database including 20 organometallic PAK1 protein inhibitors. From the results, good correlations are found between the calculated scores and the experimental inhibitor efficacies with the square of correlation coefficient R² of 0.76–0.88. This suggests a good predictive power of this scoring function. To the best of our knowledge, this is the first high level theory‐based nonfitting scoring function with such a good level of performance. This scoring function is recommended to be used in the final screening of lead structure derivatives. © 2013 Wiley Periodicals, Inc.     

Oxygen-18 surface exchange and diffusion in Li2O-deficient single crystalline lithium niobate

¹⁸O/¹⁶O isotope exchange in combination with SIMS depth profiling was used to investigate oxygen transport in Li₂O-deficient single crystalline LiNbO₃ in the temperature range 983 ≤ T/K ≤ 1188 at 200 mbar oxygen. Within the limit of experimental error and for the investigated range of temperatures no significant differences between transport parallel and transport perpendicular to the c-axis were found. The following temperature dependencies were determined: for oxygen tracer diffusion D = 6.4 × 10⁻³exp[−333 kJ/mol/(RT)] m²/s; and for oxygen surface exchange k = 7.8 × 10²exp[−288 kJ mol⁻¹/(RT)] m/s. The activation enthalpy obtained for tracer diffusion can be interpreted as the enthalpy of migration of extrinsic oxygen vacancies induced by impurities with lower valency on niobium sites.     

Kinetics and mechanism of aqua ligand substitution from cis-diaqua(cis-1,2-diaminocyclohexane)platinum(II)perchlorate by diethyldithiocarbamate anion in aqueous medium

The kinetics of the interaction of diethyldithiocarbamate (Et₂DTC) with [Pt(dach)(H₂O)₂]²⁺ (dach = cis-1,2-diaminocyclohexane) have been studied spectrophotometrically as a function of [Pt(dach)(H₂O)₂ ²⁺], [Et₂DTC] and temperature at a particular pH (4.0). The reaction proceeds via rapid outer sphere association complex formation followed by two slow consecutive steps. The first step involves the transformation of the outer sphere complex into an inner sphere complex containing a Pt–S bond and one aqua ligand, while the second step involves chelation when the second aqua ligand is replaced. The association equilibrium constant K _E and two rate constants k ₁ and k ₂ have been evaluated. Activation parameters for both the steps have been calculated (∆H ₁ ^# = 66.8 ± 3.7 kJ mol⁻¹, ∆S ₁^# = −81 ± 12 JK⁻¹ mol⁻¹ and ∆H ₂^# = 95.1 ± 2.8 kJ mol⁻¹, ∆S ₂^# = −34.4 ± 9.1 JK⁻¹ mol⁻¹). The low enthalpy of activation and negative entropy of activation indicate an associative mode of activation for both the steps.     

Cross-docking study on InhA inhibitors: a combination of Autodock Vina and PM6-DH2 simulations to retrieve bio-active conformations

InhA, the NADH-dependent enoyl-acyl carrier protein reductase from Mycobacterium tuberculosis (Mtb) is the proposed main target of the first-line antituberculosis drug isoniazid (INH). INH activity is dependent on activation by the catalase peroxidase KatG, a Mtb enzyme whose mutations are linked to clinical resistance to INH. Other inhibitors of InhA that do not require any preliminary activation are known. The design of such direct potent inhibitors represents a promising approach to circumvent this resistance mechanism. An ensemble-docking process with four known InhA X-ray crystal structures and employing the Autodock Vina software was performed. Five InhA inhibitors whose bioactive conformations are known were sequentially docked in the substrate cavity of each protein. The efficiency of the docking was assessed and validated by comparing the calculated conformations to the crystallographic structures. For a same inhibitor, the docking results differed from one InhA conformation to another; however, docking poses that matched correctly or were very close to the expected bioactive conformations could be identified. The expected conformations were not systematically well ranked by the Autodock Vina scoring function. A post-docking optimization was carried out on all the docked conformations with the AMMP force field implemented on the VEGAZZ software, followed by a single point calculation of the interaction energy, using the MOPAC PM6-DH2 semi-empirical quantum chemistry method. The conformations were subsequently submitted to a PM6-DH2 optimization in partially flexible cavities. The resulting interaction energies combined with the multiple receptor conformations approach allowed us to retrieve the bioactive conformation of each ligand.     

An atom-in-molecules and electron-localization-function study of the interaction between O2 and VxOy+/VxOy (x = 1, 2, y = 1–5) clusters

 The most stable structures of V _x O _y ⁺/V _x O _y (x=1, 2, y=1–5) clusters and their interaction with O₂ are determined by density functional calculations, the B3LYP functional with the 6-31G* basis set. The nature of the bonding of these clusters and the interaction with O₂ have been studied by topological analysis in the framework of both the atoms-in-molecules theory of Bader and the Becke–Edgecombe electron localization function. Bond critical points are localized by means of the analysis of the electron density gradient field, ∇ρ(r), and the electron localization function gradient field, ∇η(r). The values of the electron density properties, i.e., electron density, ρ(r), Laplacian of the electron density, ∇²ρ(r), and electron localization function, η(r), allow the nature of the bonds to be characterized, and linear correlation is found for the results obtained in both gradient fields. Vanadium-oxygen interactions are characterized as unshared-electron interactions, and linear correlation is observed between the electron density properties and the V–O bond length. In contrast, O₂ units involve typical shared-electron interactions, as for the dioxygen molecule. Four different vanadium–oxygen interactions are found and characterized: a molecular O₂ interaction, a peroxo O₂ ²⁻ interaction, a superoxo O₂ ⁻ interaction and a side-on O₂ ⁻ interaction. Received: 15 October 2001 / Accepted: 30 January 2002 / Published online: 24 June 2002     

Imidazole-containing farnesyltransferase inhibitors: 3D quantitative structure–activity relationships and molecular docking

One of the most promising anticancer and recent antimalarial targets is the heterodimeric zinc-containing protein farnesyltransferase (FT). In this work, we studied a highly diverse series of 192 Abbott-initiated imidazole-containing compounds and their FT inhibitory activities using 3D-QSAR and docking, in order to gain understanding of the interaction of these inhibitors with FT to aid development of a rational strategy for further lead optimization. We report several highly significant and predictive CoMFA and CoMSIA models. The best model, composed of CoMFA steric and electrostatic fields combined with CoMSIA hydrophobic and H-bond acceptor fields, had r ² = 0.878, q ² = 0.630, and r _pred² = 0.614. Docking studies on the statistical outliers revealed that some of them had a different binding mode in the FT active site based on steric bulk and available active site space, explaining why the predicted activities differed from the experimental activities. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Thermochemical properties of MnNb<Subscript>2</Subscript>O<Subscript>6</Subscript>

Homogeneous manganocolumbite (MnNb₂O₆) was synthesized from Nb₂O₅ and MnO oxides. Powder sample was orthorhombic with unit cell parameters: α = 0.5766 nm, b = 1.4439 nm, c = 0.5085 nm and V = 0.4234 nm³. Heat capacity over the temperature range of 313–1253 K was measured in an inert atmosphere with combined thermogravimetry and calorimetry using NETZSCH STA 449C Jupiter thermoanalyzer. Melting point was 1767 ± 3 K, enthalpy of melting was 144 ± 4 kJ mol⁻¹. Experimental heat capacity of MnNb₂O₆ is fitted to polynomial C _pm = 221.46 + 3.03 · 10⁻³ T + −39.79 · 10⁵ T ⁻² + 40.59 · 10⁻⁶ T ².     

CoMFA and CoMSIA studies on a new series of xanthone derivatives against the oral human epidermoid carcinoma (KB) cancer cell line

Abstract  

A new series of xanthone derivatives against the oral human epidermoid carcinoma (KB) cancer cell line is examined to determine the relationship between the structural properties and the biological activity of these compounds—the 3-D quantitative structure–activity relationship (3D-QSAR)—using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). The best CoMFA and CoMSIA models were obtained using the atom-based alignment of 33 compounds, 22 training compounds and 11 tested compounds, and these give desirable statistics; those for the CoMFA standard model were: r _cv² = 0.691, r ² = 0.998, S _press = 0.178, s = 0.014 and F = 1080.765, while CoMSIA combined steric, electrostatic, hydrophobic and hydrogen-bond acceptor fields: r _cv² = 0.600, r ² = 0.988, S _press = 0.206, s = 0.034 and F = 284.433. The 3D-QSAR models calculated satisfactory test set activities. The 3D-QSAR contour plots correlated strongly with the experimental data for the binding topology. For this reason, these results would be beneficial for predicting affinities with the compounds of interest, and they are advantageous for guiding the design and synthesis of new and more effective anticancer agents.     

Thermal decomposition and mass spectra of mixed ligand copper(II) complexes of 1,10-phenanthroline and coumarin derivatives

Four copper(II) new mix ligand complexes of the coumarin derivative (A¹ = 7-hydroxy-10,11-dihydroindeno[5,4-c]chromen-6(9H)-one, A² = 2-bromo-7-hydroxy-10,11- dihydroindeno[5,4-c]chromen-6(9H)-one, A³ = 7-hydroxy-4-methoxy-10,11-dihydroindeno[5,4-c]chromen-6(9H)-one, and A⁴ = 5-hydroxy-8,9-dihydrobenzo[f]indeno[5,4-c]chromen-4(7H)-one) and 1,10-Phenanthroline have been synthesized. The structural interpretations were confirmed from elemental analyses, magnetic susceptibility and FAB mass spectral, as well as from IR spectral studies. From the analytical, spectroscopic, and thermal data, the stoichiometry of the mentioned complexes was found to be 1:1:1 (coumarin ligand:copper metal:1,10-Phenanthroline). The thermal stabilities of these complexes were studied by thermogravimetric (TG/DTG) and the decomposition steps of these four complexes are investigated. Kinetic parameters such as order of reaction (n) and the energy of activation (E _a) were calculated using Freeman–Carroll method. The pre-exponential factor (A), the activation entropy (S*), the activation enthalpy (H*), and the free energy of activation (G*) were calculated using Horowitz–Matzger equations. Based on the E _a values, the thermal stabilities of complexes in the decreasing order are Cu(II)-2 > Cu(II)-3 > Cu(II)-4 > Cu(II)-1.     

The performance of ANI-ML potentials for ligand-n(H2O) interaction energies and estimation of hydration free energies from end-point MD simulations

Here, we investigate the performance of “Accurate NeurAl networK engINe for Molecular Energies” (ANI), trained on small organic compounds, on bulk systems including non-covalent interactions and applicability to estimate solvation (hydration) free energies using the interaction between the ligand and explicit solvent (water) from single-step MD simulations. The method is adopted from ANI using the Atomic Simulation Environment (ASE) and predicts the non-covalent interaction energies at the accuracy of wb97x/6-31G(d) level by a simple linear scaling for the conformations sampled by molecular dynamics (MD) simulations of ligand-n(H₂O) systems. For the first time, we test ANI potentials' abilities to reproduce solvation free energies using linear interaction energy (LIE) formulism by modifying the original LIE equation. Our results on ~250 different complexes show that the method can be accurate and have a correlation of R² = 0.88–0.89 (MAE <1.0 kcal/mol) to the experimental solvation free energies, outperforming current end-state methods. Moreover, it is competitive to other conventional free energy methods such as FEP and BAR with 15-20 × fold reduced computational cost.     

QSAR analysis of 1,4-dihydro-4-oxo-1-(2-thiazolyl)-1,8-naphthyridines exhibiting anticancer activity by optimal SMILES-based descriptors

A predictive model of the anticarcinogenic activity of a 1,4-dihydro-4-oxo-1-(2-thiazolyl)-1,8-naphthyridines series has been built, with statistical quality: n = 75, r ² = 0.7688, s = 0.48, F = 243 (training set); n = 25, r ² = 0.8025, s = 0,49, F = 93 (test set). The robustness of this model has been tested in three random splits into training set and test set. Correlation weights (the analogue of the contributions of substituents) of molecular attributes expressed by symbols in the simplified molecular input line entry system (SMILES) notation are able to serve as informative indicators in the search for new anticancer agents.     

Benchmark calculations with correlated molecular wave functions XII. Core correlation effects on the homonuclear diatomic molecules B2-F2

Using systematic sequences of the newly developed correlation consistent core-valence basis sets from cc-pCVDZ through cc-pCV6Z, the spectroscopic constants of the homonuclear diatomic molecules containing first row atoms, B–F, are calculated both with and without inclusion of 1s correlation. Internally contracted multireference configuration interaction (IC-MRCI) and singles and doubles coupled cluster (CCSD) theory with a perturbational estimate of connected triple excitations, CCSD(T), have been investigated. By exploiting the convergence of the correlation consistent basis sets, complete basis set (CBS) limits have been estimated for total energies, dissociation energies, equilibrium geometries, and harmonic frequencies. Based on the estimated CBS limits the effects of 1s correlation on D _e (kcal/mol), r _e (?), and ω _e (cm⁻¹) are: +1.1, −0.0070, +10 for B₂; +1.5, −0.0040, +13 for C₂; +0.9, −0.0020, +9 for N₂; +0.3, −0.0020, +6 for O₂; and −0.1, −0.0015, +1 for F₂. Received: 20 January 1997 / Accepted: 6 May 1997     

Heat capacity, enthalpy and entropy of strontium niobate Sr2Nb2O7 and calcium niobate Ca2Nb2O7

The heat capacity and the enthalpy increments of strontium niobate Sr₂Nb₂O₇ and calcium niobate Ca₂Nb₂O₇ were measured by the relaxation time method (2–300 K), DSC (260–360 K) and drop calorimetry (720–1370 K). Temperature dependencies of the molar heat capacity in the form C_pm = 248.0 + 0.04350T − 3.948 × 10⁶/T² J K⁻¹ mol⁻¹ for Sr₂Nb₂O₇ and C_pm = 257.2 + 0.03621T − 4.434 × 10⁶/T² J K⁻¹ mol⁻¹ for Ca₂Nb₂O₇ were derived by the least-square method from the experimental data. The molar entropies at 298.15 K, S_m°(298.15 K) = 238.5 ± 1.3 J K⁻¹ mol⁻¹ for Sr₂Nb₂O₇ and S_m°(298.15 K) = 212.4 ± 1.2 J K⁻¹ mol⁻¹ for Ca₂Nb₂O₇, were evaluated from the low-temperature heat capacity measurements.     

Influence of the water molecules (n?=?1–6) on the interaction between Li+, Na+, K+ cations and indole molecule as tryptophan amino acid residue

Influence of the addition of water molecules (n = 1–6) on the interaction energy between Li⁺, Na⁺, K⁺ cations and indole molecule as tryptophan amino acid residue is considered at MP2(FULL)/6-311++G(d,p)//B3LYP/6-311++G(d,p) levels of theory. The calculations suggest that the size of cation and the number of water molecules are two important factors that affect the interaction energy between the hydrated metal cation and indole molecule. The strength of cation–π interactions get substantially reduced when the metal ion is solvated or the size of metal cation increases. Quantum theory of atoms in molecules analysis of cation–π interaction indicates that there is a correlation between the electron density (ρ(r)) in the cage critical points generated upon complexation and the distance between metal cation and centroid of phenyl ring in indole molecule.     

Binding of benzene-1,2,3,4,5,6-hexacarboxylate by polyammonium cations

The interaction between mellitate (benzene-1,2,3,4,5,6-hexacarboxylate) and diethylenetriamine and spermidine was studied by potentiometric and calorimetric techniques in aqueous solution at t = 25°C, moreover by diffractometric technique in the solid state. Thermodynamic parameters of several A_pLH_q species with p = 1, q = 2…5, for both systems, were calculated; in addition the following species were found: A₂LH₆, for A = dien; ALH₆, for A = spd. The stabilities of these species are quite high; for example formation constants regarding the ALH₃³⁻ species are: logK⁰ = 5.7 for A = dien and logK⁰ = 10.1 for A = spd. Thermodynamic parameters are generally function of charges involved in the formation reaction and some linear relationships were found. The speciation profiles show that the formation percentages, for the mononuclear species in particular, are high, in a wide pH range. The sequestering ability of mlt towards polyamines was analysed, also considering the already published data regarding ethylenediamine. By considering the formation constants at various ionic strength and the enthalpy values of triamine–mellitate species, it was possible to evaluate the dependence of sequestering ability on ionic strength, temperature and pH. Solid state investigation of two cocrystals, made by mellitate trianion and triammonium cations, provides information on the formation of supramolecular anionic layers. Comparison with the stability of mellitate–alkaline earth metals species was made.