Effectiveness and safety of secukinumab in 608 patients with psoriatic arthritis in real life: a 24-month prospective, multicentre study.

OBJECTIVES: To evaluate in a multicentric Italian cohort of patients with psoriatic arthritis (PsA) on secukinumab followed for 24 months: (1) the long-term effectiveness and safety of secukinumab, (2) the drug retention rate and minimal disease activity (MDA), (3) differences in the outcomes according to the biological treatment line: biologic-naïve patients (group A) versus multifailure (group B) patients. METHODS: Consecutive patients with PsA receiving secukinumab were evaluated prospectively. Disease characteristics, previous/ongoing treatments, comorbidities and follow-up duration were collected. Disease activity/functional/clinimetric scores and biochemical values were recorded at baseline (T0), 6(T6), 12(T12) and 24(T24) months. Effectiveness was evaluated overtime with descriptive statistics; multivariate Cox and logistic regression models were used to evaluate predictors of drug-discontinuation and MDA at T6. Infections and adverse events were recorded. RESULTS: 608 patients (41.28% men; mean (SD) age 52.78 (11.33)) were enrolled; secukinumab was prescribed as first-line biological treatment in 227 (37.34%) patients, as second (or more)-line biological treatment in 381 (62.66%). Effectiveness of secukinumab was shown with an improvement in several outcomes, such as Ankylosing Spondylitis Disease Activity Score (T0=3.26 (0.88) vs T24=1.60 (0.69) ;p=0.02) and Disease Activity Index for Psoriatic Arthritis (T0=25.29 (11.14) vs T24=7.69 (4.51); p<0.01). At T24, group A showed lower Psoriasis Area Severity Index (p=0.04), erythrocyte sedimentation rate and C reactive protein (p=0.03 ;p=0.05) and joint count (p=0.03) compared with group B. At T24, MDA was achieved in 75.71% of group A and 70.37% of group B. Treatment was discontinued in 123 (20.23%) patients, mainly due to primary/secondary loss of effectiveness, and in 22 due to adverse events. Retention rate at T24 was 71% in the whole population, with some difference depending on secukinumab dosage (p=0.004) and gender (p=0.05). CONCLUSIONS: In a real-life clinical setting, secukimumab proved safe and effective in all PsA domains, with notable drug retention rate.

The interplay between dynamic heterogeneities and structure of bulk liquid water: A molecular dynamics simulation study.

In order to study the interplay between dynamical heterogeneities and structural properties of bulk liquid water in the temperature range 130-350 K, thus including the supercooled regime, we use the explicit trend of the distribution functions of some molecular properties, namely, the rotational relaxation constants, the atomic mean-square displacements, the relaxation of the cross correlation functions between the linear and squared displacements of H and O atoms of each molecule, the tetrahedral order parameter q and, finally, the number of nearest neighbors (NNs) and of hydrogen bonds (HBs) per molecule. Two different potentials are considered: TIP4P-Ew and a model developed in this laboratory for the study of nanoconfined water. The results are similar for the dynamical properties, but are markedly different for the structural characteristics. In particular, for temperatures higher than that of the dynamic crossover between "fragile" (at higher temperatures) and "strong" (at lower temperatures) liquid behaviors detected around 207 K, the rotational relaxation of supercooled water appears to be remarkably homogeneous. However, the structural parameters (number of NNs and of HBs, as well as q) do not show homogeneous distributions, and these distributions are different for the two water models. Another dynamic crossover between "fragile" (at lower temperatures) and "strong" (at higher temperatures) liquid behaviors, corresponding to the one found experimentally at T(∗) ∼ 315 ± 5 K, was spotted at T(∗) ∼ 283 K and T(∗) ∼ 276 K for the TIP4P-Ew and the model developed in this laboratory, respectively. It was detected from the trend of Arrhenius plots of dynamic quantities and from the onset of a further heterogeneity in the rotational relaxation. To our best knowledge, it is the first time that this dynamical crossover is detected in computer simulations of bulk water. On the basis of the simulation results, the possible mechanisms of the two crossovers at molecular level are discussed.

Hydrogen Bonding and Related Properties in Liquid Water: A Car-Parrinello Molecular Dynamics Simulation Study.

The local hydrogen-bonding structure and dynamics of liquid water have been investigated using the Car-Parrinello molecular dynamics simulation technique. The radial distribution functions and coordination numbers around water molecules have been found to be strongly dependent on the number of hydrogen bonds formed by each molecule, revealing also the existence of local structural heterogeneities in the structure of the liquid. The results obtained have also revealed the strong effect of the local hydrogen-bonding network on the local tetrahedral structure and entropy. The investigation of the dynamics of the local hydrogen-bonding network in liquid water has shown that this network is very labile, and the hydrogen bonds break and reform very rapidly. Nevertheless, it has been found that the hydrogen-bonding states associated with the formation of four hydrogen bonds by a water molecule exhibit the largest survival probability and corresponding lifetime. The reorientational motions of water molecules have also been found to be strongly dependent on their initial hydrogen-bonding state. Finally, the dependence of the librational and vibrational modes of water molecules on the local hydrogen-bonding network has been carefully examined, revealing a significant effect upon the libration and bond-stretching peak frequencies. The calculated low frequency peaks come in agreement with previously reported interpretations of the experimental low-frequency Raman spectrum of liquid water.

Molecular epizootiology and diagnosis of porcine babesiosis in Sardinia, Italy.

The recent characterization of the 18S ribosomal RNA (rRNA) of a pathogenic Babesia species in a domestic sow paved the way for establishing diagnostic and epidemiological tools for porcine babesiosis. Here, we developed the first specific Babesia sp. Suis PCR, and we applied this test to a panel of samples collected from animals living in a typical Mediterranean environment (Sardinia, Italy), including domestic pigs, wild boars, and ticks. In domestic pigs, PCR coupled with sequencing revealed an estimated Babesia infection frequency of 26.2% and the presence of distinct 18S sequence types. The different distribution of sequence types in symptomatic and asymptomatic subjects might suggest the existence of phylogenetically closely related strains with variable pathogenicity in pigs. Moreover, molecular identification of tick species indicated Rhipicephalus sanguineus and Rhipicephalus bursa as candidate vectors potentially involved in the transmission of this pathogen. Collectively, the data reveal the suitability of 18S rRNA PCR/sequencing for molecular diagnosis of porcine babesiosis and for large-scale investigations on the presence and geographical distribution of Babesia sp. Suis genetic variants.

Shortcomings of the standard Lennard-Jones dispersion term in water models, studied with force matching.

In this work, ab initio parametrization of water force field is used to get insights into the functional form of empirical potentials to properly model the physics underlying dispersion interactions. We exploited the force matching algorithm to fit the interaction forces obtained with dispersion corrected density functional theory based molecular dynamics simulations. We found that the standard Lennard-Jones interaction potentials poorly reproduce the attractive character of dispersion forces. This drawback can be resolved by accounting for the distinctive short range behavior of dispersion interactions, multiplying the r(-6) term by a damping function. We propose two novel parametrizations of the force field using different damping functions. Structural and dynamical properties of the new models are computed and compared with the ones obtained from the non-damped force field, showing an improved agreement with reference first principle calculations.

Boundary based on exchange symmetry theory for multilevel simulations. II. Multiple time scale approach.

The QM/MM BEST method presented in the first article of this series [M. Shiga and M. Masia, J. Chem. Phys. 139, 044120 (2013)] has been applied herein to simulate the whole series of hydrated alkali ions. In this article we show how to overcome the sampling bottleneck for QM/MM simulations by using our method with multiple time scale algorithm (MTS-BEST). We extend the use of MTS-BEST to ab initio QM/MM path integral molecular dynamics simulations, thus demonstrating that one could obtain a complete quantum description of the primary subsystem based on first principles. We highlight that the MTS-BEST approach could be generally applied to hybrid multiscale simulation of diffusive systems, thus extending its relevance to a broad class of simulation techniques beyond QM/MM. We show that it is important to account for electron correlation to better reproduce the hydration structural properties such as the ion-water radial distribution functions, and the anisotropic angular distributions around the ion.

Boundary based on exchange symmetry theory for multilevel simulations. I. Basic theory.

In this paper, we lay the foundations for a new method that allows multilevel simulations of a diffusive system, i.e., a system where a flux of particles through the boundaries might disrupt the primary region. The method is based on the use of flexible restraints that maintain the separation between inner and outer particles. It is shown that, by introducing a bias potential that accounts for the exchange symmetry of the system, the correct statistical distribution is preserved. Using a toy model consisting of non-interacting particles in an asymmetric potential well, we prove that the method is formally exact, and that it could be simplified by considering only up to a couple of particle exchanges without a loss of accuracy. A real-world test is then made by considering a hybrid MM(∗)/MM calculation of cesium ion in water. In this case, the single exchange approximation is sound enough that the results superimpose to the exact solutions. Potential applications of this method to many different hybrid QM/MM systems are discussed, as well as its limitations and strengths in comparison to existing approaches.

Influence of site-dependent pigment-protein interactions on excitation energy transfer in photosynthetic light harvesting.

A site-dependent spectral density system-bath model of the Fenna-Matthews-Olsen (FMO) pigment-protein complex is developed using results from ground-state molecular mechanics simulations together with a partial charge difference model for how the long-range contributions to the chromophore excitation energies fluctuate with environmental configuration. A discussion of how best to consistently process the chromophore excitation energy fluctuation correlation functions calculated in these classical simulations to obtain reliable site-dependent spectral densities is presented. The calculations reveal that chromophores that are close to the protein-water interface can experience strongly dissipative environmental interactions characterized by reorganization energies that can be as much as 2-3 times those of chromophores that are buried deep in the hydrophobic protein scaffolding. Using a linearized density matrix quantum propagation method, we demonstrate that the inhomogeneous system-bath model obtained from our site-dependent spectral density calculations gives results consistent with experimental dissipation and dephasing rates. Moreover, we show that this model can simultaneously enhance the energy-transfer rate and extend the decoherence time. Finally, we explore the influence of initially exciting different chromophores and mutating local environments on energy transfer through the network. These studies suggest that different pathways, selected by varying initial photoexcitation, can exhibit significantly different relaxation times depending on whether the energy-transfer path involves chromophores at the protein-solvent interface or if all chromophores in the pathway are buried in the protein.

Estimating chloride polarizability in a water solution.

The evaluation of the hydrated chloride anion polarizability is hereby addressed by using density functional theory based calculations in the condensed phase. In this study, the quantum probability associated with maximally localized Wannier functions is included to account for the spatial extent of the electronic density. It is shown that the anion polarizability is not appreciably influenced upon solvation. The method could be applied to systems where the quantum state is separable; issues related to system size dependence and about its applicability to other systems are discussed.

Characterization of the Methane-Graphene Hydrophobic Interaction in Aqueous Solution from Ab Initio Simulations.

In this article, the interaction between a methane molecule and a graphene plane in liquid water has been characterized employing DFT-based free energy Molecular Dynamics calculations. This system represents a good model to understand the generic interaction between a small hydrophobic solute (methane molecule) and an extense hydrophobic surface (graphene plane). The structural and dynamical properties of graphene and methane hydration water are analyzed and found to be closely related to the main features of the potential of mean force. The results could be used in coarse-grained models to take into account the effect of the hydrophobic interaction in realistic systems relevant to experiment.

Unraveling the role of water in the stereoselective step of aqueous proline-catalyzed aldol reactions.

A multiscale computational study was performed with the aim of tracing the source of stereoselectivity and disclosing the role of water in the stereoselective step of propionaldehyde aldol self-condensation catalyzed by proline amide in water, a reaction that serves as a model for aqueous organocatalytic aldol condensations. Solvent mixing and hydration behavior were assessed by classical molecular dynamics simulations, which show that the reaction between propanal and the corresponding enamine takes place in a fully hydrated environment. First-principles molecular dynamics simulations were used to study the free-energy profile of four possible reaction paths, each of which yields a different stereoisomer, and high-level static first-principles calculations were employed to characterize the transition states for microsolvated species. The first solvation shell of the oxygen atom of the electrophilic aldehyde at the transition states contains two water molecules, each of which donates one hydrogen bond to the nascent alkoxide and thereby largely stabilizes its excess electron density. The stereoselectivity originates in an extra hydrogen bond donated by the amido group of proline amide in two reaction paths.

Fitting properties from density functional theory based molecular dynamics simulations to parameterize a rigid water force field.

In the quest towards coarse-grained potentials and new water models, we present an extension of the force matching technique to parameterize an all-atom force field for rigid water. The methodology presented here allows to improve the matching procedure by first optimizing the weighting exponents present in the objective function. A new gauge for unambiguously evaluating the quality of the fit has been introduced; it is based on the root mean square difference of the distributions of target properties between reference data and fitted potentials. Four rigid water models have been parameterized; the matching procedure has been used to assess the role of the ghost atom in TIP4P-like models and of electrostatic damping. In the former case, burying the negative charge inside the molecule allows to fit better the torques. In the latter, since short-range interactions are damped, a better fit of the forces is obtained. Overall, the best performing model is the one with a ghost atom and with electrostatic damping. The approach shown in this paper is of general validity and could be applied to any matching algorithm and to any level of coarse graining, also for non-rigid molecules.

Seroepidemiologic survey for Chlamydia suis in wild boar (Sus scrofa) populations in Italy.

We used serology to estimate the prevalence of exposure to chlamydiae in Italian populations of wild boars (Sus scrofa). Sera from 173 hunter-killed wild boars harvested during the 2006-2009 hunting seasons in three Italian regions were tested for antibodies to Chlamydia suis, Chlamydophila pecorum, Chlamydophila abortus, and Chlamydophila psittaci by the microimmunofluorescence test. Antibody titers to chlamydiae ≥ 1:32 were detected in 110 of the 173 samples tested (63.6%). Specific reactivity could be assessed only in 44 sera with antibody titers to C. suis that were two- to threefold higher than antibody titers against the other chlamydial species; the other 66 sera had similar reactivity against all the chlamydia species tested. Antibody to C. suis was detected in sera from wild boar populations with rare or no known contact with domestic pigs. These results suggest that the wild boar could be a chlamydia reservoir and may acquire chlamydiae independent of contacts with the domestic pig.

Constructing simple yet accurate potentials for describing the solvation of HCl/water clusters in bulk helium and nanodroplets.

The infrared spectroscopy of molecules, complexes, and molecular aggregates dissolved in superfluid helium clusters, commonly called HElium NanoDroplet Isolation (HENDI) spectroscopy, is an established, powerful experimental technique for extracting high resolution ro-vibrational spectra at ultra-low temperatures. Realistic quantum simulations of such systems, in particular in cases where the solute is undergoing a chemical reaction, require accurate solute-helium potentials which are also simple enough to be efficiently evaluated over the vast number of steps required in typical Monte Carlo or molecular dynamics sampling. This precludes using global potential energy surfaces as often parameterized for small complexes in the realm of high-resolution spectroscopic investigations that, in view of the computational effort imposed, are focused on the intermolecular interaction of rigid molecules with helium. Simple Lennard-Jones-like pair potentials, on the other hand, fall short in providing the required flexibility and accuracy in order to account for chemical reactions of the solute molecule. Here, a general scheme of constructing sufficiently accurate site-site potentials for use in typical quantum simulations is presented. This scheme employs atom-based grids, accounts for local and global minima, and is applied to the special case of a HCl(H(2)O)(4) cluster solvated by helium. As a first step, accurate interaction energies of a helium atom with a set of representative configurations sampled from a trajectory following the dissociation of the HCl(H(2)O)(4) cluster were computed using an efficient combination of density functional theory and symmetry-adapted perturbation theory, i.e. the DFT-SAPT approach. For each of the sampled cluster configurations, a helium atom was placed at several hundred positions distributed in space, leading to an overall number of about 400,000 such quantum chemical calculations. The resulting total interaction energies, decomposed into several energetic contributions, served to fit a site-site potential, where the sites are located at the atomic positions and, additionally, pseudo-sites are distributed along the lines joining pairs of atom sites within the molecular cluster. This approach ensures that this solute-helium potential is able to describe both undissociated molecular and dissociated (zwitter-) ionic configurations, as well as the interconnecting reaction pathway without re-adjusting partial charges or other parameters depending on the particular configuration. Test calculations of the larger HCl(H(2)O)(5) cluster interacting with helium demonstrate the transferability of the derived site-site potential. This specific potential can be readily used in quantum simulations of such HCl/water clusters in bulk helium or helium nanodroplets, whereas the underlying construction procedure can be generalized to other molecular solutes in other atomic solvents such as those encountered in rare gas matrix isolation spectroscopy.

A molecular dynamics study and molecular level explanation of pressure dependence of ionic conductivity of potassium chloride in water.

Experimental ionic conductivity of different alkali ions in water shows markedly different dependences on pressure. Existing theories such as that of Hubbard-Onsager are unable to explain these dependences on pressure of the ionic conductivity for all ions. We report molecular dynamics investigation of potassium chloride solution at low dilution in water at several pressures between 1 bar and 2 kbar. Two different potential models have been employed. One of the models successfully reproduces the experimentally observed trend in ionic conductivity of K(+) ions in water over the 0.001-2 kbar range. We also propose a theoretical explanation, albeit at a qualitative level, to account for the dependence of ionic conductivity on pressure in terms of the previously studied Levitation Effect. It also provides a microscopic picture in terms of the pore network in liquid water.

Aggregation-induced chemical reactions: acid dissociation in growing water clusters.

Understanding chemical reactivity at ultracold conditions, thus enabling molecular syntheses via interstellar and atmospheric processes, is a key issue in cryochemistry. In particular, acid dissociation and proton transfer reactions are ubiquitous in aqueous microsolvation environments. Here, the full dissociation of a HCl molecule upon stepwise solvation by a small number of water molecules at low temperatures, as relevant to helium nanodroplet isolation (HENDI) spectroscopy, is analyzed in mechanistic detail. It is found that upon successive aggregation of HCl with H(2)O molecules, a series of cyclic heteromolecular structures, up to and including HCl(H(2)O)(3), are initially obtained before a precursor state for dissociation, HCl(H(2)O)(3)···H(2)O, is observed upon addition of a fourth water molecule. The latter partially aggregated structure can be viewed as an "activated species", which readily leads to dissociation of HCl and to the formation of a solvent-shared ion pair, H(3)O(+)(H(2)O)(3)Cl(-). Overall, the process is mostly downhill in potential energy, and, in addition, small remaining barriers are overcome by using kinetic energy released as a result of forming hydrogen bonds due to aggregation. The associated barrier is not ruled by thermal equilibrium but is generated by athermal non-equilibrium dynamics. These "aggregation-induced chemical reactions" are expected to be of broad relevance to chemistry at ultralow temperature much beyond HENDI spectroscopy.

Estimation of Partial Charges in Small Zeolite Imidazolate Frameworks from Density Functional Theory Calculations.

Zeolitic Imidazolate Frameworks (ZIFs) are the new frontier in the field of metal-organic materials. They incorporate the confining properties of the more traditional aluminosilicate zeolites together with the catalytic activity provided by transition metal ions and organic links. Computation of atomic point charges for these hybrid materials is important in the field of molecular simulations for substantial prediction of experimental results. However, due to the structural complexity of advanced materials in general, studies involving derivation of point charges for these materials are truly scarce. In this article, we have derived the atomic point charges of ZIF-8 through fitting of the quantum electrostatic potential obtained systematically from density functional theory (DFT) calculations both on finite clusters of increasing size and on the periodic system. For the periodic system, fluctuations on the atomic charges have been studied through ab initio molecular dynamics simulations. Using the latter approach, we have extended the study to ZIF-2 and ZIF-3, where it has been found that charge fluctuations are, as well as for ZIF-8, very narrow, therefore justifying the use of the point charge approximation for these materials.

The polarizable point dipoles method with electrostatic damping: implementation on a model system.

Recently, the use of polarizable force fields in Molecular Dynamics simulations has been gaining importance, since they allow a better description of heterogeneous systems compared to simple point charges force fields. Among the various techniques developed in the last years the one based on polarizable point dipoles represents one of the most used. In this paper, we review the basic technical issues of the method, illustrating the way to implement intramolecular and intermolecular damping of the electrostatic interactions, either with and without the Ewald summation method. We also show how to reduce the computational overhead for evaluating the dipoles, introducing to the state-of-the-art methods: the extended Lagrangian method and the always stable predictor corrector method. Finally we discuss the importance of screening the electrostatic interactions at short range, defending this technique against simpler approximations usually made. We compare results of density functional theory and classical force field-based Molecular Dynamics simulations of chloride in water.