Search

We designed a series of photochromic derivatives by employing density functional method (CAM-B3LYP/6-31G*). These compounds are based on DAE (diarylethenes), both sides of which are bonded with ben...

International audience; We propose a family of photonic materials based on nickel bis(dithiolene) [NiBDT] and benzene (B). Linear and planar oligomers of 1D and 2D polymers, together with several rich π-electron linkers (e.g. C14H8, C24H8, and C4O2H4), have been employed in order to demonstrate the superior performance of the proposed materials. A key property for the design of efficient photonic materials is the second hyperpolarizability. We have, thus, computed it together with several other properties, such as the dipole moment, polarizability, first excitation energy, etc. We have also used two indices to estimate the degree of the diradical character of the considered derivatives. The calculations have been performed by employing density functional theory. Considerable care has been taken to validate the computational procedure we have used. The main findings of the present work are as follows: (a) the 1D and 2D coordination polymers based on nickel bis(dithiolene) and benzene and in particular the linear ones, (B-NiBDT)n, are very likely to be efficient photonic materials, since they have gigantic second hyperpolarizability. (b) The second hyperpolarizability greatly depends on the organic linker with which NiBDT is fused and on the structure; for example, the linear oligomers have much higher second hyperpolarizability than the planar ones. The present work together with a recent article (A. Avramopoulos et al., J. Phys. Chem. C, 2016, 120, 9419-9435) demonstrates a mechanism for designing efficient photonic materials.

Protein misfolding and aggregation are common pathological features of several human diseases, including Alzheimer’s disease and type 2 diabetes. Here, we report an integrated and generalizable bacterial system for the facile discovery of chemical rescuers of disease-associated protein misfolding. In this system, large combinatorial libraries of macrocyclic molecules are biosynthesized in Escherichia coli cells and simultaneously screened for their ability to rescue pathogenic protein misfolding and aggregation using a flow cytometric assay. We demonstrate the effectiveness of this approach by identifying drug-like, head-to-tail cyclic peptides that modulate the aggregation of the Alzheimer’s disease-associated amyloid β peptide. Biochemical, biophysical and biological assays using isolated amyloid β peptide, primary neurons and various established Alzheimer’s disease nematode models showed that the selected macrocycles potently inhibit the formation of neurotoxic amyloid β peptide aggregates. We also applied the system to the identification of misfolding rescuers of mutant Cu/Zn superoxide dismutase—an enzyme linked with inherited forms of amyotrophic lateral sclerosis. Overall, the system enables the identification of molecules with therapeutic potential for rescuing the misfolding of disease-associated polypeptides. A fluorescence-based assay is used to screen cyclic peptides for their activity in preventing protein misfolding, an event that can generate pathogenic aggregates that lead to diseases such as Alzheimer’s disease or amyotrophic lateral sclerosis..

DNA is the building block of life, as it carries the biological information controlling development, function and reproduction of all organisms. However, its central role in storing and transferring genetic information can be severely hindered by molecules with structure altering abilities. Fullerenes are nanoparticles that find a broad spectrum of uses, but their toxicological effects on living organisms upon exposure remain unclear. The present study examines the interactions of a diverse array of fullerenes with DNA, by means of Molecular Dynamics and MM–PBSA methodologies, with special focus on structural deformations that may hint toxicity implications. Our results show that pristine and hydroxylated fullerenes have no unwinding effects upon DNA structure, with the latter displaying binding preference to the DNA major groove, achieved by both direct formation of hydrogen bonds and water molecule mediation. Fluorinated derivatives are capable of penetrating DNA structure, forming intercalative complexes with high binding affinities.

Water-in-oil microemulsions with biocompatible components were formulated to be used as carriers of natural antioxidants, such as hydroxytyrosol (HT) and gallic acid (GA). The system was composed of a mixture of natural surfactants, lecithin and monoglycerides, medium chain triglycerides, and aqueous phase. A dual approach was undertaken to study the structure and dynamics of these complicated systems. First, experimental data were collected by using adequate techniques, such as dynamic light scattering (DLS) and electron paramagnetic resonance (EPR) spectroscopy. Following this, a coarse-grained molecular dynamics (CGMD) study based on the experimental composition using the MARTINI force field was conducted. The simulations revealed the spontaneous formation of reverse micelles (RMs) starting from completely random initial conformations, underlying their enhanced thermodynamic stability. The location of the bioactive molecules, as well as the structure of the RM, were in accordance with the experimental findings. Furthermore, GA molecules were found to be located inside the water core, in contrast to the HT ones, which seem to lie at the surfactant interfacial layer. The difference in the antioxidants' molecular location was only revealed in detail from the computational analysis and explains the RM's swelling observed by GA in DLS measurements.

The synthesis of O‐doped polyaromatic hydro‐ carbons in which two polycyclic aromatic hydrocarbon sub units are bridged through one or two O atoms has been achieved. This includes high‐yield ring‐closure key steps that, depending on the reaction conditions, result in the formation of furanyl or pyranopyranyl linkages through intramolecular C−O bond formation. Comprehensive photophysical measurements in solution showed that these compounds have exceptionally high emission yields and tunable absorption properties throughout the UV/Vis spectral region. Electrochemical investigations showed that in all cases O annulation increases the electron‐donor capabilities by raising the HOMO energy level, whereas the LUMO energy level is less affected. Moreover, third‐order nonlinear optical (NLO) measurements on solutions or thin films containing the dyes showed very good values of the second hyperpolarizability. Importantly, poly(methyl methacrylate) films containing the pyranopyranyl derivatives exhibited weak linear absorption and NLO absorption compared to the nonlinearity and NLO refraction, respectively, and thus revealed them to be exceptional organic materials for photonic devices.

A combination of computational techniques and inhibition assay experiments was employed to identify hit compounds from commercial libraries with enhanced inhibitory potency against HIV type 1 aspartic protease (HIV PR). Extensive virtual screening with the aid of reliable pharmacophore models yielded five candidate protease inhibitors. Subsequent molecular dynamics and molecular mechanics Poisson-Boltzmann surface area free-energy calculations for the five ligand-HIV PR complexes suggested a high stability of the systems through hydrogen-bond interactions between the ligands and the protease's flaps (Ile50/50'), as well as interactions with residues of the active site (Asp25/25'/29/29'/30/30'). Binding-energy calculations for the three most promising compounds yielded values between -5 and -10 kcal mol(-1) and suggested that van der Waals interactions contribute most favorably to the total energy. The predicted binding-energy values were verified by in vitro inhibition assays, which showed promising results in the high nanomolar range. These results provide structural considerations that may guide further hit-to-lead optimization toward improved anti-HIV drugs.

International audience; The main goal of this study was the design/recognition of a series of derivatives with exceptionally large hyperpolarizabilities, the understanding of the mechanism through which these properties are derived, and the generalization of the resulting findings. Thus, we have studied the structure, a series of properties involving the excitation energies and the diradical character, but mainly the (hyper)polarizabilities of some oligomers of radiaannulene-tetrathiafulvalene (RA-TTF), radiaannulene-bis(ethylene-1,2-dithiolato)nickel (RA-NiBDT), and their lithiated analogues. The employed methodology involves MP2 and DFT techniques, approaches for the computation of static and frequency-dependent properties, and techniques for the calculation of electronic and vibrational contributions. The polarizability has been partitioned be employing the fractional occupational Hirshfeld iterative method. Indices for the calculation of the diradical character of the NiBDT oligomers have been employed. We have found that (i) oligomerization increases γzzzz (second hyperpolarizability), (ii) substitution of TTF with NiBDT leads to a very large increase of γzzzz, and (iii) lithiation leads to extremely large nonlinearities. The importance of NiBDT and lithium as building blocks for the production of NLO materials is highlighted.

Inhibition of group IIA secreted phospholipase A2 (GIIA sPLA2) has been an important objective for medicinal chemists. We have previously shown that inhibitors incorporating the 2-oxoamide functionality may inhibit human and mouse GIIA sPLA2s. Herein, the development of new potent inhibitors by molecular docking calculations using the structure of the known inhibitor 7 as scaffold, are described. Synthesis and biological evaluation of the new compounds revealed that the long chain 2-oxoamide based on (S)-valine GK241 led to improved activity (IC50 = 143 nM and 68 nM against human and mouse GIIA sPLA2, respectively). In addition, molecular dynamics simulations were employed to shed light on GK241 potent and selective inhibitory activity.

International audience; A systematic analysis of the molecular structure, energetics, electronic (hyper)​polarizabilities and their interaction-​induced counterparts of C60 with a series of molecular graphene (MG) models, CmHn, where m = 24, 84, 114, 222, 366, 546 and n = 12, 24, 30, 42, 54, 66, was performed. All the reported data were computed by employing density functional theory and a series of basis sets. The main goal of the study is to investigate how alteration of the size of the MG model affects the strength of the interaction, charge rearrangement, and polarization and interaction-​induced polarization of the complex, C60-​MG. A Hirshfeld-​based scheme has been employed in order to provide information on the intrinsic polarizability density representations of the reported complexes. It was found that the interaction energy increases approaching a limit of -​26.98 kcal​/mol for m = 366 and 546; the polarizability and second hyperpolarizability increase with increasing the size of MG. An opposite trend was observed for the dipole moment. Interestingly, the variation of the first hyperpolarizability is relatively small with m. Since polarizability is a key factor for the stability of molecular graphene with nucleobases (NB)​, a study of the magnitude of the interaction-​induced polarizability of C84H24-​NB complexes is also reported, aiming to reveal changes of its magnitude with the type of NB. The binding strength of C84H24-​NB complexes is also computed and found to be in agreement with available theoretical and experimental data. The interaction involved in C60 B12N12H24-​NB complexes has also been considered, featuring the effect of contamination on the binding strength between MG and NBs.

We investigate the binding mechanism in renin complexes, involving three drugs (remikiren, zankiren and enalkiren) and one lead compound, which was selected after screening the ZINC database. For this purpose, we used ab initio methods (the effective fragment potential, the variational perturbation theory, the energy decomposition analysis, the atoms-in-molecules), docking, molecular dynamics, and the MM-PBSA method. A biological assay for the lead compound has been performed to validate the theoretical findings. Importantly, binding free energy calculations for the three drug complexes are within 3 kcal/mol of the experimental values, thus further justifying our computational protocol, which has been validated through previous studies on 11 drug-protein systems. The main elements of the discovered mechanism are: (i) minor changes are induced to renin upon drug binding, (ii) the three drugs form an extensive network of hydrogen bonds with renin, whilst the lead compound presented diminished interactions, (iii) ligand binding in all complexes is driven by favorable van der Waals interactions and the nonpolar contribution to solvation, while the lead compound is associated with diminished van der Waals interactions compared to the drug-bound forms of renin, and (iv) the environment (H2O/Na(+)) has a small effect on the renin-remikiren interaction.

In biological media, nanoparticles acquire a coating of biomolecules (proteins, lipids, polysaccharides) from their surroundings, which reduces their surface energy and confers a biological identity to the particles. This adsorbed layer is the interface between the nanomaterial and living systems and therefore plays a significant role in determining the fate and behaviour of the nanoparticles. This review summarises the state of the art in terms of understanding the bio-nano interface and provides direction for potential future research directions and some recommendations for future priorities and strategies to support the safe implementation of nanotechnologies. The central premise is that nanomaterials must be studied as biological entities under the appropriate exposure conditions and that this should be implemented in study design and reporting for nanosafety assessment. The implications of the bio-nano interface for nanomaterials fate and behaviour are described in light of four interlinked perspectives: the coating concept; the translocation concept; the signalling concept, and the kinetics concept. A key conclusion is that nanoparticles cannot be viewed as non-interacting species, but rather must be thought of, and studied as, biological entities, where their interaction with the environment is mediated by the proteins and other biomolecules that adsorb to them, and the key parameter to characterise then becomes the nature, composition and evolution of the bio-nano interface.

The particular properties of nanomaterials have led to their rapidly increasing use in diverse fields of application. However, safety assessment is not keeping pace and there are still gaps in the understanding of their hazards. Computational models predicting nanotoxicity, such as (quantitative) structure-activity relationships ((Q)SARs), can contribute to safety evaluation, in line with general efforts to apply alternative methods in chemical risk assessment. Their development is highly dependent on the availability of reliable and high quality experimental data, both regarding the compounds' properties as well as the measured toxic effects. In particular, "nano-QSARs" should take the nano-specific characteristics into account. The information compiled needs to be well organized, quality controlled and standardized. Integrating the data in an overarching, structured data collection aims to (a) organize the data in a way to support modelling, (b) make (meta)data necessary for modelling available, and (c) add value by making a comparison between data from different sources possible.Based on the available data, specific descriptors can be derived to parameterize the nanomaterial-specific structure and physico-chemical properties appropriately. Furthermore, the interactions between nanoparticles and biological systems as well as small molecules, which can lead to modifications of the structure of the active nanoparticles, need to be described and taken into account in the development of models to predict the biological activity and toxicity of nanoparticles. The EU NanoPUZZLES project was part of a global cooperative effort to advance data availability and modelling approaches supporting the characterization and evaluation of nanomaterials.

The particular properties of nanomaterials have led to their rapidly increasing use in diverse fields of application. However, safety assessment is not keeping pace and there are still gaps in the understanding of their hazards. Computational models predicting nanotoxicity, such as (quantitative) structure-activity relationships ((Q)SARs), can contribute to safety evaluation, in line with general efforts to apply alternative methods in chemical risk assessment. Their development is highly dependent on the availability of reliable and high quality experimental data, both regarding the compounds’ properties as well as the measured toxic effects. In particular, “nano-QSARs” should take the nano-specific characteristics into account. The information compiled needs to be well organized, quality controlled and standardized. Integrating the data in an overarching, structured data collection aims to (a) organize the data in a way to support modelling, (b) make (meta)data necessary for modelling available, and (c) add value by making a comparison between data from different sources possible.

Mutations in the human immunodeficiency virus (HIV) enable virus replication even when appropriate antiretroviral therapy is followed, thus leading to the emergence of drug resistance. In a previous work, we systematically examined seven single mutations that are associated with saquinavir (SQV) resistance in HIV-1 protease (Tzoupis, H.; Leonis, G.; Mavromoustakos, T.; Papadopoulos, M. G. J. Chem. Theory Comput. 2013, 9, 1754-1764). Herein, we extend our analysis, which includes seven double (G48V-V82A, L10I-G48V, G48V-L90M, I84V-L90M, L10I-V82A, L10I-L63P, A71V-G73S) and four multiple (L10I-L63P-A71V, L10I-G48V-V82A, G73S-I84V-L90M, L10I-L63P-A71V-G73S-I84V-L90M) SQV-HIV-1 PR mutant complexes, in an attempt to generalize our findings and formulate the main elements of the SQV resistance mechanism in the protease. On the basis of molecular dynamics (MD), molecular mechanics Poisson-Boltzmann surface area (MM-PBSA), and ab initio computational approaches, we identified specific features that constitute the HIV-1 PR mechanism of resistance at the molecular level: the low flexibility of SQV in the binding cavity and the preservation of hydrogen bonding (HB) and van der Waals interactions between SQV and several active-site (Gly27/27', Asp29/29'/30/30', especially Asp25/25') and flap (Ile50/50', Gly48/48') residues of the protease contribute significantly to efficient binding. The total enthalpy loss in all mutants is mostly due to the loss in enthalpy of the active-site region. Furthermore, it was observed that mutation accumulation may induce stabilization to SQV and to the flaps through enhanced HB interactions that lead to improved inhibition (e.g., accumulation of mutations in complexes containing L10I, G48V, L63P, I84V, or L90M single mutations). It was also concluded that permanent flap closure is obtained independently of mutations and SQV binding is mostly driven by van der Waals, nonpolar, and exchange-energy contributions. Importantly, it was indicated that the optimal positioning of SQV and the structure of the binding cavity are tightly coupled, since small changes in geometry may affect the binding energy greatly. The results of our theoretical approaches are in agreement with experimental evidence and provide a reliable description of SQV resistance in HIV-1 PR.

Opioid G protein-coupled receptors (GPCRs) have been implicated in modulating pain, addiction, psychotomimesis, mood and memory, among other functions. We have employed the recently reported crystal structure of the human κ-opioid receptor (κ-OR) and performed molecular dynamics (MD), free energy, and ab initio calculations to elucidate the binding mechanism in complexes with antagonist JDTic and agonist SalA. The two systems were modeled in water and in DPPC lipid bilayers, in order to investigate the effect of the membrane upon conformational dynamics. MD and Atoms in Molecules (AIM) ab initio calculations for the complexes in water showed that each ligand was stabilized inside the binding site of the receptor through hydrogen bond interactions that involved residues Asp138 (with JDTic) and Gln115, His291, Leu212 (with SalA). The static description offered by the crystal structure was overcome to reveal a structural rearrangement of the binding pocket, which facilitated additional interactions between JDTic and Glu209/Tyr139. The role of Glu209 was emphasized, since it belongs to an extracellular loop that covers the binding site of the receptor and is crucial for ligand entrapment. The above interactions were retained in membrane complexes (SalA forms additional hydrogen bonds with Tyr139/312), except the Tyr139 interaction, which is abolished in the JDTic complex. For the first time, we report that JDTic alternates between a "V-shape" (stabilized via a water-mediated intramolecular interaction) and a more extended conformation, a feature that offers enough suppleness for effective binding. Moreover, MM-PBSA calculations showed that the more efficient JDTic binding to κ-OR compared to SalA (ΔGJDTic = -31.6 kcal mol(-1), ΔGSalA = -9.8 kcal mol(-1)) is attributed mostly to differences in electrostatic contributions. Importantly, our results are in qualitative agreement with the experiments (ΔGJDTic,exp = -14.4 kcal mol(-1), ΔGSalA,exp = -10.8 kcal mol(-1)). This study provides previously unattainable information on the dynamics of human κ-OR and insight on the rational design of drugs with improved pharmacological properties.

Static excited-state polarisabilities and hyperpolarisabilities of three Ru(II) ammine complexes are computed at the density functional theory (DFT) and several correlated ab initio levels. Most accurate modelling of the low energy electronic absorption spectrum is obtained with the hybrid functionals B3LYP, B3P86 or M06 for the complex [Ru(II)(NH3)5(MeQ(+))](3+) (MeQ(+)=N-methyl-4,4'-bipyridinium, 3) in acetonitrile. The match with experimental data is less good for [Ru(II)(NH3)5L](3+) (L=N-methylpyrazinium, 2; N-methyl-4-{E,E-4-(4-pyridyl)buta-1,3-dienyl}pyridinium, 4). These calculations confirm that the first dipole- allowed excited state (FDAES) has metal-to-ligand charge-transfer (MLCT) character. Both the solution and gas-phase results obtained for 3 by using B3LYP, B3P86 or M06 are very similar to those from restricted active-space SCF second-order perturbation theory (RASPT2) with a very large basis set and large active space. However, the time-dependent DFT λ(max) predictions from the long-range corrected functionals CAM-B3LYP, LC-ωPBE and wB97XB and also the fully ab initio resolution of identity approximate coupled-cluster method (gas-phase only) are less accurate for all three complexes. The ground state (GS) two-state approximation first hyperpolarisability β(2SA) for 3 from RASPT2 is very close to that derived experimentally via hyper-Rayleigh scattering, whereas the corresponding DFT-based values are considerably larger. The β responses calculated by using B3LYP, B3P86 or M06 increase markedly as the π-conjugation extends on moving along the series 2→4, for both the GS and FDAES species. All three functionals predict substantial FDAES β enhancements for each complex, increasing with the π-conjugation, up to about sevenfold for 4. Also, the computed second hyperpolarisabilities γ generally increase in the FDAES, but the results vary between the different functionals.

A series of symmetrically bis-substituted imidazole analogs bearing at the N-1 and N-3 two biphenyl moieties ortho substituted either with tetrazole or carboxylate functional groups was designed based on docking studies and utilizing for the first time an extra hydrophobic binding cleft of AT1 receptor. The synthesized analogs were evaluated for their in vitro antagonistic activities (pA 2 values) and binding affinities (–logIC 50 values) to the Angiotensin II AT1 receptor. Among them, the potassium (–logIC 50 = 9.04) and the sodium (–logIC 50 = 8.54) salts of 4-butyl- N , N ′-bis{[2′-(2 H -tetrazol-5-yl)biphenyl-4-yl]methyl}imidazolium bromide ( 12a and 12b , respectively) as well as its free acid 11 (–logIC 50 = 9.46) and the 4-butyl-2-hydroxymethyl- N , N ′-bis{[2′-(2 H -tetrazol-5-yl)biphenyl-4-yl]methyl}imidazolium bromide ( 14 ) (–logIC 50 = 8.37, pA 2 = 8.58) showed high binding affinity to the AT1 receptor and high antagonistic activity (potency). The potency was similar or even superior to that of Losartan (–logIC 50 = 8.25, pA 2 = 8.25). On the contrary, 2-butyl- N , N ′-bis{[2′-[2 H -tetrazol-5-yl)]biphenyl-4-yl]methyl}imidazolium bromide ( 27 ) (–logIC 50 = 5.77) and 2-butyl-4-chloro-5-hydroxymethyl- N , N ′-bis{[2′-[2 H -tetrazol-5-yl)]biphenyl-4-yl]methyl}imidazolium bromide ( 30 ) (–logIC 50 = 6.38) displayed very low binding affinity indicating that the orientation of the n -butyl group is of primary importance. Docking studies of the representative highly active 12b clearly showed that this molecule has an extra hydrophobic binding feature compared to prototype drug Losartan and it fits to the extra hydrophobic cavity. These results may contribute to the discovery and development of a new class of biologically active molecules through bis-alkylation of the imidazole ring by a convenient and cost effective synthetic strategy.

In this contribution, the advantages and limitations of two computational techniques that can be used for the investigation of nanoparticles activity and toxicity: classic nano-QSAR (Quantitative Structure–Activity Relationships employed for nanomaterials) and 3D nano-QSAR (three-dimensional Quantitative Structure–Activity Relationships, such us Comparative Molecular Field Analysis, CoMFA/Comparative Molecular Similarity Indices Analysis, CoMSIA analysis employed for nanomaterials) have been briefly summarized. Both approaches were compared according to the selected criteria, including: efficiency, type of experimental data, class of nanomaterials, time required for calculations and computational cost, difficulties in the interpretation. Taking into account the advantages and limitations of each method, we provide the recommendations for nano-QSAR modellers and QSAR model users to be able to determine a proper and efficient methodology to investigate biological activity of nanoparticles in order to describe the underlying interactions in the most reliable and useful manner. Electronic supplementary material The online version of this article (doi:10.1007/s11051-016-3564-1) contains supplementary material, which is available to authorized users.

Drug–membrane interactions of the candesartan cilexetil (TCV-116) have been studied on molecular basis by applying various complementary biophysical techniques namely differential scanning calorimetry (DSC), Raman spectroscopy, small and wide angle X-ray scattering (SAXS and WAXS), solution 1H and 13C nuclear magnetic resonance (NMR) and solid state 13C and 31P (NMR) spectroscopies. In addition, 31P cross polarization (CP) NMR broadline fitting methodology in combination with ab initio computations has been applied. Finally molecular dynamics (MD) was applied to find the low energy conformation and position of candesartan cilexetil in the bilayers. Thus, the experimental results complemented with in silico MD results provided information on the localization, orientation, and dynamic properties of TCV-116 in the lipidic environment. The effects of this prodrug have been compared with other AT1 receptor antagonists hitherto studied. The prodrug TCV-116 as other sartans has been found to be accommodated in the polar/apolar interface of the bilayer. In particular, it anchors in the mesophase region of the lipid bilayers with the tetrazole group oriented toward the polar headgroup spanning from water interface toward the mesophase and upper segment of the hydrophobic region. In spite of their localization identity, their thermal and dynamic effects are distinct pointing out that each sartan has its own fingerprint of action in the membrane bilayer, which is determined by the parameters derived from the above mentioned biophysical techniques.

(1)H NMR Saturation Transfer Difference (STD) experiments were applied to study the binding of aspirin and of an anti-inflammatory complex of Cu(I), namely [Cu(tpp)(pmt)](2) [pmt = 2-mercaptopyrimidine), synthesized in an attempt to develop novel metallotherapeutic molecules. While aspirin showed only very weak binding, the complex [Cu(tpp)(pmt)](2) clearly favored binding to LOX-1. In silico docking experiments in LOX-1 showed that aspirin does only weakly bind to LOX-1, while the complex binds with high affinity. In addition, docking experiments and molecular dynamics (MD) simulations showed that the complex binds via hydrogen bonding (HB), to an allosteric site of LOX-1, revealing that this enzyme has more than one accessible site for complex metallotherapeutic molecules. When aspirin was added in the solution containing LOX and the complex [Cu(tpp)(pmt)](2), the former was shown to hinder the binding of the Cu complex significantly. This may be interpreted as the copper complex aiding the transfer of aspirin through an acid-base reaction at the LOX enzyme which subsequently blocks its binding.

The linear and nonlinear optical properties (L&NLO) of a monolayer of (4-(N-methyl-N-(carboxypropyl)amino)-phenyl-4′-(N,N-dibutylamino)phenylsquaraine (SBA) were computed by a combination of molecular dynamics simulations, molecular quantum-mechanical, and discrete local-field model calculations to compute the macroscopic optical susceptibilities. Langmuir films on water and graphite were simulated and several structural properties investigated. In addition, SBA in water and dimethylsulfoxide (DMSO) solutions were simulated, and the aggregation behavior of SBA in these solvents was analyzed. The molecular (hyper)polarizabilities of SBA were calculated with density functional theory and validated with MP2 correlated ab initio calculations. An unusual large component perpendicular to the molecular dipole moment is obtained for the molecular first hyperpolarizability, which is a main contributor to the large in-plane anisotropy of the computed macroscopic second-harmonic generation signal of the Langmuir–Blo...

cited By 16; International audience; It is shown by density functional theory calculations that high symmetry silicon cages can be designed by coating with Li atoms. The resulting highly symmetric lithiated silicon cages (up to D 5d symmetry) are low-lying true minima of the energy hypersurface with binding energies of the order of 4.6 eV per Si atom and moderate highest occupied molecular orbital-lowest unoccupied molecular orbital gaps. Moreover, relying on a systematic study of the electric response properties obtained by ab initio (Hartree-Fock, MP2, and configuration interaction singles (CIS)) and density functional (B3LYP, B2PLYP, and CAM-B3LYP) methods, it is shown that lithium coating has a large impact on the magnitude of their second hyperpolarizabilities resulting to highly hyperpolarizable species. Such hyperpolarizable character is directly connected to the increase in the density of the low-lying excited states triggered by the interaction between the Si cage and the surrounding Li atoms. Copyright © 2012 Wiley Periodicals, Inc.

Most of current 3D-QSAR algorithms use alignments of compounds at the training set based on reference active ligands in the first step of the construction of the pharamacophore modeling. This first step mostly defines the success of constructed pharmacophore models. In this step, it is essential to find the bioactive conformation for solid and reliable 3D-QSAR models. Therefore, we have proceeded through different approaches for revealing the preferred conformations of Δ8-THC derivative AMG-3 at CB1 and CB2 receptors. In the first approach, we have applied conformational search methods in gas and in solvent phases for the ligand. The derived low energy conformers using these methodologies have been modeled through 3D-QSAR studies (first generation model). In the second approach, the low energy conformers derived from molecular docking studies have been used as input for 3D-QSAR studies (second generation model). In the current study, a new approach using MD calculations in a simulated biological environment, thus the CB receptors surrounded by a lipid bilayer environment has been used (third generation). The obtained results for different environments were compared and the approach deriving the highest statistic results was used for the generation of the novel AMG3 analogs for optimal and selective binding affinities at CB1 and CB2 receptors by the de novo drug design modeling.

Aliskiren is the first orally active, direct renin inhibitor to be approved for the treatment of hypertension. Its structure elucidation and conformational analysis were explored using 1D and 2D NMR spectroscopy, as well as random search and molecular dynamics (MD) simulations. For the first time, MD calculations have also been performed for aliskiren at the receptor site, in order to reveal its molecular basis of action. It is suggested that aliskiren binds in an extended conformation and is involved in several stabilizing hydrogen bonding interactions with binding cavity (Asp32/255, Gly34) and other binding-cavity (Arg74, Ser76, Tyr14) residues. Of paramount importance is the finding of a loop consisting of residues around Ser76 that determines the entrapping of aliskiren into the active site of renin. The details of this mechanism will be the subject of a subsequent study. Additionally molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) free energy calculations for the aliskiren-renin complex provided insight into the binding mode of aliskiren by identifying van der Waals and nonpolar contribution to solvation as the main components of favorable binding interactions.

The objectives of this study include the design of a series of novel fullerene-based inhibitors for HIV-1 protease (HIV-1 PR), by employing two strategies that can also be applied to the design of inhibitors for any other target. Additionally, the interactions which contribute to the observed exceptionally high binding free energies were analyzed. In particular, we investigated: (1) hydrogen bonding (H-bond) interactions between specific fullerene derivatives and the protease, (2) the regions of HIV-1 PR that play a significant role in binding, (3) protease changes upon binding and (4) various contributions to the binding free energy, in order to identify the most significant of them. This study has been performed by employing a docking technique, two 3D-QSAR models, molecular dynamics (MD) simulations and the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method. Our computed binding free energies are in satisfactory agreement with the experimental results. The suitability of specific fullerene derivatives as drug candidates was further enhanced, after ADMET (absorption, distribution, metabolism, excretion and toxicity) properties have been estimated to be promising. The outcomes of this study revealed important protein-ligand interaction patterns that may lead towards the development of novel, potent HIV-1 PR inhibitors.

Rational design is applied in the discovery of novel lead drugs. Its rapid development is mainly attributed to the tremendous advancements in the computer science, statistics, molecular biology, biophysics, biochemistry, medicinal chemistry, pharmacokinetics and pharmacodynamics experienced in the last few decades. The promising feature that characterizes the application of rational drug design is that it uses for developing potential leads in drug discovery all known theoretical and experimental knowledge of the system under study. The utilization of the knowledge of the molecular basis of the system ultimately aims to reduce human power cost, time saving and laboratory expenses in the drug discovery. In this review paper various strategies applied for systems which include: (i) absence of knowledge of the receptor active site; (ii) the knowledge of a homology model of a receptor, (iii) the knowledge of the experimentally determined (i.e. X-ray crystallography, NMR spectroscopy) coordinates of the active site of the protein in absence and (iv) the presence of the ligand will be analyzed.

The interactions of the antihypertensive AT(1) antagonists candesartan and losartan with membrane bilayers were studied through the application of DSC, Raman, and solid state (31)P NMR spectroscopies. (1)H and (13)C NMR resonances of candesartan were assigned on the basis of 1D and 2D NMR spectroscopy. A (31)P CP NMR broadline fitting methodology in combination with ab initio computations was implemented and, in conjunction with DSC and Raman results, provided valuable information regarding the perturbation, localization, orientation, and dynamic properties of the drugs in membrane models. In particular, results indicate that losartan anchors in the mesophase region of the lipid bilayers with the tetrazole group oriented toward the polar headgroup, whereas candesartan has less definite localization spanning from water interface toward the mesophase and upper segment of the hydrophobic region. Both sartan molecules decrease the mobilization of the phospholipids alkyl chains. Losartan exerts stronger interactions compared with candesartan, as depicted by the more prominent thermal, structural, and dipolar (1)H-(31)P changes that are caused in the lipid bilayers. At higher concentrations, candesartan strengthens the polar interactions and induces increased order at the bilayer surface. At the highest concentration used (20 mol %), only losartan induces formation of microdomains attributed to the flexibility of its alkyl chain. These results in correlation to reported data with other AT(1) antagonists strengthen the hypothesis that this class of molecules may approach the active site of the receptor by insertion in the lipid core, followed by lateral diffusion toward the binding site. Further, the similarities and differences of these drugs in their interactions with lipid bilayers establish, at least in part, their pharmacological properties.

In the version of this Article originally published, in Fig. 1c–e, on the x axes, the lines labelled ‘Aβ42’ and ‘Aβ42(F19S;L34P)’ grouped the data incorrectly; the line labelled Aβ42 should have grouped the data for Random 1–2 and Clones 1–10, and the line labelled Aβ42(F19S;L34P) should have only grouped the data for Random 1–2 on the right end of the plots and blots. These figures have now been corrected in all versions of the Article.

For the first time, a set of renin inhibitors were subjected to the 3D QSAR/CoMFA and CoMSIA studies. The utility of renin inhibitors in the treatment of cardiovascular diseases has not been fully explored yet. At the moment, aliskiren is the first and only existing renin inhibitor in the drug market. The performed 3D QSAR/CoMFA and CoMSIA in combination with docking studies included aliskiren and 37 derivatives possessing a wide variety of bioactivity. The obtained results may aid in the design of novel bioactive renin inhibitors.

In the present study, we report on the results of computations of the electronic and the vibrational contributions to the static first hyperpolarizability ( β ) of meta-dinitrobenzene molecule. It turned out that the electron correlation effects are much more important for reliable prediction of the electronic counterpart than for determining vibrational corrections: β e value is increased by about 500% passing from the HF to the CCSD(T) level of theory. The preliminary assessment of density functional theory in determination of hyperpolarizabilities shows that harmonic contributions to β , contrary to the purely electronic contributions, are substantially underestimated in comparison with the wave function theory results. Another important finding of this study is that long-range corrected functionals tend to improve upon traditional functionals both in determining electronic as well as vibrational hyperpolarizabilities. It is also demonstrated that the vibrations of the nitro groups have a predominant influence on the vibrational contributions to β vib . The mechanical and electrical anharmonicity correction terms to the vibrational hyperpolarizability were found to be substantially larger than the lowest-order harmonic term.

A database has been derived from recently reported [60]fullerene derivatives, and their binding scores with HIV-1 PR have been computed using docking techniques. Computational methods have been used to predict which derivatives may have high binding affinities, and for these compounds biological tests have been performed with purified PR. Experimental results confirm the high binding scores of fullerene derivatives predicted from the docking calculations. Our measurements showed that the fullerene derivative (Fmoc-Baa) has about three times better inhibitory binding (K(i) = 36 nM) than the most active fullerene-based inhibitor (K(i) = 103 nM) currently available.

A systematic study of the (hyper)polarizabilities of a series of Xe compounds, HXeF, AuXeF and XeAuF has been performed. A consistent hierarchy of basis sets and ab-initio methods involving HF, MP2, CCSD and CCSD(T), has been employed in order to investigate in depth the effect of Xe insertion on the above properties of HF and AuF. It was observed that the Xe position in AuF significantly modifies the (hyper)polarizability of the resulting derivative. The polarizability and first hyperpolarizability of AuXeF are remarkably larger than that of XeAuF.

The conformational properties of AT1 antagonist valsartan have been analyzed both in solution and at the binding site of the receptor. Low energy conformations of valsartan in solution were explored by NMR spectroscopy and molecular modeling studies. The NMR results showed the existence of two distinct and almost isoenergetic conformations for valsartan (cis:trans ratio around the amide bond approximately 40:60) that coalesce at the temperature range of 55-60 degrees C in agreement with previous in solution conformational analysis study (Fang et al. Magn. Reson. Chem. 2007, 45, 929-936). Quantum mechanics and ONIOM calculations revealed that the bulky valsartan substituents actually contribute to stabilization of the transition state for interconversion. In silico docking and Molecular Dynamic studies were applied to study binding of valsartan at the AT1 receptor site models, explicitly solvated and embedded in lipid bilayers and solvent molecules. These studies revealed that the majority of docked poses adopted a trans (major) conformation. Of paramount and maybe biological importance are the MD simulations results which showed that the two acidic groups of valsartan are bridged through LYS199 enabling it for multiple hydrogen bond interactions. In a lipid bilayer environment these interactions are enhanced, designating the important role of lipid bilayers for the better binding of valsartan and its stabilization at the active site.