A Comparative Molecular Dynamics, MM−PBSA and Thermodynamic Integration Study of Saquinavir Complexes with Wild-Type HIV‑1 PR and L10I, G48V, L63P, A71V, G73S, V82A and I84V Single Mutants

A great challenge toward Acquired Immunodeficiency Syndrome (AIDS) treatment is to combat the HIV-1 virus. The major problem of drug resistance has kept the virus one step ahead of the medical community, and the call for more effective drugs remains as urgent as ever. Saquinavir, the first inhibitor against HIV-1 protease, offers the most extensive clinical data regarding resistance mutations. In this work, we examine L10I, G48V, L63P, A71V, G73S, V82A, and I84V single mutant HIV-1 PR strains in complexes with saquinavir to elucidate drug–protease interactions and dynamics. A comparative analysis of these mutations at the molecular level may lead to a deeper understanding of saquinavir resistance. The G48V mutation induces structural changes to the protease that reflect upon the drug’s binding affinity, as shown by MM–PBSA and thermodynamic integration (TI) calculations (ΔΔGTI = 0.3 kcal/mol; ΔΔGMM–PBSA = 1.2 kcal/mol). It was shown that mutations, which increase the flexibility of the flaps (G48V, L63P, L10I) diminish binding. The preservation of hydrogen bonds of saquinavir with both the active site and flap residues in the wild-type and certain single mutants (A71V, V82A) is also crucial for effective inhibition. It was shown that mutations conferring major resistance (G48V, L63P, I84V) did not present these interactions. Finally, it was indicated that a water-mediated hydrogen bond between saquinavir and Asp29 in the active site (wild-type, A71V, G73S) facilitates a proper placement of the drug into the binding cavity that favors binding. Mutants lacking this interaction (G48V, V82A, I84V) demonstrated reduced binding affinities. This systematic and comparative study is a contribution to the elucidation of the drug resistance mechanism in HIV-1 PR

Conformational analysis of AT1 antagonist valsartan using 2DNMR spectroscopy and computational analysis: determination of thermodynamic parameters through dynamic NMR spectroscopy and semi-empirical calculations

AbstractArticles published in this journal are Indexed or Abstracted in Chemical Abstracts, Elsevier's Bibliographic Databases: Scopus, EMBASE, EMBiology, Elsevier BIOBASE, Compendex, GEOBASE, FLUIDEX, TEXTILE

The bio-nano-interface in predicting nanoparticle fate and behaviour in living organisms: towards grouping and categorising nanomaterials and ensuring nanosafety by design

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 and 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 interfac

Linear and nonlinear optical properties of some organoxenon derivatives

We employ a series of state-of-the-art computational techniques to study the effect of inserting one or more Xe atoms in HC2H and HC4H, on the linear and nonlinear optical (L&NLO) properties of the resulting compounds. It has been found that the inserted Xe has a great effect on the L&NLO properties of the organoxenon derivatives. We analyze the bonding in HXeC2H, and the change of the electronic structure, which is induced by inserting Xe, in order to rationalize the observed extraordinary L&NLO properties. The derivatives, which are of interest in this work, have been synthesized in a Xe matrix. Thus the effect of the local field (LF), due to the Xe environment, on the properties of HXeC2H, has also been computed. It has been found that the LF effect on some properties is significant. The calculations have been performed by employing a hierarchy of basis sets and the techniques MP2 and CCSD(T) for taking into account correlation. For the interpretation of the results we have employed the complete active space valence bond and CASSCF/CASPT2 [email protected]

Tailoring colors by O-annulation of polycyclic aromatic hydrocarbons

The synthesis of O-doped polyaromatic hydrocarbons, in which two polycyclic aromatic hydrocarbon subunits are bridged through one or two O atoms, has been achieved. This includes high-yielding ring-closure key steps that, depending on the reaction conditions, yield the formation of either furanyl or pyranopyranyl linkages through intramolecular C-O bond formation. Comprehensive photophysical measurements in solution showed that these molecules feature exceptionally high emission yields and tunable absorption properties throughout the UV-vis spectral region. Electrochemical investigations showed that in all cases the O-annulation increases the electron donor capabilities by raising the HOMO energy level with the LUMO energy level being less affected. Moreover, third-order NLO measurements of solutions or thin films containing the dyes displayed very good second hyperpolarizibility values. Importantly, PMMA films containing the pyranopyranyl derivatives displayed weak linear absorption and NLO absorption compared to the nonlinearity and NLO refraction, respectively, revealing to be exceptional organic materials for photonic devices

Linear and nonlinear optical properties of a series of Ni-dithiolene derivatives

Some linear and nonlinear optical (NLO) properties of Ni(SCH)4 and several of its derivatives have been computed by employing a series of basis sets and a hierarchy of methods (e.g., HF, DFT, coupled cluster, and multiconfigurational techniques). The electronic structure of Ni(SCH)4 has been also analyzed by using CASSCF/CASPT2, ab initio valence bond, and DFT methods. In particular we discuss how the diradicaloid character (DC) of Ni(SCH)4 significantly affects its NLO properties. The quasidegeneracy of the two lowest-energy singlet states 1 mathg and 1 math1u, the clear DC nature of the former, and the very large number of low-lying states enhance the NLO properties values. These particular features are used to interpret the NLO properties of Ni(SCH)4. The DC of the considered derivatives has been estimated and correlated with the NLO properties. CASVB computations have shown that the structures with Ni(II) are the dominant ones, while those with Ni(0) and Ni(IV) have negligible weight. The weights of the four diradical structures were discussed in connection with the weight of the structures, where all the electrons are paired. Comparative discussion of the properties of Ni(SCH)4 with those of tetrathia fulvalene demonstrates the very large effect of Ni on the properties of the Ni-dithiolene derivatives. A similar remarkable effect on the NLO properties is produced by one or two methyl or C3S groups. The considered Ni-dithiolene derivatives have exceptionally large NLO properties. This feature in connection with their other physical properties makes them ideal candidates for photonic [email protected]

Application of 3D QSAR CoMFA/CoMSIA and in silico docking studies on novel renin inhibitors against cardiovascular diseases

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

Comparative study of the AT1 receptor prodrug antagonist candesartan cilexetil with other sartans on the interactions with membrane bilayers

AbstractDrug–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

Rational design, efficient syntheses and biological evaluation of N,N′-symmetrically bis-substituted butylimidazole analogs as a new class of potent Angiotensin II receptor blockers

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 (pA2 values) and binding affinities (–logIC50 values) to the Angiotensin II AT1 receptor. Among them, the potassium (–logIC50 = 9.04) and the sodium (–logIC50 = 8.54) salts of 4-butyl-N,N′-bis{[2′-(2H-tetrazol-5-yl)biphenyl-4-yl]methyl}imidazolium bromide (12a and 12b, respectively) as well as its free acid 11 (–logIC50 = 9.46) and the 4-butyl-2-hydroxymethyl-N,N′-bis{[2′-(2H-tetrazol-5-yl)biphenyl-4-yl]methyl}imidazolium bromide (14) (–logIC50 = 8.37, pA2 = 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 (–logIC50 = 8.25, pA2 = 8.25). On the contrary, 2-butyl-N,N′-bis{[2′-[2H-tetrazol-5-yl)]biphenyl-4-yl]methyl}imidazolium bromide (27) (–logIC50 = 5.77) and 2-butyl-4-chloro-5-hydroxymethyl-N,N′-bis{[2′-[2H-tetrazol-5-yl)]biphenyl-4-yl]methyl}imidazolium bromide (30) (–logIC50 = 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

Tests of the Equivalence Principle with Neutral Kaons

We test the Principle of Equivalence for particles and antiparticles, using CPLEAR data on tagged K0 and K0bar decays into pi^+ pi^-. For the first time, we search for possible annual, monthly and diurnal modulations of the observables |eta_{+-}| and phi_{+-}, that could be correlated with variations in astrophysical potentials. Within the accuracy of CPLEAR, the measured values of |eta_{+-}| and phi_{+-} are found not to be correlated with changes of the gravitational potential. We analyze data assuming effective scalar, vector and tensor interactions, and we conclude that the Principle of Equivalence between particles and antiparticles holds to a level of 6.5, 4.3 and 1.8 x 10^{-9}, respectively, for scalar, vector and tensor potentials originating from the Sun with a range much greater than the distance Earth-Sun. We also study energy-dependent effects that might arise from vector or tensor interactions. Finally, we compile upper limits on the gravitational coupling difference between K0 and K0bar as a function of the scalar, vector and tensor interaction range.Comment: 15 pages latex 2e, five figures, one style file (cernart.csl) incorporate