Nadtanet Nunthaboot

Susceptibility of antiviral drugs against 2009 influenza A (H1N1) virus

The recent outbreak of the novel strain of influenza A (H1N1) virus has raised a global concern of the future risk of a pandemic. To understand at the molecular level how this new H1N1 virus can be inhibited by the current anti-influenza drugs and which of these drugs it is likely to already be resistant to, homology modeling and MD simulations have been applied on the H1N1 neuraminidase complexed with oseltamivir, and the M2-channel with adamantanes bound. The H1N1 virus was predicted to be susceptible to oseltamivir, with all important interactions with the binding residues being well conserved. In contrast, adamantanes are not predicted to be able to inhibit the M2 function and have completely lost their binding with the M2 residues. This is mainly due to the fact that the M2 transmembrane of the new H1N1 strain contains the S31N mutation which is known to confer resistance to adamantanes.

Simultaneous analysis of ultrafast fluorescence decays of FMN binding protein and its mutated proteins by molecular dynamic simulation and electron transfer theory.

Ultrafast fluorescence decays of FMN binding proteins (FBP) from Desulfovibrio vulgaris (Miyazaki F) were analyzed with an electron transfer (ET) theory by Kakitani and Mataga (KM theory). Time-dependent distances among isoalloxazine (Iso) and Trp-32, Tyr-35, and Trp-106 in wild-type FBP (WT), among Iso and Tyr-32, Tyr-35, and Trp-106 in W32Y (Trp-32 was replaced by Tyr-32), and among Iso and Tyr-35 and Trp-106 in W32A (Trp-32 was replaced by Ala-32) were determined by molecular dynamic simulation (MD). Electrostatic energies between Iso anion and all other ionic groups, between Trp-32 cation and all other ionic groups, and between Tyr-32 cation and all other ionic groups were calculated in WT, W32Y, and W32A, from the MD coordinates. ET parameters contained in KM theory, such as frequency (nu 0), a coefficient of the ET process (beta), a critical distance of the ET process ( R 0), standard free energy related to the electron affinity of the excited Iso ( G Iso (0)), and the static dielectric constant in FBP species (epsilon 0), were determined with and without inclusion of the electrostatic energy, so as to fit the calculated fluorescence decays with the observed decays of all FBP species, by a nonlinear least-squares method according to the Marquardt algorithm. In the analyses the parameters, nu 0, beta, and R 0 were determined separately between Trp residues and Tyr residues among all FBP species. Calculated fluorescence intensities with the inclusion of the electrostatic energy fit quite well with the observed ones of all WT, W32Y, and W32A.

Evolution of Human Receptor Binding Affinity of H1N1 Hemagglutinins from 1918 to 2009 Pandemic Influenza A Virus

The recent outbreak of the novel 2009 H1N1 influenza in humans has focused global attention on this virus, which could potentially have introduced a more dangerous pandemic of influenza flu. In the initial step of the viral attachment, hemagglutinin (HA), a viral glycoprotein surface, is responsible for the binding to the human SIA alpha2,6-linked sialopentasaccharide host cell receptor (hHAR). Dynamical and structural properties, based on molecular dynamics simulations of the four different HAs of Spanish 1918 (H1-1918), swine 1930 (H1-1930), seasonal 2005 (H1-2005), and a novel 2009 (H1-2009) H1N1 bound to the hHAR were compared. In all four HA-hHAR complexes, major interactions with the receptor binding were gained from HA residue Y95 and the conserved HA residues of the 130-loop, 190-helix, and 220-loop. However, introduction of the charged HA residues K145 and E227 in the 2009 HA binding pocket was found to increase the HA-hHAR binding efficiency in comparison to the three previously recognized H1N1 strains. Changing of the noncharged HA G225 residue to a negatively charged D225 provides a larger number of hydrogen-bonding interactions. The increase in hydrophilicity of the receptor binding region is apparently an evolution of the current pandemic flu from the 1918 Spanish, 1930 swine, and 2005 seasonal strains. Detailed analysis could help the understanding of how different HAs effectively attach and bind with the hHAR.

Density functional investigation of hydrogen gas adsorption on Fe−doped pristine and Stone−Wales defected single−walled carbon nanotubes

AbstractThe adsorptions of hydrogen molecule of the Fe − doped pristine and Stone − Wales defected armchair (5,5) single − walled carbon nanotubes (SWCNTs) compared with the pristine SWCNT were investigated by using the density functional theory at the B3LYP/LanL2DZ level. The doping of Fe atom into SWCNTs occurring via an exothermic process was found. The adsorptions of hydrogen molecule on the Fe − doped structures of either perfect or SW defected SWCNTs are stronger than on their corresponding undoped structures. The structural and electronic properties of the pristine and SW defected SWCNTs, their Fe − doped structures and their hydrogen molecule adsorptions are reported. FigureThe adsorptions of hydrogen molecule of the Fe−doped pristine and defected (5,5) single−walled carbon nanotubes (SWCNTs) compared with the pristine SWCNT were computed. The adsorptions of hydrogen molecule on the Fe−doped structures of either perfect or defected SWCNTs are stronger than on their corresponding undoped structures

How does each substituent functional group of oseltamivir lose its activity against virulent H5N1 influenza mutants

To reveal the source of oseltamivir-resistance in influenza (A/H5N1) mutants, the drug-target interactions at each functional group were investigated using MD/LIE simulations. Oseltamivir in the H274Y mutation primarily loses the electrostatic and the vdW interaction energies at the -NH(3)(+) and -OCHEt(2) moieties corresponding to the weakened hydrogen-bonds and changed distances to N1 residues. Differentially, the N294S mutation showed small changes of binding energies and intermolecular interactions. Interestingly, the presence of different conformations of E276 positioned between the -OCHEt(2) group and the mutated residue is likely to play an important role in oseltamivir-resistant identification. In the H274Y mutant, it moves towards the -OCHEt(2) group leading to a reduction in hydrophobicity and pocket size, whilst in the N294S mutant it acts as the hydrogen network center bridging with R224 and the mutated residue S294. The molecular details have answered a question of how the H274Y and N294S mutations confer the high- and medium-level of oseltamivir-resistance to H5N1.

Binding pattern of the long acting neuraminidase inhibitor laninamivir towards influenza A subtypes H5N1 and pandemic H1N1.

Influenza A H5N1 and pH1N1 viruses have broadly emerged and become widespread in various countries around the world. Oseltamivir, the most commonly used antiviral drug against the seasonal and pandemic influenza viruses, is targeted at the viral neuraminidase (NA), but some isolates of this virus have become highly resistant to this drug. The novel long-acting drug, laninamivir, was recently developed to inhibit influenza A and B viruses of either the wild-type (WT) or the oseltamivir resistant mutant of NA. To understand the high efficiency of laninamivir, all-atom molecular dynamics simulations were performed on the WT and H274Y mutant of H5N1 and pH1N1 NAs with laninamivir bound. As a result, the novel drug was found to directly interact with 11 binding residues mainly through salt bridge and hydrogen bond formation (as also seen by electrostatic contribution). These are comprised of 7 of the catalytic residues (R118, D151, R152, R224, E276, R292 and R371), and 4 of the framework residues (E119, W178, E227 and E277). Laninamivir showed a similar binding pattern to all four NAs, but strong hydrogen bonding interactions were only found in the WT strain, with a slightly lowered contribution at some drug contact residues being observed in the H274Y mutation. This is in good agreement with the experimental data that the H274Y mutant has a small increase (1.3-7.5-fold, which was not statistically significant) in the IC₅₀ value of laninamivir.

Structural basis for the temperature-induced transition of D-amino acid oxidase from pig kidney revealed by molecular dynamic simulation and photo-induced electron transfer.

The structural basis for the temperature-induced transition in the D-amino acid oxidase (DAAO) monomer from pig kidney was studied by means of molecular dynamic simulations (MDS). The center to center (Rc) distances between the isoalloxazine ring (Iso) and all aromatic amino acids (Trp and Tyr) were calculated at 10 °C and 30 °C. Rc was shortest in Tyr224 (0.82 and 0.88 nm at 10 and 30 °C, respectively), and then in Tyr228. Hydrogen bonding (H-bond) formed between the Iso N1 and Gly315 N (peptide), between the Iso N3H and Leu51 O (peptide) and between the Iso N5 and Ala49 N (peptide) at 10 °C, whilst no H-bond was formed at the Iso N1 and Iso N3H at 30 °C. The H-bond of Iso O4 with Leu51 N (peptide) at 10 °C switched to that with Ala49 N (peptide) at 30 °C. The reported fluorescence lifetimes (228 and 182 ps at 10 and 30 °C, respectively) of DAAO were analyzed with Kakitani and Mataga (KM) ET theory. The calculated fluorescence lifetimes displayed an excellent agreement with the observed lifetimes. The ET rate was fastest from Tyr224 to the excited Iso (Iso*) at 10 °C and from Tyr314 at 30 °C, despite the fact that the Rc was shortest between Iso and Tyr224 at both temperatures. This was explained by the electrostatic energy in the protein. The differences in the observed fluorescence lifetimes at 10 and 30 °C were ascribed to the differences in electron affinity of the Iso* at both temperatures, in which the free energies of the electron affinity of Iso* at 10 and 30 °C were -8.69 eV and -8.51 eV respectively. The other physical quantities related to ET did not differ appreciably at both temperatures. The electron affinities at both temperatures were calculated with a semi-empirical molecular orbital method (MO) of PM6. Mean calculated electron affinities over 100 snapshots with 0.1 ps intervals were -7.69 eV at 10 °C and -7.59 eV at 30 °C. The difference in the calculated electron affinities, -0.11 eV, was close to the observed difference in the free energies, -0.18 eV. The present quantitative analysis predicts that the highest ET rate can occur from a donor with longer donor-acceptor distance, which was explained by differences in electrostatic energy.

Quantum mechanical study of photoinduced charge transfer in FMN binding protein.

CT interactions between Iso* and nearby aromatic amino acids in FBP were investigated by a semiempirical MO method. Atomic coordinates of lumiflavin as Iso, 3-methylindole as Trp, and 4-methylphenol as Tyr, used for MO calculations, were obtained from crystal, 20 NMR structures and 40 MD structures (20 ps time intervals). Geometries of Iso-Trp32, Iso-Trp106 and Iso-Tyr35 systems were optimized by the PM3 method. The interaction energies (kcal/mol) of crystal structure were -16.9 in the Iso-Trp32 system, -7.4 in the Iso-Trp106 system and 1.4 in the Iso-Tyr35 system. The interaction energies (kcal/mol) of NMR structures were -16.5 +/- 0.28 in the Iso-Trp32 system, -10.6 +/- 0.14 in the Iso-Trp106 system, and 0.97 +/- 0.09 in the Iso-Tyr35 system. The interaction energies (kcal/mol) of MD structures were -24.3 +/- 0.19 in the Iso-Trp32 system, -10.2 +/- 0.49 in the Iso-Trp106 system, and 0.285 +/- 0.037 in the Iso-Tyr35 system. CT interaction from the aromatic amino acids to Iso* was judged from negative charge at Iso*. The charge in the Iso-Trp32 system was -0.490 in crystals, -0.439 +/- -0.099 in NMR structures, -0.454 +/- 0.048 in MD structures. The charge in the Iso and Trp106 system was -0.011 +/- 0.004 in MD structures, but negligible in other structures. CT interactions in Iso-Tyr35 system were also negligible. The ET rate obtained with Kakitani and Mataga theory and MD decreased as the magnitude of the interaction energy decreased. Correlation between the ET rate and CT interaction in FBP was examined. The interaction energy (Y) was approximated with ln(ET rate) (X) by a function, Y = 0.0036X(3) + 0.0306X(2) - 1.7822X - 21.177.

Computational studies of influenza A virus at three important targets: hemagglutinin, neuraminidase and M2 protein.

While the seasonal influenza viruses spreading around the world cause the annual epidemics, the recent outbreaks of influenza A virus subtype H5N1 and pandemic H1N1 have raised a global human health concerns. In this review, the applicability of computational techniques focused on three important targets in the viral life cycle: hemagglutinin, neuraminidase and M2 proton channel are summarized. Protein mechanism of action, substrate binding specificity and drug resistance, ligand-target interactions of substrate/inhibitor binding to these three proteins either wild-type or mutant strains are discussed and compared. Advances on the novel anti-influenza agents designed specifically to combat the avian H5N1 and pandemic H1N1 viruses are introduced. A better understanding of molecular inhibition and source of drug resistance as well as a set of newly designed compounds is greatly useful as a rotational guide for synthetic and medicinal chemists to develop a new generation of anti-influenza drugs.

Theoretical analyses of the fluorescence lifetimes of the D-amino acid oxidase–benzoate complex dimer from porcine kidney: molecular dynamics simulation and photoinduced electron transfer

The mechanism of photoinduced electron transfer (ET) from benzoate (Bz) and aromatic amino acids to the excited isoalloxazine (Iso*) in the D-amino acid oxidase–benzoate complex (DAOB) dimer from porcine kidney was studied using molecular dynamics simulation (MDS) and an electron transfer theory, and compared with that in the DAOB monomer. The DAOB dimer displayed two fluorescent lifetime components of 0.85 ps and 4.8 ps, as reported. The ET parameters contained in the Kakitani and Mataga (KM) model were determined so as to reproduce these lifetimes with MDS atomic coordinates. The Bz–isoalloxazine (Iso) distances were 0.66 nm in subunit A (Sub A), 0.68 nm in subunit B (Sub B) and 0.61 nm in the monomer. The fluorescent lifetimes of 4.8 ps and 0.85 ps were found to originate from Sub A and Sub B, respectively. In Sub A, Tyr228 was the fastest ET donor followed by Bz and Tyr55, while Bz was followed by Tyr228 and Tyr314 in Sub B. The ET rate from Bz was fastest in Sub B, followed by that in Sub A and the DAOB monomer. The static dielectric constants obtained near Iso were 2.4–2.6 in the DAOB dimer and monomer and 5.8–5.9 in holo D-amino oxidase (DAAO). The different dielectric constants could account for the experimental fluorescence peak observed for DAOB (524 nm) and DAAO (530 nm). Logarithmic ET rates decreased linearly with the donor–acceptor distance expressed by both center to center distance (Rc) and edge to edge distance (Re) in Sub A and Sub B of DAOB dimer and monomer, which reveals that the conventional Dutton rule holds in the ET processes in DAOB. The logarithmic ET rates were decomposed into the electronic coupling (EC), square root (SQ) and exponential (GTRAM) terms. It was found that both the EC term and the GTRAM term also decreased linearly with Rc. The sum of the slopes in the EC and GTRAM vs. Rc plots coincided with the slopes in the logarithmic ET rate vs. Rc functions, suggesting that the GTRAM term makes a significant contribution to the linear relations between logarithmic ET rate and Rc.