Position of the Third Na+ Site in the Aspartate Transporter GltPh and the Human Glutamate Transporter, EAAT1

Glutamate transport via the human excitatory amino acid transporters is coupled to the co-transport of three Na+ ions, one H+ and the counter-transport of one K+ ion. Transport by an archaeal homologue of the human glutamate transporters, GltPh, whose three dimensional structure is known is also coupled to three Na+ ions but only two Na+ ion binding sites have been observed in the crystal structure of GltPh. In order to fully utilize the GltPh structure in functional studies of the human glutamate transporters, it is essential to understand the transport mechanism of GltPh and accurately determine the number and location of Na+ ions coupled to transport. Several sites have been proposed for the binding of a third Na+ ion from electrostatic calculations and molecular dynamics simulations. In this study, we have performed detailed free energy simulations for GltPh and reveal a new site for the third Na+ ion involving the side chains of Threonine 92, Serine 93, Asparagine 310, Aspartate 312, and the backbone of Tyrosine 89. We have also studied the transport properties of alanine mutants of the coordinating residues Threonine 92 and Serine 93 in GltPh, and the corresponding residues in a human glutamate transporter, EAAT1. The mutant transporters have reduced affinity for Na+ compared to their wild type counterparts. These results confirm that Threonine 92 and Serine 93 are involved in the coordination of the third Na+ ion in GltPh and EAAT1

A candidate ion-retaining state in the inward-facing conformation of sodium/galactose symporter: Clues from atomistic simulations

The recent Vibrio parahaemolyticus sodium/galactose (vSGLT) symporter crystal structure captures the protein in an inward-facing substrate-bound conformation, with the sodium ion placed, by structural alignment, in a site equivalent to the Na2 site of the leucine transporter (LeuT). A recent study, based on molecular dynamics simulations, showed that the sodium ion spontaneously leaves its initial position diffusing outside vSGLT, toward the intracellular space. This suggested that the crystal structure corresponds to an ion-releasing state of the transporter. Here, using metadynamics, we identified a more stable Na+ binding site corresponding to a putative ion-retaining state of the transporter. In addition, our simulations, consistently with mutagenesis studies, highlight the importance of D189 that, without being one of the NA(+)-coordinating residues, regulates its binding/release

Strength of Hydrogen Bond Network Takes Crucial Roles in the Dissociation Process of Inhibitors from the HIV-1 Protease Binding Pocket

To understand the underlying mechanisms of significant differences in dissociation rate constant among different inhibitors for HIV-1 protease, we performed steered molecular dynamics (SMD) simulations to analyze the entire dissociation processes of inhibitors from the binding pocket of protease at atomistic details. We found that the strength of hydrogen bond network between inhibitor and the protease takes crucial roles in the dissociation process. We showed that the hydrogen bond network in the cyclic urea inhibitors AHA001/XK263 is less stable than that of the approved inhibitor ABT538 because of their large differences in the structures of the networks. In the cyclic urea inhibitor bound complex, the hydrogen bonds often distribute at the flap tips and the active site. In contrast, there are additional accessorial hydrogen bonds formed at the lateral sides of the flaps and the active site in the ABT538 bound complex, which take crucial roles in stabilizing the hydrogen bond network. In addition, the water molecule W301 also plays important roles in stabilizing the hydrogen bond network through its flexible movement by acting as a collision buffer and helping the rebinding of hydrogen bonds at the flap tips. Because of its high stability, the hydrogen bond network of ABT538 complex can work together with the hydrophobic clusters to resist the dissociation, resulting in much lower dissociation rate constant than those of cyclic urea inhibitor complexes. This study may provide useful guidelines for design of novel potent inhibitors with optimized interactions

Cytostatic agents. 9. Relations between physicochemical properties and antimicrobial activity of beta -amino ketones

The relation between antibacterial and antifungal activities of 6 aliphatic beta -amino ketones, 5 alpha -phenyl-beta -amino ketones, 8 beta -amino propiophenones, and 9 alpha -phenyl-beta -amino propiophenones and partition coeff., H2O soly. of the base, and total soly. was studied. The bacteriostatic effect of all investigated beta -amino ketones was small, but the fungistatic effect, with the exception of aliphatic compds., was good. Aliphatic beta -amino ketones of lower mol. size, 1-dimethylamino-2-isopropylpropan-3-one, 1-dimethylamino-2-isobutylpropan-3-one, and 1-dimethylamino-2,3-dimethylpropan-3-one, showed good H2O soly. and a partition coeff. <0.1 but had weak antifungal activity. Increasing the length of the alkyl residue, as in 1-dimethylamino-2-hexyl-3-methylpropan-3-one and 1-dimethylamino-2-octyl-3-methylpropan-3-one, increased lipid soly. but reduced antifungal activity. Of the alpha -phenyl-beta -amino ketones, 1-dimethylamino-2-phenylbutan-3-one and 1-pyrrolidinyl-2-phenylbutan-3-one had the greatest H2O soly. and their partition coeff. was <0.4; both compds. had good antifungal activity. Increasing lipid soly. did not increase antifungal properties. 1-Diethylamino-2-phenylbutan-3-one had the greatest fungistatic activity. Also in the beta -amino propiophenone series no relation between the phys.-ch em. properties and fungistatic activity was noted. Good lipid sol. compds., such as 1-piperidino-3-p-propoxyphenylpropan-3-on e and 1-dimethylamino-2-dimethyl-3-phenylpropan-3-one, had the least activity, while hydrophilic compds., such as 1-dimethylamino-2-methyl-3-phenylpropan-3-one, were quite effective. All of the alpha -phenyl-beta -amino propiophenones, with the exception of 1-dimethylamino-2-(3-methoxyphenyl)-3-(3-methoxyphenyl)propan-3-one, showed good to very good fungistatic effects independent of their phys.-chem. properties; 1-dimethylamino-2-phenyl-3-phenylpropan-3-one, 1-dimethylamino-2-(4-chlorophenyl)-3-phenylpropan-3-one, and 1-piperidino-2-phenyl-3-phenylpropan-3-one were the most active. Chelation with Cu2+ or Fe3+ was excluded as the mechanism of action of beta -amino ketones

Cytostatics. 15. Antimicrobial and antitumor properties of nitrogen-containing stilbestrol analogs

Me2NCH2C(C6H4R-p):C(C6H4R-p)Et [I, R = H (II) or OMe (III)] were prepd. by reaction of Me2NCH2CH(C6H4R-p)COC6H4R-p with EtMgBr and dehydration of the resulting alc. with PCl3. Ether cleavage of III with AlBr3 in C6H6 gave I [R = OH (IV)]. II and IV had no estrogenic properties. II, III, and IV showed no antibacterial effects in vitro and only low activity against mouse sarcoma 180 and rat Yoshida sarcoma in vivo. II caused good inhibition of rat mammary carcinoma. The i.p. LD50 values of II, III, and IV were 120, 160, and 150 mg/kg, resp., in rats

Cytostatic drugs. 10. Relations between stability and antimicrobial activity of beta-aminoketones

The antimicrobial activity of 6 beta -aminopropio-phenones (I), 4 alpha -phenyl-beta -aminopropiophenones (II), and 2 alpha -phenyl-beta -aminoketones (III) increased with increasing in-stability in aq. solns. at pH 7.35 and 37 Deg. Compds. which did not decomp. under these physiol. conditions also showed no biol. activity. The effect of I and III was due to release of an alpha ,beta -unsatd. ketone, whereas II formed CH2O and alpha ,beta -unsatd. ketones under physiol. conditions

Relativistic effects on atomic and molecular properties of the heaviest elements

Interaction of superheavy element 112 and its homolog Hg with inert and gold surfaces was studied on the basis of atomic and molecular fully-relativistic (4-component) DFT electronic structure calculations. Performance of additional non-relativistic calculations allowed one to demonstrate the role and magnitude of relativistic effects on adsorption energies and bond distances of the studied systems. For example, on quartz, element 112 will be stronger adsorbed than Hg by about 5 kJ/mol (or at 5 degrees higher temperatures) due to the stronger van der Waals interaction. This is caused by the relativistically contracted smallest atomic radius of element 112. Non-relativistically, the trend would be opposite. On surface of gold, element 112 will be about 20 kJ/mol weaker adsorbed than Hg (i.e., it will be deposited at about 100 degrees lower temperatures than Hg). Such a decrease in ΔHads comes at the account of the weaker interaction of the relativistically stabilized 7s1/2(112) orbital with valence orbitals of gold. Still, the relatively large adsorption energy of element 112 is indicative that it is a transition metal forming intermetallic compounds with Au and other metals due to the involvement of the relativistically destabilized 6d orbitals. The influence of relativistic effects on the adsorption energy depends, however, on the adsorption position