Selectively Fluorinated Citronellol Analogues Support a Hydrogen Bonding Donor Interaction with the Human OR1A1 Olfactory Receptor.
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ABSTRACT:
SUBMITTER: He M
PROVIDER: S-EPMC9237825 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Archaeal family-B DNA polymerases stall replication on encountering the pro-mutagenic bases uracil and hypoxanthine. This publication describes an X-ray crystal structure of Thermococcus gorgonarius polymerase in complex with a DNA containing hypoxanthine in the single-stranded region of the template, two bases ahead of the primer-template junction. Full details of the specific recognition of hypoxanthine are revealed, allowing a comparison with published data that describe uracil binding. The two bases are recognized by the same pocket, in the N-terminal domain, and make very similar protein-DNA interactions. Specificity for hypoxanthine (and uracil) arises from a combination of polymerase-base hydrogen bonds and shape fit between the deaminated bases and the pocket. The structure with hypoxanthine at position 2 explains the stimulation of the polymerase 3'-5' proofreading exonuclease, observed with deaminated bases at this location. A beta-hairpin element, involved in partitioning the primer strand between the polymerase and exonuclease active sites, inserts between the two template bases at the extreme end of the double-stranded DNA. This denatures the two complementary primer bases and directs the resulting 3' single-stranded extension toward the exonuclease active site. Finally, the relative importance of hydrogen bonding and shape fit in determining selectivity for deaminated bases has been examined using nonpolar isosteres. Affinity for both 2,4-difluorobenzene and fluorobenzimidazole, non-hydrogen bonding shape mimics of uracil and hypoxanthine, respectively, is strongly diminished, suggesting polar protein-base contacts are important. However, residual interaction with 2,4-difluorobenzene is seen, confirming a role for shape recognition.
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Project description:A series of 1,5-disubstituted tetrazole-tethered combretastatin analogues with extended hydrogen-bond donors at the ortho-positions of the aryl A and B rings were developed and evaluated for their antitubulin and antiproliferative activity. We wanted to test whether intramolecular hydrogen-bonding used as a conformational locking element in these analogues would improve their activity. The correlation of crystal structures with the antitubulin and antiproliferative profiles of the modified analogues suggested that hydrogen-bond-mediated conformational control of the A ring is deleterious to the bioactivity. In contrast, although there was no clear evidence that intramolecular hydrogen bonding to the B ring enhanced activity, we found that increased substitution on the B ring had a positive effect on antitubulin and antiproliferative activity. Among the various analogues synthesized, compounds 5d and 5e, having hydrogen-bonding donor groups at the ortho and meta-positions on the 4-methoxy phenyl B ring, are strong inhibitors of tubulin polymerization and antiproliferative agents having IC50 value in micromolar concentrations.
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Project description:DNA complementarity is expressed by way of three hydrogen bonds for a G:C base pair and two for A:T. As a result, careful control of the denaturation temperature of PCR allows selective amplification of AT-rich alleles. Yet for the same reason, the converse is not possible, selective amplification of GC-rich alleles. Inosine (I) hydrogen bonds to cytosine by two hydrogen bonds while diaminopurine (D) forms three hydrogen bonds with thymine. By substituting dATP by dDTP and dGTP by dITP in a PCR reaction, DNA is obtained in which the natural hydrogen bonding rule is inversed. When PCR is performed at limiting denaturation temperatures, it is possible to recover GC-rich viral genomes and inverted Alu elements embedded in cellular mRNAs resulting from editing by dsRNA dependent host cell adenosine deaminases. The editing of Alu elements in cellular mRNAs was strongly enhanced by type I interferon induction indicating a novel link mRNA metabolism and innate immunity.
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Project description:Chemical sensors are powerful for the fast recognition of chiral compounds. However, the established sensing systems are less effective for chiral tertiary alcohols. The chiral tertiary alcohol group is an important structural unit in natural products and drug molecules, and its enantioselective recognition represents a significant and challenging task. In this paper, a novel type of chiral bisselenourea sensor was first synthesized and used as a strong hydrogen-bonding donor for highly efficient chiral recognition of a diverse range of tertiary alcohols. The obtained sharply split NMR signals are well-distinguishable with a large (up to 0.415 ppm) chemical shift nonequivalence. The NMR signal of the hydroxyl hydrogen atom was first employed for enantiomeric excess determination of tertiary alcohols, giving accurate results with <2% absolute errors. The 2D NOESY spectra and computational studies suggest that the geometrical differentiation of the formed diastereomeric complexes between the sensor and tertiary alcohols enables the chiral discrimination of the hydroxyl hydrogen signals of the tertiary alcohol in the 1H NMR spectrum.
| S-EPMC5953003 | biostudies-literature
Project description:Synthetic polypeptides have received increasing attention due to their ability to form higher ordered structures similar to proteins. The control over their secondary structures, which enables dynamic conformational changes, is primarily accomplished by tuning the side-chain hydrophobic or ionic interactions. Herein we report a strategy to modulate the conformation of polypeptides utilizing donor-acceptor interactions emanating from side-chain H-bonding ligands. Specifically, 1,2,3-triazole groups, when incorporated onto polypeptide side-chains, serve as both H-bond donors and acceptors at neutral pH and disrupt the α-helical conformation. When protonated, the resulting 1,2,3-triazolium ions lose the ability to act as H-bond acceptors, and the polypeptides regain their α-helical structure. The conformational change of triazole polypeptides in response to the donor-acceptor pattern was conclusively demonstrated using both experimental-based and simulation-based methods. We further showed the utility of this transition by designing smart, cell-penetrating polymers that undergo acid-activated endosomal escape in living cells.Hydrogen bonding plays a major role in determining the tridimensional structure of biopolymers. Here, the authors show that control over a polypeptide conformation can be achieved by altering the donor-acceptor properties of side-chain triazole units via protonation-deprotonation.
| S-EPMC5522480 | biostudies-literature
Project description:For the first time, the intermolecular orbital interaction between benzene and methane in the benzene-methane complex, a representative of weak interaction system, has been studied by us using ab initio calculations based on different methods and basis sets. Our results demonstrate obvious intermolecular orbital interaction between benzene and methane involving orbital overlaps including both occupied and unoccupied orbitals. Similar to interatomic orbital interaction, the intermolecular interaction of orbitals forms "bonding" and "antibonding" orbitals. In the interaction between occupied orbitals, the total energy of the complex increases because of the occupation of the antibonding orbital. The existence of the CH-π hydrogen bond between benzene and methane causes a decrease in rest energy level, leading to at least -1.51 kcal/mol intermolecular interaction energy. Our finding extends the concept of orbital interaction from the intramolecular to the intermolecular regime and gives a reliable explanation of the deep orbital reformation in the benzene-methane complex.
| S-EPMC4772115 | biostudies-literature
Project description:Fluoro- and chloro-phosphasilynes [X-Si[triple bond, length as m-dash]P (X = F, Cl)] belong to a class of illusive chemical species which are expected to have Si[triple bond, length as m-dash]P multiple bonds. Theoretical investigations of the bonding and stability of the corresponding Lewis base-stabilized species (L')PSi(X)(L) [L' = cAACMe (cyclic alkyl(amino) carbene); L = cAACMe, NHCMe (N-heterocyclic carbene), PMe3, aAAC (acyclic alkyl(amino) carbene); X = Cl, F] have been studied using the energy decomposition analysis-natural orbitals for chemical valence (EDA-NOCV) method. The variation of the ligands (L) on the Si-atom leads to different bonding scenarios depending on their σ-donation and π-back acceptance properties. The ligands with higher lying HOMOs prefer profoundly different bonding scenarios than the ligands with lower lying HOMOs. The type of halogen (Cl or F) on the Si-atom was also found to have a significant influence on the overall bonding scenario. The reasonably higher value and endergonic nature of the dissociation energies along with the appreciable HOMO-LUMO energy gap may corroborate to the synthetic viability of the homo and heteroleptic ligand-stabilized elusive PSi(Cl/F) species in the laboratory.
| S-EPMC8694932 | biostudies-literature
Project description:The anhydrous salts morpholinium (tetra-hydro-2-H-1,4-oxazin-4-ium) phen-oxy-acetate, C4H10NO(+)·C8H7O3 (-), (I), morpholinium (4-fluoro-phen-oxy)acetate, C4H10NO(+)·C8H6 FO3 (-), (II), and isomeric morpholinium (3,5-di-chloro-phen-oxy)acetate (3,5-D), (III), and morpholinium (2,4-di-chloro-phen-oxy)acetic acid (2,4-D), C4H10NO(+)·C8H5Cl2O3 (-), (IV), have been determined and their hydrogen-bonded structures are described. In the crystals of (I), (III) and (IV), one of the the aminium H atoms is involved in a three-centre asymmetric cation-anion N-H⋯O,O' R 1 (2)(4) hydrogen-bonding inter-action with the two carboxyl O-atom acceptors of the anion. With the structure of (II), the primary N-H⋯O inter-action is linear. In the structures of (I), (II) and (III), the second N-H⋯Ocarbox-yl hydrogen bond generates one-dimensional chain structures extending in all cases along [100]. With (IV), the ion pairs are linked though inversion-related N-H⋯O hydrogen bonds [graph set R 4 (2)(8)], giving a cyclic hetero-tetra-meric structure.
| S-EPMC4645053 | biostudies-literature
Project description:Substrate-support interactions play an important role in the catalytic hydrogenation of phenolic compounds by ceria-supported palladium (Pd/CeO2). Here, we combine surface contrast solution NMR methods and reaction kinetic assays to investigate the role of substrate-support interactions in phenol (PhOH) hydrogenation catalyzed by titania-supported palladium (Pd/TiO2). We show that PhOH adsorbs on the catalyst via a weak hydrogen-bonding interaction between the -OH group of the substrate and one oxygen atom on the support. Interestingly, we observe that the addition of 20 mM inorganic phosphate results in a ∼2-fold destabilization of the PhOH-support interaction and a corresponding ∼2-fold inhibition of the catalytic reaction, suggesting an active role of the PhOH-TiO2 hydrogen bond in catalysis. A comparison of the data measured here with the results previously reported for a Pd/CeO2 catalyst indicates that the efficiency of the Pd-supported catalysts is correlated to the amount of PhOH hydrogen bonded to the metal oxide support. Since CeO2 and TiO2 have similar ability to uptake activated hydrogen from a noble metal site, these data suggest that hydrogen spillover is the main mechanism by which Pd-activated hydrogens are shuttled to the PhOH adsorbed on the surface of the support. Consistent with this hypothesis, Pd supported on a non-reducible metal oxide (silica) displays negligible hydrogenation activity. Therefore, we conclude that basic and reducible metal oxides are active supports for the efficient hydrogenation of phenolic compounds due to their ability to hydrogen bond to the substrate and mediate the addition of the activated hydrogens to the adsorbed aromatic ring.
| S-EPMC10717535 | biostudies-literature
Project description:The conformational equilibria of selectively halogenated cyclohexanes are explored both experimentally (VT-NMR) for 1,1,4,-trifluorocyclohexane 7 and by computational analysis (M06-2X/aug-cc-pVTZ level), with the latter approach extending to a wider range of more highly fluorinated cyclohexanes. Perhaps unexpectedly, 7ax is preferred over the 7eq conformation by ΔG = 1.06 kcal mol-1, contradicting the accepted norm for substituents on cyclohexanes. The axial preference is stronger again in 1,1,3,3,4,5,5,-heptafluorocyclohexane 9 (ΔG = 2.73 kcal mol-1) as the CF2 groups further polarize the isolated CH2 hydrogens. Theoretical decomposition of electrostatic and hyperconjugative effects by natural bond orbital analysis indicated that nonclassical hydrogen bonding (NCHB) between the C-4 fluorine and the diaxial hydrogens at C-2 and C-6 in cyclohexane 7 and 9 largely accounts for the observed bias. The study extended to changing fluorine (F) for chlorine (Cl) and bromine (Br) at the pseudoanomeric position in the cyclohexanes. Although these halogens do not become involved in NCHBs, they polarize the geminal -CHX- hydrogen at the pseudoanomeric position to a greater extent than fluorine, and consequent electrostatic interactions influence conformer stabilities.
| S-EPMC10949234 | biostudies-literature