Search results for "conformation"

Exploring kainate receptor pharmacology using molecular dynamics simulations.

2010

Ionotropic glutamate receptors (iGluRs) are enticing targets for pharmaceutical research; however, the search for selective ligands is a laborious experimental process. Here we introduce a purely computational procedure as an approach to evaluate ligand–iGluR pharmacology. The ligands are docked into the closed ligand-binding domain and during the molecular dynamics (MD) simulation the bi-lobed interface either opens (partial agonist/antagonist) or stays closed (agonist) according to the properties of the ligand. The procedure is tested with closely related set of analogs of the marine toxin dysiherbaine bound to GluK1 kainate receptor. The modeling is set against the abundant binding data …

Structural Mechanism of N-Methyl-D-Aspartate Receptor Type 1 Partial Agonism

2012

N-methyl-D-aspartate (NMDA) receptors belong to a family of ionotropic glutamate receptors that contribute to the signal transmission in the central nervous system. NMDA receptors are heterotetramers that usually consist of two GluN1 and GluN2 monomers. The extracellular ligand-binding domain (LBD) of a monomer is comprised of discontinuous segments that form the functional domains D1 and D2. While the binding of a full agonist glycine to LBD of GluN1 is linked to cleft closure and subsequent ion-channel opening, partial agonists are known to activate the receptor only sub-maximally. Although the crystal structures of the LBD of related GluA2 receptor explain the mechanism for the partial a…

Conformational studies into N-methylation of alanine diamide models: A quantitative approach

2006

Abstract A systematic theoretical analysis was performed on N -acetyl- l -alanine N ′-methylamide (Ac- l -Ala-NHMe) and the analogues methylated on the N-terminus (Ac- l -(Me)Ala-NHMe), C-terminus (Ac- l -Ala-NMe 2 ), and both N/C-termini (Ac- l -(Me)Ala-NMe 2 ), to evaluate the influence of methylation of the amide group on the conformational properties of the affected residues. The ϕ , ψ potential energy surfaces were calculated at the B3LYP/6-31+G**//HF/3-21G level of theory with inclusion of the solvent (water) effect (SCRF method). The conformers localised were fully optimised at the B3LYP/6-31+G** in vacuo. The accessible areas of the potential energy surfaces; the number of conformer…

Synthesis of terpenoid unsaturated 1,4-dialdehydes. Pi-facial selectivity in the Diels-Alder reaction of the 1-vinyl-2-methylcyclohexene moiety of po…

2000

Unsaturated syn- and anti-1,2-Amino Alcohols by Cyclization of Allylic Bis-trichloroacetimidates. Stereoselectivity Dependence on Substrate Configura…

2014

Disubstituted allylic bis-imidates undergo Lewis acid catalyzed or spontaneous cyclization to oxazolines, which are precursors of unsaturated amino alcohols. Stereoselectivity of the cyclization is mainly determined by the substrate configuration. Highly selective cis-oxazoline formation is achieved starting from anti-E-bis-imidates while trans-oxazoline predominantly forms from anti-Z-bis-imidates. On the basis of DFT calculations, the stereoselectivity trends can be explained by the formation of the energetically most stable carbenium ion conformation, followed by the cyclization via most favorable bond rotations.

Design of P-Chirogenic Aminophosphine-Phosphinite Ligands at Both Phosphorus Centers: Origin of Enantioselectivities in Pd-Catalyzed Allylic Reaction…

2020

International audience; We have recently patented an unprecedented stereospecific N→O phosphinyl migration process which transforms P-chirogenic aminophosphines into phosphinites. A fine design of aminophosphine phosphinite ligands (AMPP*) derived from ephedrine and bearing a P-chirogenic center either at the aminophosphine or phosphinite moiety, was performed. The synthesis of AMPP* ligands with P-chirogenic aminophosphine moiety was based on the well-established stereospecific reaction of oxazaphospholidine-borane with organolithium reagents, followed by trapping with a chlorophosphine and borane decomplexation. Concurrently, the preparation of AMPP* ligands with P-chirogenic phosphinite …

Design and synthesis of new trehalose-conjugated pentapeptides as inhibitors of Aβ(1-42) fibrillogenesis and toxicity

2009

Aggregation of the amyloid A? peptide and its accumulation into insoluble deposits (plaques) are believed to be the main cause of neuronal dysfunction associated with Alzheimer's disease (AD); small molecules that can interfere with the A? amyloid fibril formation are therefore of interest for a potential therapeutic strategy. Three new trehalose-conjugated peptides of the well known ?-sheet breaker peptide iA?5p,were synthesized. The disaccharide was covalently attached to different sites of the LPFFD peptide chain, i.e. at the N-terminus, C-terminus or at the Asp side chain. CD spectroscopy in different solvents was used to assess changes in the peptide conformation of these compounds. Th…

Thermodynamic versus Conformational Metastability in Fibril-Forming Lysozyme Solutions

2012

The role of intermolecular interaction in fibril-forming protein solutions and its relation with molecular conformation is a crucial aspect for the control and inhibition of amyloid structures. Here, we study the fibril formation and the protein-protein interactions of lysozyme at acidic pH and low ionic strength. The amyloid formation occurs after a long lag time and is preceded by the formation of oligomers, which seems to be off-pathway with respect to fibrillation. By measuring the osmotic isothermal compressibility and the collective diffusion coefficient of lysozyme in solution, we observe that the monomeric solution is kept in a thermodynamically metastable state by strong electrosta…

Oligonucleotides in Sensing and Diagnostic Applications

2015

Highlights on contemporary recognition and sensing of fluoride anion in solution and in the solid state

2012

The fluoride anion has recently gained well deserved attention among the scientific community for its importance in many fields of human activities, but also for concerns on its effect on health and the environment. Although surprisingly overlooked in systematic studies in the past, fluoride has nowadays become a topical target in the field of anion recognition. A multitude of scientific reports are published every year where the establishment of efficient and specific interaction with fluoride is sought in polar and aqueous media. Here, the emphasis is directed to a detailed description of the most interesting contemporary studies in the field, with a particular focus given to those publis…