Positive allosteric modulation of the cannabinoid CB receptor potentiates endocannabinoid signalling and changes ERK1/2 phosphorylation kinetics.

Background And Purpose: Activation of CB by exogenous agonists causes adverse effects in vivo. Positive allosteric modulation may offer improved therapeutic potential and a reduced on-target adverse effect profile compared with orthosteric agonists, due to reduced desensitisation/tolerance, but this has not been directly tested. This study investigated the ability of PAMs/ago-PAMs to induce receptor regulation pathways, including desensitisation and receptor internalisation.

Remarkable Reactivity Differences between Glucosides with Identical Leaving Groups.

Two isomeric aryl 2-deoxy-2-fluoro-β-glucosides react with a β-glucosidase at rates differing by 10-fold, despite the fact that they release the same aromatic aglycone. In contrast, the equivalent glucoside substrates react with essentially identical rate constants. Insight into the source of these surprising rate differences was obtained through a comprehensive study of the nonenzymatic (spontaneous) hydrolysis of these same substrates, wherein an approximate 10-fold difference in rates was measured, clarifying that the differences were inherent rather than being due to specific interactions with the enzyme.

Solvent effects on isotope effects: methyl cation as a model system.

The isotopic sensitivity (CH3(+) vs CD3(+)) of the equilibrium between the methyl cation in vacuum and in solution has been investigated. Two alternative options for describing the shape of the solute cavity within the widely used polarized continuum model for implicit solvation were compared; the UFF and UA0 methods give equilibrium isotope effects (EIEs) that vary as a function of the dielectric constant in opposite directions. The same isotope effect was also obtained as the average over 40 structures from a hybrid quantum mechanical/molecular mechanical molecular dynamics simulation for the methyl cation explicitly solvated by many water molecules; the inverse value of the EIE agrees with UFF but not UA0.

Tuning mechanism-based inactivators of neuraminidases: mechanistic and structural insights.

3-Fluorosialosyl fluorides are inhibitors of sialidases that function by the formation of a long-lived covalent active-site adduct and have potential as therapeutics if made specific for the pathogen sialidase. Surprisingly, human Neu2 and the Trypanosoma cruzi trans-sialidase are inactivated more rapidly by the reagent with an equatorial fluorine at C3 than by its axial epimer, with reactivation following the same pattern. To explore a possible stereoelectronic basis for this, rate constants for spontaneous hydrolysis of the full series of four 3-fluorosialosyl fluorides were measured, and ground-state energies for each computed.

Structural, mechanistic, and computational analysis of the effects of anomeric fluorines on anomeric fluoride departure in 5-fluoroxylosyl fluorides.

The effects of fluorine substitution at the C-5 center of pyranosyl fluorides on the reactivity at the C-1 anomeric center was probed by studying a series of 5-fluoroxylosyl fluoride derivatives. X-ray structures of their per-O-acetates detailed the effects on the ground-state structures. First-order rate constants for spontaneous hydrolysis, in conjunction with computational studies, revealed that changes in the stereochemistry of the 5-fluorine had minimal effects on the solvolysis rate constants and that the observed rate reductions were broadly similar to those caused by additional fluorine substitution at C-1 but significantly less than those due to substitution at C-2.

The analysis of enzymic free energy relationships using kinetic and computational models.

Free energy relationships are a ubiquitous means of characterizing trends in rates of reaction with changing molecular structure. They may be used to quantify the extent of progress along a reaction coordinate at a reaction's transition state or alternatively the extent of similarity between a reaction's transition state and some reference transformation. This critical review outlines correlative procedures for the treatment of experimentally-determined free energy relationships with a particular focus on enzyme-catalyzed group transfers.

Mechanism of glycoside hydrolysis: A comparative QM/MM molecular dynamics analysis for wild type and Y69F mutant retaining xylanases.

Computational simulations have been performed using hybrid quantum-mechanical/molecular-mechanical potentials to investigate the catalytic mechanism of the retaining endo-beta-1, 4-xylanase (BCX) from B. circulans. Two-dimensional potential-of-mean-force calculations based upon molecular dynamics with the AM1/OPLS method for wild-type BCX with a p-nitrophenyl xylobioside substrate in water clearly indicates a stepwise mechanism for glycosylation: the rate-determining step is nucleophilic substitution by Glu78 to form the covalently bonded enzyme-substrate intermediate without protonation of the leaving group by Glu172.

Probing synergy between two catalytic strategies in the glycoside hydrolase O-GlcNAcase using multiple linear free energy relationships.

Human O-GlcNAcase plays an important role in regulating the post-translational modification of serine and threonine residues with beta-O-linked N-acetylglucosamine monosaccharide unit (O-GlcNAc). The mechanism of O-GlcNAcase involves nucleophilic participation of the 2-acetamido group of the substrate to displace a glycosidically linked leaving group. The tolerance of this enzyme for variation in substrate structure has enabled us to characterize O-GlcNAcase transition states using several series of substrates to generate multiple simultaneous free-energy relationships.

Computational mutagenesis reveals the role of active-site tyrosine in stabilising a boat conformation for the substrate: QM/MM molecular dynamics studies of wild-type and mutant xylanases.

Molecular dynamics simulations have been performed for non-covalent complexes of phenyl beta-xylobioside with the retaining endo-beta-1,4-xylanase from B. circulans (BCX) and its Tyr69Phe mutant using a hybrid QM/MM methodology. A trajectory initiated for the wild-type enzyme-substrate complex with the proximal xylose ring bound at the -1 subsite (adjacent to the scissile glycosidic bond) in the (4)C(1) chair conformation shows spontaneous transformation to the (2,5)B boat conformation, and potential of mean force calculations indicate that the boat is approximately 30 kJ mol(-1) lower in free energy than the chair.

Elucidating the nature of the Streptomyces plicatus beta-hexosaminidase-bound intermediate using ab initio molecular dynamics simulations.

By using all-atom ab initio molecular dynamics simulations, the solution pK(a) of the oxazolinium ion intermediate formed during the Streptomyces plicatus beta-hexosaminidase (SpHex)-catalyzed hydrolysis of beta-D-N-acetylglucosaminides is estimated as pK(a) = 7.7. The structure and protonation state of the enzyme-bound intermediate have also been investigated, using hybrid QM/MM methods.

Glycosidase inhibitors as conformational transition state analogues.

A method for estimating the conformational similarity between hexopyranose rings is presented and used to probe the behaviour of various glycosyl hydrolase inhibitors as conformational transition state analogues.

Analysis of PUGNAc and NAG-thiazoline as transition state analogues for human O-GlcNAcase: mechanistic and structural insights into inhibitor selectivity and transition state poise.

O-GlcNAcase catalyzes the cleavage of beta-O-linked 2-acetamido-2-deoxy-beta-d-glucopyranoside (O-GlcNAc) from serine and threonine residues of post-translationally modified proteins. Two potent inhibitors of this enzyme are O-(2-acetamido-2-deoxy-d-glucopyranosylidene)amino-N-phenylcarbamate (PUGNAc) and 1,2-dideoxy-2'-methyl-alpha-d-glucopyranoso[2,1-d]-Delta2'-thiazoline (NAG-thiazoline). Derivatives of these inhibitors differ in their selectivity for human O-GlcNAcase over the functionally related human lysosomal beta-hexosamindases, with PUGNAc derivatives showing modest selectivities and NAG-thiazoline derivatives showing high selectivities.

Identification of 3-(acylamino)azepan-2-ones as stable broad-spectrum chemokine inhibitors resistant to metabolism in vivo.

3-(acylamino)glutarimides, a class of broad spectrum chemokine inhibitors, are rapidly hydrolyzed in serum, despite being stable in aqueous solution. Synthesis and high-performance liquid chromatography analysis of the proposed N-acyl-glutamate and -glutamine metabolites establish the enzyme-catalyzed breakdown pathways. In vitro assays suggest that despite their short half-life in vivo, the parent acylamino-glutarimides, not the ring-opened hydrolysis products, are the source of the antiinflammatory activity.