Evangelia D. Chrysina

Bio: Evangelia D. Chrysina is an academic researcher from University of Bath. The author has contributed to research in topics: Glycogen phosphorylase & Ligand (biochemistry). The author has an hindex of 23, co-authored 61 publications receiving 1684 citations. Previous affiliations of Evangelia D. Chrysina include University of Oxford.

New Inhibitors of Glycogen Phosphorylase as Potential Antidiabetic Agents

Abstract: The protein glycogen phosphorylase has been linked to type 2 diabetes, indicating the importance of this target to human health Hence, the search for potent and selective inhibitors of this enzyme, which may lead to antihyperglycaemic drugs, has received particular attention Glycogen phosphorylase is a typical allosteric protein with five different ligand binding sites, thus offering multiple opportunities for modulation of enzyme activity The present survey is focused on recent new molecules, potential inhibitors of the enzyme The biological activity can be modified by these molecules through direct binding, allosteric effects or other structural changes Progress in our understanding of the mechanism of action of these inhibitors has been made by the determination of high-resolution enzyme inhibitor structures (both muscle and liver) The knowledge of the three-dimensional structures of protein-ligand complexes allows analysis of how the ligands interact with the target and has the potential to facilitate structure-based drug design In this review, the synthesis, structure determination and computational studies of the most recent inhibitors of glycogen phosphorylase at the different binding sites are presented and analyzed

Kinetic and crystallographic studies on 2-(beta-D-glucopyranosyl)-5-methyl-1, 3, 4-oxadiazole, -benzothiazole, and -benzimidazole, inhibitors of muscle glycogen phosphorylase b. Evidence for a new binding site.

Abstract: Glycogen phosphorylase (GP), because of its central role in glycogen metabolism, has been exploited as a potential target for structure-based design of potent inhibitors, that may be relevant to the control of blood glucose concentrations in type 2 diabetes (Aiston et al. 2001, 2003; Latsis et al. 2002). Several regulatory binding sites, identified in GP, have been used as molecular targets (for review, see Oikonomakos 2002). These are the allosteric site that binds the activator AMP and the inhibitor glucose-6-P, the catalytic site that binds substrates glucose-1-P and glycogen, and the inhibitor glucose, the caffeine binding site, which binds caffeine and related compounds, and the new allosteric inhibitor or indole binding site that binds indole-2 carboxamides and β-D-glucopyranosyl ureas. More specifically, the catalytic site has been probed with glucose analog inhibitors, designed on the basis of information derived from the crystal structure of T-state GPb–α-D-glucose complex (Martin et al. 1991; Watson et al. 1994, 1995; Bichard et al. 1995; Oikonomakos et al. 1995, 2002a, b; Gregoriou et al. 1998; Somsak et al. 2001, 2003; Chrysina et al. 2003, 2004; Gyorgydeak et al. 2004). A common feature of these compounds is that upon binding at the catalytic site, they promote the (less active) T-state conformation of the enzyme through stabilization of the closed position of 280s loop (residues 282–287), which blocks access of the substrate to the catalytic site. We report here on the kinetic and crystallographic study of three new lead compounds, derivatives of β-D-glucopy-ranose, 2-(β-D-glucopyranosyl)-5-methyl-1,3,4-oxadiazole, 2-(β-D-glucopyranosyl)-benzothiazole, and 2-(β-D-gluco-pyranosyl)-benzimidazole with GPb. The kinetic experiments reveal that the three compounds are potent competitive inhibitors with respect to the substrate Glc-1-P, whereas the crystallographic results show that each of the compounds binds at the catalytic site and stabilizes the closed position of the 280s loop. Additionally, benzimidazole can occupy the indole binding site and also a novel site that has not been observed previously. Benzimidazole is the first compound to show binding at this novel site.

Role of conserved residues in structure and stability: Tryptophans of human serum retinol-binding protein, a model for the lipocalin superfamily

Abstract: Serum retinol binding protein (RBP) is a member of the lipocalin family, proteins with up-and-down β-barrel folds, low levels of sequence identity, and diverse functions. Although tryptophan 24 of RBP is highly conserved among lipocalins, it does not play a direct role in activity. To determine if Trp24 and other conserved residues have roles in stability and/or folding, we investigated the effects of conservative substitutions for the four tryptophans and some adjacent residues on the structure, stability, and spectroscopic properties of apo-RBP. Crystal structures of recombinant human apo-RBP and of a mutant with substitutions for tryptophans 67 and 91 at 1.7 A and 2.0 A resolution, respectively, as well as stability measurements, indicate that these relatively exposed tryptophans have little influence on structure or stability. Although Trp105 is largely buried in the wall of the β-barrel, it can be replaced with minor effects on stability to thermal and chemical unfolding. In contrast, substitutions of three different amino acids for Trp24 or replacement of Arg139, a conserved residue that interacts with Trp24, lead to similar large losses in stability and lower yields of native protein generated by in vitro folding. The results and the coordinated nature of natural substitutions at these sites support the idea that conserved residues in functionally divergent homologs have roles in stabilizing the native relative to misfolded structures. They also establish conditions for studies of the kinetics of folding and unfolding by ideying spectroscopic signals for monitoring the formation of different substructures.

Chemistry and Biology Of Multicomponent Reactions

Abstract: Multicomponent reactions (MCRs) are one-pot reactions employing more than two starting materials, e.g. 3, 4, … 7, where most of the atoms of the starting materials are incorporated in the final product.1 Several descriptive tags are regularly attached to MCRs (Fig. 1): they are atom economic, e.g. the majority if not all of the atoms of the starting materials are incorporated in the product; they are efficient, e.g. they efficiently yield the product since the product is formed in one-step instead of multiple sequential steps; they are convergent, e.g. several starting materials combine in one reaction to form the product; they exhibit a very high bond-forming-index (BFI), e.g. several non-hydrogen atom bonds are formed in one synthetic transformation.2 Therefore MCRs are often a useful alternative to sequential multistep synthesis. Open in a separate window Figure 1 Above: multistep syntheses can be divergent (sequential) or convergent; below: in analogy MCR reactions are convergent and one or two component reactions are divergent or less convergent.

Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields

Abstract: : The unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio. Harmonic force fields are obtained using Density Functional Theory (DFT), MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set. DFT calculations use the Local Spin Density Approximation (LSDA), BLYP, and Becke3LYP (B3LYP) density functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with experiment. The MP2 force field yields spectra in slightly worse agreement with experiment than the B3LYP force field. The SCF force field yields spectra in poor agreement with experiment.The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreements with experiment. jg

Calculation of protein-ligand binding affinities.

Abstract: Accurate methods of computing the affinity of a small molecule with a protein are needed to speed the discovery of new medications and biological probes. This paper reviews physics-based models of binding, beginning with a summary of the changes in potential energy, solvation energy, and configurational entropy that influence affinity, and a theoretical overview to frame the discussion of specific computational approaches. Important advances are reported in modeling protein-ligand energetics, such as the incorporation of electronic polarization and the use of quantum mechanical methods. Recent calculations suggest that changes in configurational entropy strongly oppose binding and must be included if accurate affinities are to be obtained. The linear interaction energy (LIE) and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) methods are analyzed, as are free energy pathway methods, which show promise and may be ready for more extensive testing. Ultimately, major improvements in modeling accuracy will likely require advances on multiple fronts, as well as continued validation against experiment.