Dominique Dehareng

Mercaptophosphonate Compounds as Broad-Spectrum Inhibitors of the Metallo-β-lactamases

Although commercialized inhibitors of active site serine beta-lactamases are currently used in coadministration with antibiotic therapy, no clinically useful inhibitors of metallo-beta-lactamases (MBLs) have yet been discovered. In this paper, we investigated the inhibitory effect of mercaptophosphonate derivatives against the three subclasses of MBLs (B1, B2, and B3). All 14 tested mercaptophosphonates, with the exception of 1a, behaved as competitive inhibitors for the three subclasses. Apart from 13 and 21, all the mercaptophosphonates tested exhibit a good inhibitory effect on the subclass B2 MBL CphA with low inhibition constants (K(i) < 15 muM). Interestingly, compound 18 turned out to be a potent broad spectrum MBL inhibitor. The crystallographic structures of the CphA-10a and CphA-18 complexes indicated that the sulfur atom of 10a and the phosphonato group of 18 interact with the Zn(2+) ion, respectively. Molecular modeling studies of the interactions between compounds 10a and 18 and the VIM-4 (B1), CphA (B2), and FEZ-1 (B3) enzymes brought to light different binding modes depending on the enzyme and the inhibitor, consistent with the crystallographic structures.

Dynamical study of non adiabatic unimolecular reactions: The conical intersection between the B 2B2 and à 2A1 states of H2O+.

The conical intersection connecting the B 2A′ and A 2A′ states of the H2O+ ion is studied. The two potential energy surfaces are calculated ab initio by the SCF/CI method within the CS point group. The nonadiabatic coupling matrix elements 〈A‖∂/∂q‖B〉 are computed for several cross sections throughout the potential energy surfaces. A transformation to the diabatic representation is performed. The linear model is found to be a good approximation in the region close to the apex of the cone. The global functions t(s) and T(S) governing the nonadiabatic transition probability are calculated; their shapes are those predicted by the Landau–Zener model (in the Nikitin bidimensional version). A dynamical study is undertaken by means of classical trajectory calculations on the upper adiabatic potential energy surface. An averaged transition probability Ptr is derived. Excitation of rotation or of the bending mode of H2O before photon impact has no influence on Ptr. Excitation of the symmetrical or antisymmetr...

NMR Structure of Citrobacter freundii AmpD, Comparison with Bacteriophage T7 Lysozyme and Homology with PGRP Domains

AmpD is a bacterial amidase involved in the recycling of cell-wall fragments in Gram-negative bacteria. Inactivation of AmpD leads to derepression of beta-lactamase expression, presenting a major pathway for the acquisition of constitutive antibiotic resistance. Here, we report the NMR structure of AmpD from Citrobacter freundii (PDB accession code 1J3G). A deep substrate-binding pocket explains the observed specificity for low molecular mass substrates. The fold is related to that of bacteriophage T7 lysozyme. Both proteins bind zinc at a conserved site and require zinc for amidase activity, although the enzymatic mechanism seems to differ in detail. The structure-based sequence alignment identifies conserved features that are also conserved in the eukaryotic peptidoglycan recognition protein (PGRP) domains, including the zinc-coordination site in several of them. PGRP domains thus belong to the same fold family and, where zinc-binding residues are conserved, may have amidase activity. This hypothesis is supported by the observation that human serum N-acetylmuramyl-L-alanine amidase seems to be identical with a soluble form of human PGRP-L.

Energy analysis on small to medium sized H-bonded complexes

SummaryDimers (water-methanol, guanine-cytosine) as well as trimers (methanol-water-imidazole, formamide-methylformate-formamide), are studied as H-bonded complexes of increasing complexity. All the investigated conformations have been fully optimized. In particular, it is the first time that all the intra-and intermolecular parameters of the guanine-cytosine complex are left variable. In minimal basis sets, the planar conformation has been found to be a first-order critical point. The minimal basis set MINI-1 has been adapted to provide nearly planar amides. The stability of the complexes is accounted for by four energy components of the same order: the first-order term (electrostatic + exchange), the polarization, the charge transfer and the correlation terms. In the case of the studied trimers, the energy components, apart from the electrostatic one, have been found to be nearly additive.

Constructing approximately diabatic states from LCAO‐SCF‐CI calculations

We consider here two approaches which have been proposed in the literature to obtain diabatic states from ab initio calculations. First, by calculating explicitly the coupling vector g=〈ψ2‖∇ψ1〉 which describes the nonadiabatic interaction between two adiabatic states ψ1 and ψ2. Second, by some extrapolation process of the wave functions obtained at a particular reference point. The coupling vector g is the sum of three contributions: g=gCI+gLCAO+gAO. The first two represent the change in character of the adiabatic states in the region of nonadiabatic coupling due to the variation of the CI and LCAO coefficients, whereas gAO results from the translation of the atomic orbitals with the moving nuclear centers. Criteria have been given to recognize when it is possible to transform a set of CI wave functions into a pair of useful diabatic states. A particularly favorable situation is obtained when the interacting electronic states are doubly excited with respect to each other. Within the two‐state approximatio...

Critical role of tryptophan 154 for the activity and stability of class D beta-lactamases.

The catalytic efficiency of the class D beta-lactamase OXA-10 depends critically on an unusual carboxylated lysine as the general base residue for both the enzyme acylation and deacylation steps of catalysis. Evidence is presented that the interaction between the indole group of Trp154 and the carboxylated lysine is essential for the stability of the posttranslationally modified Lys70. Substitution of Trp154 by Gly, Ala, or Phe yielded noncarboxylated enzymes which displayed poor catalytic efficiencies and reduced stability when compared to the wild-type OXA-10. The W154H mutant was partially carboxylated. In addition, the maximum values of k(cat) and k(cat)/K(M) were shifted toward pH 7, indicating that the carboxylation state of Lys70 is dependent on the protonation level of the histidine. A comparison of the three-dimensional structures of the different proteins also indicated that the Trp154 mutations did not modify the overall structures of OXA-10 but induced an increased flexibility of the Omega-loop in the active site. Finally, the deacylation-impaired W154A mutant was used to determine the structure of the acyl-enzyme complex with benzylpenicillin. These results indicate a role of the Lys70 carboxylation during the deacylation step and emphasize the importance of Trp154 for the ideal positioning of active site residues leading to an optimum activity.

Importance of the Conserved Residues in the Peptidoglycan Glycosyltransferase Module of the Class A Penicillin-binding Protein 1b of Escherichia coli

The peptidoglycan glycosyltransferase (GT) module of class A penicillin-binding proteins (PBPs) and monofunctional GTs catalyze glycan chain elongation of the bacterial cell wall. These enzymes belong to the GT51 family, are characterized by five conserved motifs, and have some fold similarity with the phage λ lysozyme. In this work, we have systematically modified all the conserved amino acid residues of the GT module of Escherichia coli class A PBP1b by site-directed mutagenesis and determined their importance for the in vivo and in vitro activity and the thermostability of the protein. To get an insight into the GT active site of this paradigm enzyme, a model of PBP1b GT domain was constructed based on the available crystal structures (PDB codes 2OLV and 2OLU). The data show that in addition to the essential glutamate residues Glu233 of motif 1 and Glu290 of motif 3, the residues Phe237 and His240 of motif 1 and Gly264, Thr267, Gln271, and Lys274 of motif 2, all located in the catalytic cavity of the GT domain, are essential for the in vitro enzymatic activity of the PBP1b and for its in vivo functioning. Thus, the first three conserved motifs contain most of the residues that are required for the GT activity of the PBP1b. The residues Asp234, Phe237, His240, Thr267, and Gln271 are proposed to maintain the structure of the active site and the positioning of the catalytic Glu233.

Mutational analysis of the catalytic centre of the Citrobacter freundii AmpD N-acetylmuramyl-L-alanine amidase

Citrobacter freundii AmpD is an intracellular 1,6-anhydro-N-acetylmuramyl-L-alanine amidase involved in both peptidoglycan recycling and beta-lactamase induction. AmpD exhibits a strict specificity for 1,6-anhydromuropeptides and requires zinc for enzymic activity. The AmpD three-dimensional structure exhibits a fold similar to that of another Zn2+ N-acetylmuramyl-L-alanine amidase, the T7 lysozyme, and these two enzymes define a new family of Zn-amidases which can be related to the eukaryotic PGRP (peptidoglycan-recognition protein) domains. In an attempt to assign the different zinc ligands and to probe the catalytic mechanism of AmpD amidase, molecular modelling based on the NMR structure and site-directed mutagenesis were performed. Mutation of the two residues presumed to act as zinc ligands into alanine (H34A and D164A) yielded inactive proteins which had also lost their ability to bind zinc. By contrast, the active H154N mutant retained the capacity to bind the metal ion. Three other residues which could be involved in the AmpD catalytic mechanism have been mutated (Y63F, E116A, K162H and K162Q). The E116A mutant was inactive, but on the basis of the molecular modelling this residue is not directly involved in the catalytic mechanism, but rather in the binding of the zinc by contributing to the correct orientation of His-34. The K162H and K162Q mutants retained very low activity (0.7 and 0.2% of the wild-type activity respectively), whereas the Y63F mutant showed 16% of the wild-type activity. These three latter mutants exhibited a good affinity for Zn ions and the substituted residues are probably involved in the binding of the substrate. We also describe a new method for generating the N-acetylglucosaminyl-1,6-anhydro-N-acetylmuramyl-tripeptide AmpD substrate from purified peptidoglycan by the combined action of two hydrolytic enzymes.

Electrostatic potential maps at the quantum chemistry level of the active sites of the serine peptidases, α-chymotrypsin and subtilisin

The electronic properties of the active-sites of the structurally unrelated serine peptidases, alpha-chymotrypsin and subtilisin, have been expressed in the form of three-dimensional electrostatic potential maps derived from integrals calculated at the quantum chemistry level. As a consequence of the asymmetrical distribution of the secondary structures that occur within a 7 A sphere around the serine of the catalytic triad, the active sites are highly polarized entities and exhibit large dipole moments. One part of the active sites generates a nucleophilic suction-pump. Its isocontour at -10 kcal mol-1 defines an impressive, negatively-charged volume which bears a narrow channel in the immediate vicinity of the active-site serine 195 in alpha-chymotrypsin or 221 in subtilisin. In native alpha-chymotrypsin, there is a perfect complementation between this nucleophilic suction-pump and the positively-charged electrophilic hole that is generated by the backbone NH of Ser 195 and Gly 193. In subtilisin, generation of the complementing electrophilic hole requires binding of a carbonyl donor ligand and may be achieved by rotation of the side-chain amide of Asn 155 towards the backbone NH of Ser 221. Small variations in the atomic co-ordinates of alpha-chymotrypsin used for the calculations, the presence of water molecules in its active site and the occurrence of point mutations in the amino acid sequence of subtilisin have little effects on the shape and characteristics of the electrostatic potential.

Critical points and reaction paths characterization on a potential energy hypersurface

Most of the time, the definitions of minima, saddle points or more generally order p (p=0,…,n) critical points, do not mention the possibility of having zero Hessian eigenvalues. This feature reflects some flatness of the potential energy hypersurface in a special eigendirection which is not often taken into account. Thus, the definitions of critical points are revisited in a more general framework within this context. The concepts of bifurcation points, branching points, and valley ridge inflection points are investigated. New definitions based on the mathematical formulation of the reaction path are given and some of their properties are outlined.