Rational design of a beta-lactamase inhibitor achieved via stabilization of the trans-enamine intermediate: 1.28 A crystal structure of wt SHV-1 complex with a penam sulfone

beta-Lactamases are one of the major causes of antibiotic resistance in Gram negative bacteria. The continuing evolution of beta-lactamases that are capable of hydrolyzing our most potent beta-lactams presents a vexing clinical problem, in particular since a number of them are resistant to inhibitors. The efficient inhibition of these enzymes is therefore of great clinical importance. Building upon our previous structural studies that examined tazobactam trapped as a trans-enamine intermediate in a deacylation deficient SHV variant, we designed a novel penam sulfone derivative that forms a more stable trans-enamine intermediate. We report here the 1.28 A resolution crystal structure of wt SHV-1 in complex with a rationally designed penam sulfone, SA2-13. The compound is covalently bound to the active site of wt SHV-1 similar to tazobactam yet forms an additional salt-bridge with K234 and hydrogen bonds with S130 and T235 to stabilize the trans-enamine intermediate. Kinetic measurements show that SA2-13, once reacted with SHV-1 beta-lactamase, is about 10-fold slower at being released from the enzyme compared to tazobactam. Stabilizing the trans-enamine intermediate represents a novel strategy for the rational design of mechanism-based class A beta-lactamase inhibitors.     

Highly convergent three component benzyne coupling: the total synthesis of ent-clavilactone B

The first total synthesis of (+)-clavilactone B, a potent antifungal agent and novel tyrosine kinase inhibitor, is described. The absolute configuration of clavilactones has been unambiguously established by using Sharpless asymmetric epoxidation to generate the enantiomerically pure substrate. The strategy highlights the use of a powerful and convergent three-component benzyne coupling with a methylallyl Grignard and a chiral epoxy-aldehyde to generate two C-C bonds and install the carbon skeleton of clavilactone. Oxidative lactonization, ten-membered ring construction by ring closing metathesis, and oxidation gave clavilactone B.     

Development of novel statistical potentials describing cation-pi interactions in proteins and comparison with semiempirical and quantum chemistry approaches

Novel statistical potentials derived from known protein structures are presented. They are designed to describe cation-pi and amino-pi interactions between a positively charged amino acid or an amino acid carrying a partially charged amino group and an aromatic moiety. These potentials are based on the propensity of residue types to be separated by a certain spatial distance or to have a given relative orientation. Several such potentials, describing different kinds of correlations between residue types, distances, and orientations, are derived and combined in a way that maximizes their information content and minimizes their redundancy. To test the ability of these potentials to describe cation-pi and amino-pi systems, we compare their energies with those computed with the CHARMM molecular mechanics force field and with quantum chemistry calculations at the Hartree-Fock level (HF) and at the second order of the M?ller-Plesset perturbation theory (MP2). The latter calculations are performed in the gas phase and in acetone, in order to mimic the average dielectric constant of protein environments. The energies computed with the best of our statistical potentials and with gas-phase HF or MP2 show correlation coefficients up to 0.96 when considering one side-chain degree of freedom in the statistical potentials and up to 0.94 when using a totally simplified model excluding all side-chain degrees of freedom. These potentials perform as well as, or better than, the CHARMM molecular mechanics force field that uses a much more detailed protein representation. The good performance of our cation-pi statistical potentials suggests their utility in protein structure and stability prediction and in protein design.     

Recent trends in the liquid chromatography–mass spectrometry analysis of organic contaminants in environmental samples

An overview of liquid chromatography–mass spectrometry methods used for the determination of trace organic contaminants in environmental samples is presented. Among the organic contaminants the focus is given on five groups of emerging contaminants that raised most concern as environmental contaminants and therefore attracted attention of a research community: pharmaceuticals, drugs of abuse, polar pesticides, perfluorinated compounds and nanoparticles. Various aspects of current LC–MS methodology, using tandem and hybrid MS instruments, including sample preparation, are discussed.     

Cell-penetrant, nanomolar O-GlcNAcase inhibitors selective against lysosomal hexosaminidases

Posttranslational modification of metazoan nucleocytoplasmic proteins with N-acetylglucosamine (O-GlcNAc) is essential, dynamic, and inducible and can compete with protein phosphorylation in signal transduction. Inhibitors of O-GlcNAcase, the enzyme removing O-GlcNAc, are useful tools for studying the role of O-GlcNAc in a range of cellular processes. We report the discovery of nanomolar OGA inhibitors that are up to 900,000-fold selective over the related lysosomal hexosaminidases. When applied at nanomolar concentrations on live cells, these cell-penetrant molecules shift the O-GlcNAc equilibrium toward hyper-O-GlcNAcylation with EC?? values down to 3 nM and are thus invaluable tools for the study of O-GlcNAc cell biology.     

Effects of surface site distribution and dielectric discontinuity on the charging behavior of nanoparticles: a grand canonical Monte Carlo study

The surface site distribution and the dielectric discontinuity effects on the charging process of a spherical nanoparticle (NP) have been investigated. It is well known that electrostatic repulsion between charges on neighbouring sites tends to decrease the effective charge of a NP. The situation is more complicated close to a dielectric breakdown, since here a charged site is not only interacting with its neighbours but also with its own image charge and the image charges of all its neighbours. Coexistence of opposite charges, titration sites positions, and pH dependence are systematically studied using a grand canonical Monte Carlo method. A Tanford and Kirkwood approach has been applied to describe the interaction potentials between explicit discrete ampholytic charging sites. Homogeneous, heterogeneous and patch site distributions were considered to reproduce the titration site distribution at the solid/solution interface of natural NPs. Results show that the charging process is controlled by the balance between Coulomb interactions and the reaction field through the solid-liquid interface. They also show that the site distribution plays a crucial role in the charging process. In patch distributions, charges accumulate at the perimeter of each patch due to finite size effects. When homogeneous and heterogeneous distributions are compared, three different charging regimes are obtained. In homogeneous and heterogeneous (with quite low polydispersity indexes) distributions, the effects of the NP dielectric constant on Coulomb interactions are counterbalanced by the reaction field and in this case, the dielectric breakdown has no significant effect on the charging process. This is not the case in patch distributions, where the dielectric breakdown plays a crucial role in the charging process.     

Tropical matrix groups

We study the structure of groups of finitary tropical matrices under multiplication. We show that the maximal groups of \(n \times n\) tropical matrices are precisely the groups of the form \(G \times \mathbb {R}\) where G is a group admitting a 2-closed permutation representation on n points. Each such maximal group is also naturally isomorphic to the full linear automorphism group of a related tropical polytope. Our results have numerous corollaries, including the fact that every automorphism of a projective (as a module) tropical polytope of full rank extends to an automorphism of the containing space.     

Sense and nonsense of laboratory accreditation

 An open mind is essential for the implementation and improvement of total quality management. Leadership, as such, is of no value without a vision concerning corporate culture and human resources. Therefore, constant communication between partners within a corporate body is the cornerstone for empowerment. The evaluation of ideas and complaints is considered to be essential for the identification of strengths and weaknesses of a system, whereas, competition and benchmarking may reveal surprising opportunities for improvement. We discuss the idea that customer-oriented efficiency in a hospital environment may be classified as a critical success factor.     

Starch‐graft‐(synthetic copolymer) latexes initiated with Ce4+ and stabilized by amylopectin

A method is presented for synthesizing surfactant‐free latexes comprising starch‐graft‐(vinyl polymer) starting with a suspension of amylopectin, either native or modified, then using cerium(IV) with either potassium persulfate or glucose to create grafting sites on the starch. Latex particles comprising polystyrene, poly(styrene‐co‐(n‐butyl acrylate)) and poly(vinyl acetate) grafted onto high molecular weight amylopectin were developed, with up to 80% of the starch effectively grafted to the particles. These latexes were colloidally stable against electrolyte (several months in 4 M NaCl). Reaction rates of Ce⁴⁺ with simple sugars and polysaccharides were investigated, as well as the gelation mechanism of the latex. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 4185–4192, 2007     

Development of a fast liquid chromatography/mass spectrometry screening method for angiotensin‐converting enzyme (ACE) inhibitors in complex natural mixtures like snake venom

A new robust high‐performance liquid chromatography/electrospray ionization mass spectrometry (HPLC/ESI‐MS)‐based screening method for angiotensin‐converting enzyme (ACE)‐inhibiting substances in crude samples is described. The ACE assay is carried out in a typical offline setup by incubation of the samples with ACE and angiotensin I (AI), followed by stopping the reaction with acetonitrile containing val⁵‐AI serving as internal standard (I.S.). AI and the product angiotensin II (AII) are extracted from the incubation mixture by turbulent‐flow chromatography (TFC) applied in backflush mode as online solid‐phase extraction and are directly quantified by ESI(+)‐MS. The presence of ACE inhibitors (ACEi) is detected by an increase in AI signal intensity and a corresponding decrease of AII signal, as compared to the blank assay. The overall time of analysis of the TFC/ESI‐MS method was 5 min, thus making the described setup suitable for a rapid screening method. The assay was validated using a known ACE inhibitor and the IC₅₀ values found were in good accordance with a common HPLC/UV method and literature data. The method was successfully applied for the screening of size‐exclusion chromatography fractions of the venom of the pitviper Bothrops moojeni. Three of 18 analyzed fractions inhibited ACE, due to peptides present as components of this snake venom. These compounds were extracted from the two most‐active fractions by means of TFC and isolated by means of HPLC. Three peptides with ACE inhibitory activity were characterized and their structures were elucidated with ESI‐MS/MS‐based de novo sequencing to be ZKWPPGKVPP, ZKWPRPGPEIPP and ZNWPRPGPEIPP, respectively (Z = pyroglutamic acid). Copyright © 2010 John Wiley & Sons, Ltd.