Bacterial Peptide deformylase inhibitors: a new class of antibacterial agents

Peptide deformylase (PDF) is a prokaryotic metalloenzyme that is essential for bacterial growth but is not required by mammalian cells. Thus, it represents a selective and promising target for the development of new antibacterial agents. Since deformylase inhibitors have yet to be used clinically as antibacterial drugs, compounds targeting this enzyme should avoid cross-resistance with currently used antibacterial agents. The PDF enzyme is a ferrous ion-containing metallohydrolase, but a nickel-containing surrogate is routinely used in the laboratory for testing inhibitors due to its better stability. Enzymes from several bacterial species have been cloned and both their three-dimensional structures and co-crystal structures with bound inhibitor have been determined. As a metallo enzyme, PDF lends itself to the well-precedented mechanism-based rational drug design approach. Using structural and mechanistic information together with high throughput screening, several types of potent PDF inhibitors have been identified. PDF inhibitors identified to date share a common structural feature of a "chelator + peptidomimetic" scaffold. Although compounds with many different chelators inhibit the cell free enzyme, only compounds containing hydroxamic acid or N-formyl hydroxylamine exhibit appreciable antibacterial activity. Several lead inhibitors have demonstrated in vivo efficacy and an excellent safety profile. Two PDF inhibitors, VIC-104959 (LBM415) and BB-83698, have progressed to Phase I clinical trials. In this review, different PDF inhibitors are compared and their biological activities are discussed. Structure-activity relationships have been established and the implications of this work in the design of future PDF inhibitors are considered.

Increased expression of Mycobacterium tuberculosis 19 kDa lipoprotein obliterates the protective efficacy of BCG by polarizing host immune responses to the Th2 subtype

Mycobacterium tuberculosis can not only neutralize immune effector functions, but also has the ability to modulate host-signalling cascades involved in the development of these responses. The 19 kDa antigen (Rv3763), a lipoprotein of M. tuberculosis, elicits high levels of interleukin (IL)-12 from macrophages in addition to its powerful immunomodulatory properties, leading to suppression of antigen-presentation signalling cascades. The present study was aimed at analysing the effect of overexpression of this antigen on the immunostimulatory properties of M. bovis Bacille Calmette-Guerin (BCG). We have constructed a recombinant BCG strain (rBCG19N) producing higher levels of the 19 kDa antigen in both the cytoplasmic (approximately eightfold) and extracellular (approximately fivefold) fractions as compared to the wildtype BCG. Immunization of mice with rBCG19N elicited high levels of interferon-gamma (IFN-gamma) and relatively low levels of IL-10 against the purified 19 kDa antigen. However, in response to total BCG sonicate, mice immunized with rBCG19N produced significantly high levels of IL-10 with relatively very low levels of IFN-gamma. This polarization of the host immune responses towards T-helper 2 subtype resulted in complete abrogation of the protective efficacy of BCG, when rBCG19N was used as a live vaccine against M. tuberculosis challenge in guinea pigs.

Structures of E. coli peptide deformylase bound to formate: insight into the preference for Fe2+ over Zn2+ as the active site metal

E. coli peptide deformylase (PDF) catalyzes the deformylation of nascent polypeptides generated during protein synthesis. While PDF was originally thought to be a zinc enzyme, subsequent studies revealed that the active site metal is iron. In an attempt to understand this unusual metal preference, high-resolution structures of Fe-, Co-, and Zn-PDF were determined in complex with its deformylation product, formate. In all three structures, the formate ion binds the metal and forms hydrogen-bonding interactions with the backbone nitrogen of Leu91, the amide side chain of Gln50, and the carboxylate side chain of Glu133. One key difference, however, is how the formate binds the metal. In Fe-PDF and Co-PDF, formate binds in a bidentate fashion, while in Zn-PDF, it binds in a monodentate fashion. Importantly, these structural results provide the first clues into the origins of PDF's metal-dependent activity differences. On the basis of these structures, we propose that the basis for the higher activity of Fe-PDF stems from the better ability of iron to bind and activate the tetrahedral transition state required for cleavage of the N-terminal formyl group.

Blood salvage in total hip and knee arthroplasty in a community hospital: a retrospective study

PURPOSES

To assess the results of postoperative and intra-operative blood salvage in patients undergoing total knee and hip arthroplasty, respectively, and to determine if both methods of blood salvage reduce allogeneic transfusion.

METHODS

Of 229 patients who attempted blood salvage, 114 of 152 patients who underwent total knee arthroplasty received the salvaged blood postoperatively, 35 of 77 patients who underwent total hip arthroplasty received the salvaged blood intra-operatively. Various data were collected to assess whether certain factors resulted in autologous and/or allogeneic blood transfusions.

RESULTS

Patients that received postoperative salvaged blood after total knee arthroplasty generally had higher postoperative levels of haemoglobin and haematocrit compared to those who did not. Patients with autologous blood transfusion following cemented knee surgery were less likely to require allogeneic blood transfusion. For hip arthroplasty patients, postoperative levels of haemoglobin and haematocrit were similar in both groups who received and did not receive salvaged blood. Lower preoperative haemoglobin and haematocrit levels correlated with a greater likelihood of autologous and/or allogeneic blood transfusion for both knee and hip arthroplasty patients.

CONCLUSIONS

Although total knee arthroplasty patients who received salvaged blood had higher haemoglobin levels on the first postoperative day, the receipt of salvaged blood did not significantly reduce the incidence of allogeneic blood transfusion, because salvaged blood was a kind of blood loss. However, reinfusion of salvaged blood may reduce the number of units of allogeneic blood used. Given the short supply of allogeneic blood and its risks of transmitting disease, intra-operative and postoperative blood salvage carries clear advantages.

SBS threshold for single mode and multimode GRIN fibers in an all fiber configuration

We investigate stimulated Brillouin scattering (SBS) threshold in single mode and multimode fibers in an all fiber network. The pump is a single mode fiber pigtail attached to a diode. We find the theory and experiment agree for both single mode and multimode GRIN fibers. We modify the bulk SBS threshold equation for use with fibers by properly accounting for mode sizes and modal dispersion.

A comparative study of fuzzy classification methods on breast cancer data

In this paper, we examine the performance of four fuzzy rule generation methods on Wisconsin breast cancer data. The first method generates fuzzy if-then rules using the mean and the standard deviation of attribute values with 92.2% correct classification rate. The second approach generates fuzzy if-then rules using the histogram of attributes values with 86.7% correct classification rate. The third procedure generates fuzzy if-then rules with certainty of each attribute into homogeneous fuzzy sets with 99.73% correct classification rate. In the fourth approach, only overlapping areas are partitioned with 62.57% correct classification rate. The first two approaches generate a single fuzzy if-then rule for each class by specifying the membership function of each antecedent fuzzy set using the information about attribute values of training patterns. The other two approaches are based on fuzzy grids with homogeneous fuzzy partitions of each attribute. The performance of each approach is evaluated on breast cancer data sets. Simulation results show that the simple grid approach has a high classification rate of 99.73%.

The Macrolide Antibiotics: A Pharmacokinetic and Pharmacodynamic Overview

The macrolide antimicrobial family is comprised of 14, 15 and 16 member-ringed compounds that are characterized by similar chemical structures, mechanisms of action and resistance, but vary in the different pharmacokinetic parameters, and spectrum of activity. The macrolides accumulate in many tissues such as the epithelial lining fluid and easily enter the host defense cells, predominantly macrophages and polymorphonuclear leukocytes (PMNs). Concentrations of the macrolides in respiratory tract tissues and extracellular fluids are in almost all cases higher than simultaneously measured serum concentrations, making them useful for respiratory tract infections. This review will focus on pharmacokinetic and pharmacodynamic aspects of the clinical relevant macrolides including azithromycin, clarithromycin, dirithromycin, erythromycin and roxithromycin.

Cold chain monitoring of OPV at transit levels in India: correlation of VVM and potency status

We have conducted a study to analyze monitoring of the cold chain of 674 OPV field samples collected at four different levels of vaccine distribution viz., immunization clinics, district stores, hospitals and Primary Health Centers (PHC) from states of Uttar Pradesh, Madhya Pradesh, and Delhi. The study design included: collection and scoring of vaccine vial monitor (VVM) status of the samples and testing for total oral polio virus concentration (TOPV) by standard WHO protocol. Ten samples each were exposed to 25 degrees C and 37 degrees C, and 10 samples as controls were kept at -20 degrees C. VVM were scored daily till they attained grade 4 and each sample was subsequently subjected to potency testing for individual polio serotypes 1, 2 and 3, and TOPV. Of the 674 samples tested it was observed that: samples from immunization clinics and district stores had an acceptable VVM score of grade 1 and 2; however the probable risk that a sub potent vaccine could have been administered was 2.15%. In 2.5% samples received from district stores vaccine had a VVM score of grade 3 (i.e., discard point), although vaccine when tested was found to be potent (i.e., leading to the vaccine wastage). With exposure to higher temperatures, VVM changed score to grade 2 and 3 when the vaccine was kept at 25 degrees C/37 degrees C, and the titres of individual serotypes 1, 2 and 3 and TOPV were beyond the acceptable limits. Important observations at the different levels of vaccine distribution network and correlation of VVM and potency status of OPV are discussed in the paper which will be of help to the EPI program managers at different transit levels.

Correlation of percutaneous liver biopsy fragmentation with the degree of fibrosis

BACKGROUND

Although fragmentation of a liver biopsy specimen has been considered to be suggestive of cirrhosis, the evidence for this is difficult to find in the published literature.

AIM

To determine whether fragmentation of percutaneous liver biopsy specimens correlates with the degree of fibrosis.

METHODS

One hundred and eighty-six patients underwent percutaneous liver biopsy prospectively. The specimens were measured for the length and number of fragments. The extent of fibrosis was scored by a pathologist blind to the clinical data. Length and fragmentation data were compared between the different stages.

RESULTS

The overall median fragment length was 1.85 cm and the median fragment number was four. Specimens with advanced fibrosis (stages III-IV) had more fragments than those with no or mild fibrosis (stages 0-II) (P < 0.0001). The aggregate fragment length decreased with increasing stage of fibrosis (P < 0.0001). Specimens with greater than 12 fragments were seen only with advanced fibrosis.

CONCLUSIONS

Fragmentation of percutaneous liver biopsy specimens is common and increases with progression from early to advanced fibrosis. Fibrotic specimens fragment more often and more extensively.

Peptide deformylase inhibitors as antibacterial agents: identification of VRC3375, a proline-3-alkylsuccinyl hydroxamate derivative, by using an integrated combinatorial and medicinal chemistry approach

Peptide deformylase (PDF), a metallohydrolase essential for bacterial growth, is an attractive target for use in the discovery of novel antibiotics. Focused chelator-based chemical libraries were constructed and screened for inhibition of enzymatic activity, inhibition of Staphylococcus aureus growth, and cytotoxicity. Positive compounds were selected based on the results of all three assays. VRC3375 [N-hydroxy-3-R-butyl-3-(2-S-(tert-butoxycarbonyl)-pyrrolidin-1-ylcarbonyl)propionamide] was identified as having the most favorable properties through an integrated combinatorial and medicinal chemistry effort. This compound is a potent PDF inhibitor with a K(i) of 0.24 nM against the Escherichia coli Ni(2+) enzyme, possesses activity against gram-positive and gram-negative bacterial pathogens, and has a low cytotoxicity. Mechanistic experiments demonstrate that the compound inhibits bacterial growth through PDF inhibition. Pharmacokinetic studies of this drug in mice indicate that VRC3375 is orally bioavailable and rapidly distributed among various tissues. VRC3375 has in vivo activity against S. aureus in a murine septicemia model, with 50% effective doses of 32, 17, and 21 mg/kg of body weight after dosing by intravenous (i.v.), subcutaneous (s.c.), and oral (p.o.) administration, respectively. In murine single-dose toxicity studies, no adverse effects were observed after dosing with more than 400 mg of VRC3375 per kg by i.v., p.o., or s.c. administration. The in vivo efficacy and low toxicity of VRC3375 suggest the potential for developing this class of compounds to be used in future antibacterial drugs.

α-Substituted hydroxamic acids as novel bacterial deformylase inhibitor-based antibacterial agents

We report the synthesis and biological activity of analogues of VRC3375 (N-hydroxy-3-R-butyl-3-[(2-S-(tert-butoxycarbonyl)-pyrrolidin-1-ylcarbonyl]propionamide), an orally active peptide deformylase inhibitor. This study explores the structure-activity relationship of various chelator groups, alpha substituents, P(2)' and P(3)' substituents in order to achieve optimal antibacterial activity with minimal toxicity liability.

Micromanipulator: Effectiveness in Minimally Invasive Neurosurgery

Minimally invasive surgeries by innovative approaches are practiced in all fields. The evolution of microneurosurgery has revolutionized the results in neurosurgery. Use of endoscopes and navigation has made microsurgery less invasive. Another development to make minimally invasive microneurosurgery further lesser invasive is the use of micromanipulator. The use and effectiveness of manually controlled micromanipulator system is presented. The manually controlled micromanipulator system consists of three parts, i.e., a basic micromanipulator, manipulator supporting device and the manual control. The micromanipulator fitted in supporting device is arranged before the start of surgery. The supporting device used is pneumatically driven powered endoscopic holding device (Mitaka Kohki Co., Tokyo) In maximum number of times we used the system for endoscopic assisted cerebrovascular microneurosurgery. In a span of two months we used it in thirty aneurysm clipping surgeries. The endoscope fitted in system has three ranges of motions (forward/backward, upside/down and sideways). We use MACHIDA rigid endoscope with internal diameter of 2.7 mm (smallest diameter endoscope available). Special features of this endoscope are accurate visualization at a deeper plane, stable movements and availability of single focus point for long time. All these features are valuable during pre- and postoperative clipping observation. The aim of development of micromanipulator system was to further reduce invasiveness. A significant improvement in manual dexterity is possible when working through the micromanipulator interface, which dampens human physiological tremor. The physiological tremor would render the manual dexterity unsafe at the end of lever arm of long instruments. Thus, the use endoscope becomes practical. The minimally invasive microneurosurgery can be further made lesser invasive by use of micromanipulator and we are convinced that this will facilitate more accurate and promising results in microneurosurgery.

Photocatalytic degradation of 2-chlorophenol: a study of kinetics, intermediates and biodegradability

The kinetics of photocatalytic (TiO(2)/UV) degradation of 2-chlorophenol (2-CP), characterization of intermediates and induction of biodegradability in treated chlorophenol solutions is reported. Approximately 95% of the 2-CP is removed in approximately 2h at pH 5 and 0.2g TiO(2)l(-1) when the 2-CP concentration is < or =100mgl(-1); the pseudo-first-order rate constant (k) is estimated to be 0.0183 min(-1). GC-MS analyses detected phenol, catechol, hydroxyhydroquinone (HHQ), and chlorohydroquinone (CHQ) intermediates during the short irradiation time (<1h); however two other higher carbon intermediates 2-hydroxy-benzaldehyde (HB) and [1.1'-biphenyl]-2,2'-diol (BPD) are found as major intermediates over longer irradiation times. The biochemical oxygen demand (BOD) of treated 2-CP solutions improved substantially. A tentative mechanistic pathway to explain formation of higher carbon intermediates is presented.