Phenyl Esters Are Potent Inhibitors of Caseinolytic Protease P and Reveal a Stereogenic Switch for Deoligomerization.

Caseinolytic protease P (ClpP) represents a central bacterial degradation machinery that is involved in cell homeostasis and pathogenicity. The functional role of ClpP has been studied by genetic knockouts and through the use of beta-lactones, which remain the only specific inhibitors of ClpP discovered to date. Beta-lactones have served as chemical tools to manipulate ClpP in several organisms; however, their potency, selectivity and stability is limited. Despite detailed structural insights into the composition and conformational flexibility of the ClpP active site, no rational efforts to design specific non-beta-lactone inhibitors have been reported to date. In this work, an unbiased screen of more than 137 000 compounds was used to identify five phenyl ester compounds as highly potent ClpP inhibitors that were selective for bacterial, but not human ClpP. The potency of phenyl esters largely exceeded that of beta-lactones in ClpP peptidase and protease inhibition assays and displayed unique target selectivity in living S. aureus cells. Analytical studies revealed that while phenyl esters are cleaved like native peptide substrates, they remain covalently trapped as acyl-enzyme intermediates in the active site. The synthesis of 36 derivatives and subsequent structure-activity relationship (SAR) studies provided insights into conserved structural elements that are important for inhibition potency and acylation reactivity. Moreover, the stereochemistry of a methyl-substituent at the alpha position to the ester, resembling amino acid side chains in peptide substrates, impacted ClpP complex stability, causing either dissociation into heptamers or retention of the tetradecameric state. Mechanistic insights into this intriguing stereo switch and the phenyl ester binding mode were obtained by molecular docking experiments.

Modelling antibiotic and cytotoxic isoquinoline effects in Staphylococcus aureus, Staphylococcus epidermidis and mammalian cells.

Isoquinolines (IQs) are natural substances with an antibiotic potential we aim to optimize. Specifically, IQ-238 is a synthetic analog of the novel-type N,C-coupled naphthylisoquinoline (NIQ) alkaloid ancisheynine. Recently, we developed and tested other IQs such as IQ-143. By utilizing genome-wide gene expression data, metabolic network modelling and Voronoi tessalation based data analysis - as well as cytotoxicity measurements, chemical properties calculations and principal component analysis of the NIQs - we show that IQ-238 has strong antibiotic potential for staphylococci and low cytotoxicity against murine or human cells. Compared to IQ-143, systemic effects are less pronounced. Most enzyme activity changes due to IQ-238 are located in the carbohydrate metabolism. Validation includes metabolite measurements on biological replicates. IQ-238 delineates key properties and a chemical space for a good therapeutic window. The combination of analysis methods allows suggestions for further lead development and yields an in-depth look at staphylococcal adaptation and network changes after antibiosis. Results are compared to eukaryotic host cells.

Amythiamicin†D and related thiopeptides as inhibitors of the bacterial elongation factor EF-Tu: modification of the amino acid at carbon atom C2 of ring†C dramatically influences activity.

Three analogues of amythiamicin D, which differ in the substitution pattern at the methine group adjacent to C2 of the thiazole ring C, were prepared by de novo total synthesis. In amythiamicin D, this carbon atom is (S)-isopropyl substituted. Two of the new analogues carry a hydroxymethyl in place of the isopropyl group, one at an S- (compound 3 a) and the other at an R-configured stereogenic center (3 b). The third analogue, 3 c, contains a benzyloxymethyl group at an S-configured stereogenic center. Compounds 3 b and 3 c showed no inhibitory effect toward various bacterial strains, nor did they influence the translation of firefly luciferase. In stark contrast, compound 3 a inhibited the growth of Gram-positive bacteria Staphylococcus aureus (strains NCTC and Mu50) and Listeria monocytogenes EGD. In the firefly luciferase assay it proved more potent than amythiamicin D, and rescue experiments provided evidence that translation inhibition is due to binding to the bacterial elongation factor Tu (EF-Tu). The results were rationalized by structural investigations and by molecular dynamics simulations of the free compounds in solution and bound to the EF-Tu binding site. The low affinity of compound 3 b was attributed to the absence of a critical hydrogen bond, which stabilizes the conformation required for binding to EF-Tu. Compound 3 c was shown not to comply with the binding properties of the binding site.

Mode-of-action studies of the novel bisquaternary bisnaphthalimide MT02 against Staphylococcus aureus.

Screening of various bisquaternary bisnaphthalimides against a variety of human pathogens revealed one compound, designated MT02, with strong inhibitory effects against Gram-positive bacteria. The MICs ranged from 0.31 µg/ml against community-acquired methicillin-resistant Staphylococcus aureus (MRSA) lineage USA300 to 20 µg/ml against Streptococcus pneumoniae. Radioactive whole-cell labeling experiments indicated a strong impact of MT02 on bacterial DNA replication. DNA microarray studies generated a transcriptional signature characterized by stronger expression of genes involved in DNA metabolism, DNA replication, SOS response, and transport of positively charged compounds. Furthermore, surface plasmon resonance and gel retardation experiments demonstrated direct binding of MT02 to DNA in a concentration-dependent, reversible, and non-sequence-specific manner. The data presented suggest that the bisquaternary bisnaphthalimide MT02 exerts anti-Gram-positive activity by binding to DNA and thereby preventing appropriate DNA replication.

Pseudolymphomatous cutaneous angiosarcoma: a rare variant of cutaneous angiosarcoma readily mistaken for cutaneous lymphoma.

Cutaneous angiosarcoma is probably the most malignant neoplasm involving the skin. Three clinical variants of cutaneous angiosarcoma are recognized, including angiosarcoma of the scalp and face of elderly patients, angiosarcoma associated with chronic lymphedema, and postirradiation angiosarcoma. Histopathologically, these three variants of angiosarcoma show similar features, which consist of poorly circumscribed, irregularly dilated, and anastomosing vascular channels lined by prominent endothelial cells that dissect through the dermis. Focally, neoplastic endothelial cells show large, hyperchromatic, and pleomorphic nuclei, protruding within vascular lumina and creating small papillations. Usually, inflammatory infiltrate is sparse and consists of a patchy, perivascular lymphoid infiltrate around the neoformed vessels. In rare instances, cutaneous angiosarcomas may exhibit prominent inflammatory infiltrate, and the neoplasm may be mistaken for an inflammatory process, both from clinical and histopathologic points of view. We describe four examples of cutaneous angiosarcomas with dense lymphocytic infiltrates involving the neoplasm. Immunohistochemically, lymphocytes expressed immunoreactivity for CD3, CD5, and CD45 markers, whereas the germinal centers were positive for CD20, CD79a, and Bcl-6. The neoplastic endothelial cells expressed immunoreactivity for the CD31, CD34, podoplanin, Prox-1, Lyve-1, and D2-40. We discuss the possible relationship between neoplastic endothelial lymphatic cells and reactive lymphocytes. Cutaneous angiosarcoma with prominent lymphocytic infiltrate may be readily mistaken for cutaneous follicle center cell lymphoma or cutaneous pseudolymphoma.

Metastatic signet ring cell gastric carcinoma presenting as an infrarenal aortic aneurysm.

Metastases to liver, lungs, bone, and adrenal glands are common events in advanced gastric carcinoma. Occasionally, metastases to other parts of the body, such as the prostate gland [1] the gluteal muscle [2], or the cervix [3] are described. However, these are rare events in the natural history of the disease. We report an unusual case of a signet ring cell gastric carcinoma, initially presenting as an infrarenal aortic aneurysm. Following resection of the aneurysm, the spread of lymphangiosis carcinomatosa into the aortic wall and infiltration of signet ring cells into an adjacent lymph node were noted. The primary tumor, a signet ring cell gastric carcinoma, was detected by a subsequent esophago-gastro-duodenoscopy.

SKY and genetic fingerprinting reveal a cross-contamination of the putative normal colon epithelial cell line NCOL-1.

In vitro studies addressing the primary prevention of colon carcinoma are preferably conducted using normal colonic cells, because these cells are more likely to represent the potential target for prevention in vivo. Established cell lines of normal colonic origin are mostly lacking; however, this is probably due to the difficulties associated with establishment of such cell lines. Cross-contamination with malignant cells is a frequent event, and so any successfully established cell line of normal origin should be scrutinized prior to further investigation. We performed a cytogenetic (spectral karyotyping) and genetic fingerprint (Promega PowerPlex ES multiplex system and Applied Biosystems AmpFlSTR SGM Plus multiplex system) analysis of the putative normal colon epithelial cell line NCOL-1, derived from two different sources (NCOL-1a and 1b). We show that NCOL-1a and 1b are probably derived from the colon carcinoma cell line LoVo, with a matching probability of 99.9995, most probably through cross-contamination. Karyotypes of LoVo and NCOL-1a were identical; NCOL-1b displayed additional marker chromosomes. Our findings highlight the importance of molecular and cytogenetic characterization of established cell lines to avoid drawing misleading conclusions from the original findings.

Histone-deacetylase inhibitors induce the cathelicidin LL-37 in gastrointestinal cells.

UNLABELLED: Histone-deacetylase (HDAC) -inhibitors enhance acetylation of core proteins and this is linked to formation of transcriptionally active chromatin in various cells. In this study, the effect of HDAC inhibitors (butyrate, trichostatin A (TSA)) on the expression of the cathelicidin LL-37 in colon, gastric and hepatocellular cells was investigated. METHODS: LL-37 expression was assessed in colon, gastric and hepatocellular cancer cells after treatment with HDAC-inhibitors. In parallel, histone H4 and HMGN2, a non-histone protein, acetylation was evaluated. In addition, the intracellular signalling pathway MEK-ERK was explored. RESULTS: In contrast to normal colon epithelial cells, gastrointestinal cancer cells lacked LL-37 expression. LL-37 was induced following treatment with HDAC-inhibitors in all investigated cell lines. This induction was time-dependent in butyrate-treated cells while TSA exerted a transient effect. Induction of LL-37 by butyrate was paralleled by acetylation of the histone H4 and the non-histone HMGN2. Again, TSA resulted in transient acetylation. Furthermore, inhibition of MEK-ERK blocked HDAC inhibitor-induced LL-37 expression in colonic and gastric cells. CONCLUSIONS: We have previously shown that butyrate induces LL-37 in colon epithelial cells. In the present study, we demonstrate that cathelicidin expression is modulated by HDAC-inhibitors in various gastrointestinal cells including gastric and hepatocellular cells. This is paralleled by changes in the acetylation of distinct core proteins suggesting a common regulatory mechanism of cathelicidin LL-37 regulation in these cells.

Butyrate inhibits leukocyte adhesion to endothelial cells via modulation of VCAM-1.

BACKGROUND: Leukocyte recruitment to areas of inflammation depends on Integrin-VCAM/ICAM interaction. Blocking the vascular cell adhesion molecule (VCAM-1) and the intracellular adhesion molecule (ICAM-1) may have therapeutic benefit for the inflammatory component of bowel disease. Notably, the induction of ICAM and VCAM is mediated by a nuclear factor kappaB (NF-kappaB)-dependent mechanism. We investigated whether the anti-inflammatory properties of butyrate are mediated via the modulation of VCAM and ICAM on human endothelial cells. METHODS: VCAM-1 and ICAM-1 expression on human endothelial cells upon tumor necrosis factor-alpha (TNF-alpha) stimulation was assessd by FACS analysis. A monocyte adhesion assay was performed to evaluate the relevance of a modulated CAM-expression. Electrophoretic mobility shift assays were applied to investigate NF-kappaB activation. RESULTS: The observed butyrate-associated inhibition of monocyte adhesion to endothelial cells is associated with an inhibition of NF-kappaB activation in human endothelial cells. In this context, the observed suppression of the TNF-alpha induced VCAM-1 expression is likely to play an essential role. CONCLUSIONS: Butyrate inhibits VCAM-1 mediated leukocyte adhesion to human endothelial cells. This inhibition may contribute to the anti-inflammatory effects of butyrate in patients with distal ulcerative colitis.

A diagnostic expert system for structured reports, quality assessment, and training of residents in sonography.

BACKGROUND: The quality of medical reports on diagnostic procedures has a considerable impact on the quality of medical care. Handwritten or otherwise unstructured reports tend to be incomplete, whereas structured questionnaires are of limited flexibility and not considered case-adequate. Thus, medical reports of this kind may promote an incomplete and misleading documentation and, therefore, be problematic with respect to their reliability. METHODS: SonoConsult (SC), an expert system for structured and case-adequate documentation of sonographic findings with an additional diagnostic component, was evaluated with respect to user acceptance and suitability for enhancing the quality of reports and supporting sonographic beginners. The expectations and the attitudes of the users toward the program were evaluated by anonymous questionnaires. The documentation of findings and the diagnostic conclusions in 103 free text reports made by experienced examiners were evaluated by subjecting their information to a subsequent input into SC. Free text reports were checked for information that was asked by SC but not mentioned in the reports. In a series of 150 cases, the system diagnoses were blinded during input of findings into SC-questionnaires and the examiners' diagnostic conclusions were compared with the uncovered SC-diagnoses with respect to forgotten diagnoses. RESULTS: The structured and data-driven acquisition of information by the program was well accepted by the users. However, only a medium interest in the system-delivered diagnoses was noted. The program-generated reports were characterized by a more detailed description of the findings and a higher number of diagnoses in comparison to the unstructured reports before introduction of SC as the only documentation system. When unaware of the system diagnoses, information was entered into the questionnaires, and SC generated some diagnoses which were not mentioned by the examiners in their conclusions. The possibility to inspect the system diagnoses led to an enhancement of the number of diagnoses the examiners mentioned in their conclusions. By contrast, the examiners meant that the influence of the program on their conclusions was minimal or dispensable. Beginners in sonography acknowledged that the program led them to perform a complete examination in an adequate sequence. CONCLUSION: An expert system for the data-driven, case-adequate information acquisition of abdominal ultrasound examinations may enhance the quality of the reports and, potentially, of the examinations at the same time. In addition, it may help beginners to learn a structured problem- and finding-adequate examination sequence.

Establishment of a colonic adenoma cell line (GEKI-2): spectral karyotype analysis and functional characterization.

BACKGROUND AND AIMS: On the genetic level colonic carcinogenesis is best described by the adenoma-carcinoma sequence, but it may be modulated by exogenous factors, particularly by dietary factors and chemopreventive agents. The protective effects of exogenous factors are thought to be exerted rather in the early stages of the adenoma-carcinoma sequence. Thus, an in vitro model consisting of cells stemming from an colon adenoma would be desirable. However, establishing such a cell line has proven difficult. MATERIALS AND METHODS: We report the establishment of a colon adenoma cell line. The cells were generated from a colon adenoma and propagated as a stable cell line for more than 40 passages. The cells are microsatellite stable and confirmed to be of epithelial origin by cytokeratin staining. RESULTS: In contrast to commercially available colon cancer cell lines, cytogenetic analysis with spectral karyotype analysis revealed no chromosomal alterations in this adenoma cell line. Incubation with butyrate resulted in a time- and dose-dependent inhibition of proliferation and in an significant increase in cellular differentiation. The cdk inhibitor p21/waf which plays a pivotal role in growth inhibition and differentiation is expressed consecutively in GEKI-2 cells. The expression of cdk1 and cdk2, important regulatory elements in the cell cycle, is downregulated following treatment with butyrate. CONCLUSION: The presented colon adenoma cell line GEKI-2 may prove a versatile tool for further exploring the underlying mechanisms of protective and promoting factors in early colon cancerogenesis.

Ultrastructural alterations of primary human liver sinusoidal cells in patients treated for peritonitis.

Acute peritonitis is still associated with a high mortality rate. Bacterial toxins are rapidly cleared from the peritoneal cavity and may induce general sepsis. The hepatic sinusoidal cells are part of the primary defence against these toxins. The object of this study was to examine ultrastructural alterations of human sinusoidal liver cells from patients undergoing surgical treatment for peritonitis. Liver specimens, obtained from five patients treated with programmed interval peritoneal lavages for peritonitis, were analyzed by electron microscopy. Despite interindividual differences in etiology of peritonitis, the detected ultrastructural alterations displayed a high degree of similarity. Kupffer cells displayed enhanced phagocytotic activity. Numerous Kupffer cell-lymphocyte contacts were observed. Notably, the morphological appearance of the endothelial cells resembled that of an activated phagocytotic cell. The ultrastructural alterations peaked on day 7, and regressed during the course of treatment. Our findings demonstrate that major changes occur in the ultrastructural appearance of both Kupffer cells and sinusoidal endothelial cells in patients with acute peritonitis treated successfully with programmed interval peritoneal lavages. Our data suggest that in peritonitis, a septic spread of toxins and antigens may be modulated by sinusoidal liver cells.

Butyrate-enhanced TNFalpha-induced apoptosis is associated with inhibition of NF-kappaB.

BACKGROUND: Tumor necrosis factor (TNFalpha)-induced apoptosis is limited by concomitant activation of nuclear factor kappa B (NF-kappaB)-dependent anti-apoptotic genes. Butyrate inhibits NF-kappaB activation so that co-treatment with butyrate effectively enhances TNFalpha-induced apoptosis. In this context, the inhibition of NF-kappaB activation and subsequent modulation of (NF-kappaB)-dependent genes was assessed MATERIALS AND METHODS: Human colon adenocarcinoma cells (SW620) were incubated with TNFalpha and butyrate. Apoptosis was determined by annexin V/propidium iodide staining and flow cytometry. NF-kappaB activation was detected by electrophoretic mobility shift assay. The expression of NF-kappaB-dependent genes was assessed by RNase protection assay (RPA) RESULTS: The TNFalpha/butyrate combination yielded an additive increase in the number of apoptotic cells. NF-kappaB nuclear translocation was successfully inhibited by co-incubation with butyrate. However, the expression pattern of NF-kappaB-dependent genes remained essentially unchanged CONCLUSION: Butyrate enhances TNFalpha-induced apoptosis in the human adenocarcinoma cell line SW620. This additive effect may, at least in part, be mediated by the inhibition of NF-kappaB activation, presumably by impairing the anti-apoptotic properties of NF-kappaB.

Improvement of tricuspid regurgitation after pulmonary thromboendarterectomy.

BACKGROUND: For patients with chronic thromboembolic pulmonary hypertension who undergo pulmonary thromboendarterectomy (PTE) it has not yet been systematically investigated how operation affects the severity of tricuspid regurgitation (TR). This study sought (1) to evaluate the extent of TR reversibility after operation, (2) to identify potential predictors of the reversibility of TR, and (3) to investigate the influence of geometric and hemodynamic alterations on the extent of TR severity. METHODS: Thirty-nine patients (55+/-12 years) undergoing PTE without tricuspid valve repair were investigated before and 13+/-8 days after operation by Doppler color flow mapping. Geometry of the tricuspid valve as well as right ventricular size and function were determined with echocardiography. Mean pulmonary arterial pressure was determined invasively. RESULTS: After PTE, mean pulmonary arterial pressure was significantly lower (48+/-10 versus 25+/-7 mm Hg, p < 0.05). Most of the patients had a distinct reduction of TR, and the improvement trend showed on the severity scale: number of patients with 4+TR (23 --> 4), 3+TR (12 --> 12), 2+TR (2 --> 13), and 1+TR (2 --> 10). Examination after PTE revealed profound reduction of right ventricular size and annulus diameter, with a normalization of the valvular geometry. However, none of the study variables were useful as indicators of the postoperative outcome. CONCLUSIONS: After PTE without additional valve repair most patients show significantly reduced severity of TR soon afterward; the very few cases in which TR does not improve remain unidentifiable before operation. Our recommendation is consequently to refrain from additional tricuspid repair in patients undergoing PTE.

Assessment of cardiac performance using Tei indices in patients undergoing pulmonary thromboendarterectomy.

BACKGROUND: This study was designed to evaluate left and right ventricular performance using Tei indices in patients with severe chronic thromboembolic pulmonary hypertension undergoing pulmonary thromboendarterectomy (PTE). The Doppler-derived indices are easily measurable indicators of ventricular function based on nongeometric assessment, which helps overcome some of the difficulties entailed in the geometric assessment of left ventricular (LV) and right ventricular (RV) function in pulmonary hypertension. METHODS: The indices were derived for 24 patients (aged 54+/-14 years) before and after PTE. Calculation of these indices was based on the duration of two time intervals using the formula (A - B)/B, where A is the interval between cessation and onset of mitral inflow (or tricuspid inflow) and B is LV or RV ejection time. In addition, LV and RV end-diastolic and end-systolic chamber areas were determined using two-dimensional echocardiography, and systolic function was calculated. Mean pulmonary artery pressure was determined invasively. RESULTS: PTE led to a significant reduction of mean pulmonary artery pressure (46+/-10 versus 25+/-6 mm Hg; p < 0.05). LV and RV indices were abnormally high before surgery, declined significantly afterwards, and then almost matched normal values (0.61+/-0.26 versus 0.37+/-0.18; p < 0.05 and 0.55+/-0.22 versus 0.37+/-0.13; p < 0.05). Geometric assessment of the left and right ventricle also showed impaired systolic function before PTE, with significant improvement after surgery. CONCLUSIONS: LV and RV Tei indices allow a quantitative assessment of ventricular function in patients undergoing PTE. Lower indices after surgery reflect an improvement of the previously impaired cardiac function. Our results emphasize the value of PTE in the treatment of chronic thromboembolic pulmonary hypertension.

Modulation of HMG-N2 binding to chromatin by butyrate-induced acetylation in human colon adenocarcinoma cells.

Butyrate, a short chain fatty acid (SCFA), is generated by anaerobic fermentation of undigested carbohydrates within the colon. Butyrate enhances acetylation of core histones, a process directly linked to the formation of active chromatin and gene expression. However, additional chromatin components also contribute to the formation of transcriptionally active chromatin. The high mobility group protein N2 (HMG-N2), a nonhistone protein, is involved in chromatin structure modulation. We examined the effects of butyrate on HMG-N2 expression, hyperacetylation and chromatin binding. HT29 human adenocarcinoma cells were incubated with butyrate. Levels of HMG-N2 mRNA and of total or acetylated HMG-N2 protein were analyzed. Protein dynamics were investigated with transfected cells expressing HMG-N2-EGFP fusion proteins. Treatment of HT29 cells with butyrate led to significant hyperacetylation of HMG-N2. Levels of HMG-N2 protein remained unchanged. Northern blot analysis revealed a significant reduction in HMG-N2 mRNA levels after treatment with butyrate. Analysis of HMG-N2-EGFP transfected HT29 cells demonstrated that butyrate treatment changes the binding properties of HMG-N2-EGFP to chromatin. In addition, butyrate treatment resulted in solubilization of endogenous acetylated HMG-N2 into the supernatant of permeabilized cells. We demonstrate that butyrate treatment is associated with hyperacetylation of HMG-N2 protein in HT29 cells. The modulation of this nonhistone chromatin protein resulted in altered binding properties to chromatin. This may represent an additional step in changing chromatin structure and composition with subsequent consequences for transcription and gene expression. Modulation of nonhistone chromatin proteins, like the ubiquitous HMG-N2 proteins, may be partly responsible for the wide range of butyrate-associated effects.

Type I nitric oxide synthase in the human lung is predominantly expressed in capillary endothelial cells.

Nitric oxide (NO) has important functions in the regulation of pulmonary smooth muscle tone. In the human lung, published data on the expression and distribution of neuronal nitric oxide synthase (NOS-I) are contradictory. The aim of this study, therefore, was to determine the predominant cells expressing NOS-I in the human lung. Immunofluorescence double staining techniques were applied to normal human lung tissue using established monospecific antibodies directed against NOS-I. Suprisingly, capillary endothelial cells in the alveolar septa were identified as the major sites of NOS-I expression. Neither alveolar nor bronchiolar epithelium, nor the alveolar macrophages, expressed NOS-I. These results indicate that the predominant sites of NOS-I expression in the human lung are confined to non-neuronal, i.e. capillary endothelial cells and suggest a role for NO in the regulation of pulmonary endothelial cell permeability.