Efficient parallel linear scaling construction of the density matrix for Born-Oppenheimer molecular dynamics.

We present an algorithm for the calculation of the density matrix that for insulators scales linearly with system size and parallelizes efficiently on multicore, shared memory platforms with small and controllable numerical errors. The algorithm is based on an implementation of the second-order spectral projection (SP2) algorithm [ Niklasson, A. M. N. Phys. Rev. B 2002 , 66 , 155115 ] in sparse matrix algebra with the ELLPACK-R data format. We illustrate the performance of the algorithm within self-consistent tight binding theory by total energy calculations of gas phase poly(ethylene) molecules and periodic liquid water systems containing up to 15,000 atoms on up to 16 CPU cores. We consider algorithm-specific performance aspects, such as local vs nonlocal memory access and the degree of matrix sparsity. Comparisons to sparse matrix algebra implementations using off-the-shelf libraries on multicore CPUs, graphics processing units (GPUs), and the Intel many integrated core (MIC) architecture are also presented. The accuracy and stability of the algorithm are illustrated with long duration Born-Oppenheimer molecular dynamics simulations of 1000 water molecules and a 303 atom Trp cage protein solvated by 2682 water molecules.

Determinants of bistability in induction of the Escherichia coli lac operon.

The authors have developed a mathematical model of regulation of expression of the Escherichia coli lac operon, and have investigated bistability in its steady-state induction behaviour in the absence of external glucose. Numerical analysis of equations describing regulation by artificial inducers revealed two natural bistability parameters that can be used to control the range of inducer concentrations over which the model exhibits bistability. By tuning these bistability parameters, the authors found a family of biophysically reasonable systems that are consistent with an experimentally determined bistable region for induction by thio-methylgalactoside (TMG) (in Ozbudak et al. Nature, 2004, 427; p. 737). To model regulation by lactose, the authors developed similar equations in which allolactose, a metabolic intermediate in lactose metabolism and a natural inducer of lac, is the inducer. For biophysically reasonable parameter values, these equations yield no bistability in response to induction by lactose - only systems with an unphysically small permease-dependent export effect can exhibit small amounts of bistability for limited ranges of parameter values. These results cast doubt on the relevance of bistability in the lac operon within the natural context of E. coli, and help shed light on the controversy among existing theoretical studies that address this issue. The results also motivate a deeper experimental characterisation of permease-independent transport of lac inducers, and suggest an experimental approach to address the relevance of bistability in the lac operon within the natural context of E. coli. The sensitivity of lac bistability to the type of inducer emphasises the importance of metabolism in determining the functions of genetic regulatory networks.

Early responses to mechanical load in tendon: role for calcium signaling, gap junctions and intercellular communication.

Tendon and other connective tissue cells are subjected to diverse mechanical loads during daily activities. Thus, fluid flow, strain, shear and combinations of these stimuli activate mechanotransduction pathways that modulate tissue maintenance, repair and pathology. Early mechanotransduction events include calcium (Ca2+) signaling and intercellular communication. These responses are mediated through multiple mechanisms involving stretch-activated channels, voltage-activated channels such as Ca(v)1, purinoceptors, adrenoceptors, ryanodine receptor-mediated Ca2+ release, gap junctions and connexin hemichannels. Calcium, diacylglycerol, inositol (1,4,5)-trisphosphate, nucleotides and nucleosides play intracellular and/or extracellular signaling roles in these pathways. In addition, responses to mechanical loads in tendon cells vary among species, tendon type, anatomic location, loading conditions and other factors. This review includes a synopsis of the immediate responses to mechanical loading in connective tissue cells, particularly tenocytes. These responses involve Ca2+ signaling, gap junctions and intercellular communication.

Macharistol, a new cytotoxic cinnamylphenol from the stems of Machaerium aristulatum.

A new cinnamylphenol, macharistol (1), along with a known pterocarpan, (+)-medicarpin (2), were isolated as cytotoxic constituents from the stems of Machaerium aristulatum. In addition, a known pterocarpan, (+)-maackiain (3), and a known isoflavone, formononetin (4), were identified as inactive constituents. Compound 1 was evaluated in the in vivo hollow fiber assay with KB, Col-2, and hTERT-RPE1 cells and found to be inactive at the highest dose (25 mg/kg body weight) tested.

Isolation of symlandine from the roots of common comfrey (Symphytum officinale) using countercurrent chromatography.

Three pyrrolizidine alkaloids, symlandine, symphytine, and echimidine (1-3), were isolated from the roots of Symphytum officinale using a one-step countercurrent chromatography procedure. The structures of 1-3 were confirmed by several spectroscopic techniques including 2D NMR methods. This is the first description of the separation of symlandine (1) from its stereoisomer, symphytine (2).

SVDMAN--singular value decomposition analysis of microarray data.

SUMMARY: We have developed two novel methods for Singular Value Decomposition analysis (SVD) of microarray data. The first is a threshold-based method for obtaining gene groups, and the second is a method for obtaining a measure of confidence in SVD analysis. Gene groups are obtained by identifying elements of the left singular vectors, or gene coefficient vectors, that are greater in magnitude than the threshold W N(-1/2), where N is the number of genes, and W is a weight factor whose default value is 3. The groups are non-exclusive and may contain genes of opposite (i.e. inversely correlated) regulatory response. The confidence measure is obtained by systematically deleting assays from the data set, interpolating the SVD of the reduced data set to reconstruct the missing assay, and calculating the Pearson correlation between the reconstructed assay and the original data. This confidence measure is applicable when each experimental assay corresponds to a value of parameter that can be interpolated, such as time, dose or concentration. Algorithms for the grouping method and the confidence measure are available in a software application called SVD Microarray ANalysis (SVDMAN). In addition to calculating the SVD for generic analysis, SVDMAN provides a new means for using microarray data to develop hypotheses for gene associations and provides a measure of confidence in the hypotheses, thus extending current SVD research in the area of global gene expression analysis.

Bioactive constituents of the roots of Licania intrapetiolaris.

Fractionation of a methanol extract of the roots of Licania intrapetiolaris, as directed by activity against the KB assay, has led to the isolation of two novel clerodane diterpenoids, intrapetacins A (1) and B (2), and the known triterpenoid cucurbitacin B (3). The structures of 1 and 2 were deduced from one- and two-dimensional NMR experiments, including relative stereochemical assignments based on NOESY correlations and COSY coupling constants. Compound 3 was the most potent against the KB assay, but both 1 and 2 displayed moderate cytotoxicity. When evaluated against an antifungal assay using Aspergillus niger, 2 caused a significant zone of inhibition of fungal growth, while 1 was completely inactive. To the best of our knowledge, this is the first report of the isolation of bioactive compounds from the genus Licania.

Selective drug resistant human osteosarcoma cell lines.

Chemotherapy in combination with surgery has been shown to be effective for the control of osteosarcoma. Development of resistance to chemotherapeutic agents is a recurring clinical problem. To investigate this phenomena, human osteosarcoma cells, TE-85, were exposed to increasing doses of Taxol or Taxotere during a 9-month period. Highly resistant subclones (TE-85TXL; TE-85TXR, respectively) were developed. Chemosensitivities are presented for TE-85 cell line and these new lines to Taxol, Taxotere, doxorubicin, cisplatin, and topotecan. Drug concentrations that inhibited cell growth by 50% compared with untreated cells were determined. The TE-85TXL cells showed resistance greater than 1,000-fold to Taxol and Taxotere and 60-fold to doxorubicin. The TE-85TXR cells showed resistance greater than 1,000-fold to Taxol, 800-fold to Taxotere, and 90-fold to doxorubicin. There was little cross resistance to topotecan and enhanced sensitivity to cisplatin. The role of P-170 glycoprotein in Taxol and Taxotere resistance was explored. Coincubation with verapamil, to block the actions of P-170 glycoprotein, partly reversed resistance to Taxol, Taxotere, and doxorubicin in both cell lines. Anti-P-170 glycoprotein antibodies revealed positive staining in TE-85TXL and TE-85TXR cell lines. Flow cytometry revealed reduced accumulation of doxorubicin in resistant cells. These data indicate that a human osteosarcoma cell line will develop resistance to Taxol and Taxotere, which is mediated in part by the P-170 glycoprotein.

Dual role of glutathione in modulating camptothecin activity: depletion potentiates activity, but conjugation enhances the stability of the topoisomerase I-DNA cleavage complex.

Depletion of glutathione (GSH) in MCF-7 and MDA-MB-231 cell lines by pretreatment with the GSH synthesis inhibitor buthionine sulfoximine potentiated the activity of 10,11-methylenedioxy-20(S)-camptothecin, SN-38 [7-ethyl-10-hydroxy-20(S)-camptothecin], topotecan, and 7-chloromethyl-10,11-methylenedioxy-20(S)-camptothecin (CMMDC). The greatest potentiation was observed with the alkylating camptothecin CMMDC. Buthionine sulfoximine pretreatment also increased the number of camptothecin-induced DNA-protein crosslinks, indicating that GSH affects the mechanism of action of camptothecin. We also report that GSH interacts with CMMDC to form a stable conjugate, 7-(glutathionylmethyl)-10,11-methylenedioxy-20(S)-camptothecin (GSMMDC), which is formed spontaneously in buffered solutions and in MCF-7 cells treated with CMMDC. GSMMDC was synthesized and found to be nearly as active as 10,11-methylenedioxy-20(S)-camptothecin in a topoisomerase (topo) I-mediated DNA nicking assay. The resulting topo I cleavage complexes were remarkably stable. In cell culture, GSMMDC displayed potent growth-inhibitory activity against U937 and P388 leukemia cell lines. GSMMDC was not active against a topo I-deficient P388 cell line, indicating that topo I is its cellular target. Peptide-truncated analogues of GSMMDC were prepared and evaluated. All three derivatives [7-(gamma-glutamylcysteinylmethyl)-10,11-methylenedioxy-20(S)-camptothecin, 7-(cysteinylglycylmethyl)-10,11-methylenedioxy-20(S)-camptothecin, and 7-(cysteinylmethyl)-10,11-methylenedioxy-20(S)-camptothecin] displayed topo I and cell growth-inhibitory activity. These results suggest that 7-peptidyl derivatives represent a new class of camptothecin analogues.

Camptothecin analogues with enhanced antitumor activity at acidic pH.

BACKGROUND: Camptothecin (CPT) is a specific inhibitor of the nuclear enzyme topoisomerase I, which is involved in cellular DNA replication and transcription. Topoisomerase I is therefore an attractive target for anticancer drug development, and two analogues of CPT, topotecan (TPT) and irinotecan (CPT-11), have demonstrated significant antitumor activity in the clinic. This activity is limited, however, by lability of the CPT E ring lactone, which forms the inactive hydroxy acid at physiological pH. The reaction is reversible at acidic pH, which provides a rationale for selectivity, because many solid tumors create an acidic extracellular environment while maintaining a normal intracellular pH. PURPOSE: To exploit the tumor-selective pH gradient to improve the efficacy of CPT-based chemotherapy. METHODS: CPT analogues were evaluated by growth inhibition assay in three human breast cancer cell lines that had been adapted to in vitro culture at acidic pH versus the respective cells cultured at physiological pH. The MCF-7, MDA-MB-231, and MCF-7/hc cell lines represent the hormone-dependent and hormone-independent stages of the disease, and a MCF-7 variant that is resistant to the alkylating agent 4-hydroperoxycyclophosphamide (4-HC), respectively. Antiproliferative activity of SN-38 (the active metabolite of CPT-11), and TPT was compared to that of CPT and two CPT analogues, 10,11-methylenedioxy-CPT (MDC), and the alkylating derivative, 7-chloromethyl-10,11-MDC (CMMDC). RESULTS: In general, MDC was the most potent and TPT or CPT the least potent analogue, regardless of pH. However, if the comparison was based on magnitude of potentiation by pH, a different rank order emerged. CPT was modulated 4-fold; MDC, SN-38, and TPT were each modulated 5- to 6-fold, while the activity of CMMDC was increased 10- to 11-fold by acidic pH in MCF-7 lines, and 65-fold in MDA-MB-231 cells. Thus MDC was the superior CPT analogue based on potency, but CMMDC was the best candidate for pH modulation. Drug specificity was also observed. While the alkylating agent, 4-HC, was 2- to 3-fold more active at acidic pH, modulation was not observed for 5-fluorouracil, doxorubicin, or paclitaxel. Preliminary mechanism studies indicated that pH modulation of CPT analogues was directly correlated to intracellular levels of glutathione. In addition, protein-associated DNA strand breaks were more rapidly induced at acidic pH. CONCLUSION: These results suggest that CPT-based drug development and resulting chemotherapy could benefit from evaluation of differential activity at acidic versus physiological pH. Analogues have been identified that could have improved therapeutic indices based on the pH gradient that selectively exists in human tumors.

New bioactive aromatic compounds from Vismia guianensis.

Five benzophenones, vismiaguianones A-E, and two benzocoumarins, vismiaguianins A and B were isolated from the CHCl3 extract of the roots of Vismia guianensis by bioassay-directed fractionation using the DNA strand-scission assay and KB cell line. Of the isolates obtained, vismiaguianone B exhibited DNA strand-scission activity, whereas vismiaguianones D and E and vismiaguianin A were found to be significantly cytotoxic.

Large-scale shape changes in proteins and macromolecular complexes.

Proteins and RNA undergo intricate motions as they carry out functions in biological systems. These motions frequently entail large-scale conformational changes that induce changes in the surface structure, or shape, of a molecule. This review describes the experimental characterization of large-scale shape changes in proteins and macromolecular complexes and the effects of such changes on macromolecular behavior. We describe several important results that have been obtained by using small-angle scattering, which is emerging as a powerful technique for determining macromolecular shapes and elucidating the quaternary structure of macromolecular assemblies.

A model of troponin-I in complex with troponin-C using hybrid experimental data: the inhibitory region is a beta-hairpin.

We present a model for the skeletal muscle troponin-C (TnC)/troponin-I (TnI) interaction, a critical molecular switch that is responsible for calcium-dependent regulation of the contractile mechanism. Despite concerted efforts by multiple groups for more than a decade, attempts to crystallize troponin-C in complex with troponin-I, or in the ternary troponin-complex, have not yet delivered a high-resolution structure. Many groups have pursued different experimental strategies, such as X-ray crystallography, NMR, small-angle scattering, chemical cross-linking, and fluorescent resonance energy transfer (FRET) to gain insights into the nature of the TnC/TnI interaction. We have integrated the results of these experiments to develop a model of the TnC/TnI interaction, using an atomic model of TnC as a scaffold. The TnI sequence was fit to each of two alternate neutron scattering envelopes: one that winds about TnC in a left-handed sense (Model L), and another that winds about TnC in a right-handed sense (Model R). Information from crystallography and NMR experiments was used to define segments of the models. Tests show that both models are consistent with available cross-linking and FRET data. The inhibitory region TnI(95-114) is modeled as a flexible beta-hairpin, and in both models it is localized to the same region on the central helix of TnC. The sequence of the inhibitory region is similar to that of a beta-hairpin region of the actin-binding protein profilin. This similarity supports our model and suggests the possibility of using an available profilin/actin crystal structure to model the TnI/actin interaction. We propose that the beta-hairpin is an important structural motif that communicates the Ca2+-activated troponin regulatory signal to actin.

7- and 10-substituted camptothecins: dependence of topoisomerase I-DNA cleavable complex formation and stability on the 7- and 10-substituents.

7-Alkyl, 7-alkyl-10-hydroxy, 7-alkyl-10-methoxy, and 7-alkyl-10, 11-methylenedioxy analogs of camptothecin have been synthesized and evaluated for their ability to trap human DNA topoisomerase I in cleavable complexes. The 7-alkyl chain lengths varied linearly from methyl to butyl. The concentration required to produce cleavable complexes with purified topoisomerase I in 50% of the plasmid DNA (EC(50)) was reduced by 1 order of magnitude by the introduction of a 10-methoxy or 7-alkyl group compared with camptothecin. The EC(50) values were reduced by 2 orders of magnitude with a 10-hydroxy or 10, 11-methylenedioxy moiety compared with camptothecin. The steady-state EC(50) concentrations for all of the analogs tested were slightly dependent on substitution at the 7-position, but this dependence was least with the 10-methoxy series. The kinetics of the reversibility of the complexes formed with all analogs was only slightly influenced by the length of the 7-substitution, with the trend that ethyl or greater lengths led to slightly reduced rate constants for cleavable complex reversal. These results were also observed for DNA-protein cross-link formation by the analogs in isolated CEM cell nuclei. Our data indicate that in vitro cleavable complex stability, as determined by the apparent rate constants for complex dissociation, does not reflect the in vitro biological activity of these camptothecin analogs. However, complex stability in vivo may be important for the antitumor activity of the compounds.

Comparison of in vitro activities of camptothecin and nitidine derivatives against fungal and cancer cells.

The activities of a series of camptothecin and nitidine derivatives that might interact with topoisomerase I were compared against yeast and cancer cell lines. Our findings reveal that structural modifications to camptothecin derivatives have profound effects on the topoisomerase I-drug poison complex in cells. Although the water-soluble anticancer agents topotecan and irinotecan are less active than the original structure, camptothecin, other derivatives or analogs with substitutions that increase compound solubility have also increased antifungal activities. In fact, a water-soluble prodrug appears to penetrate into the cell and release its active form; the resulting effect in complex with Cryptococcus neoformans topoisomerase I is a fungicidal response and also potent antitumor activity. Some of the compounds that are not toxic to wild-type yeast cells are extremely toxic to the yeast cells when the C. neoformans topoisomerase I target is overexpressed. With the known antifungal mechanism of a camptothecin-topoisomerase I complex as a cellular poison, these findings indicate that drug entry may be extremely important for antifungal activity. Nitidine chloride exhibits antifungal activity against yeast cells through a mechanism(s) other than topoisomerase I and appears to be less active than camptothecin analogs against tumor cells. Finally, some camptothecin analogs exhibit synergistic antifungal activity against yeast cells in combination with amphotericin B in vitro. Our results suggest that camptothecin and/or nitidine derivatives can exhibit potent antifungal activity and that the activities of camptothecin derivatives with existing antifungal drugs may be synergistic against pathogenic fungi. These new compounds, which exhibit potent antitumor activities, will likely require further structural changes to find more selective activity against fungal versus mammalian cells to hold promise as a new class of antifungal agents.

New biphenyl compounds with DNA strand-scission activity from Clusia paralicola.

Three new biphenyl derivatives, clusiparalicolines A (1), B (2), and C (3), were isolated from the roots of Clusia paralicola by bioassay-directed fractionation using the DNA strand-scission and the KB human cancer cell line cytotoxicity assays. Compounds 1 and 2 were found to be active in the DNA strand-scission assay, whereas all three compounds exhibited modest cytotoxicity against the KB cell line. The structures of 1-3 were elucidated by spectroscopic methods including 1D and 2D NMR techniques.

Pre-clinical evaluation of SN-38 and novel camptothecin analogs against human chronic B-cell lymphocytic leukemia lymphocytes.

The topoisomerase I inhibitor camptothecin and its analogs have potent activity against a wide range of solid tumors and several hematologic malignancies. Previous studies with these compounds using the MTT metabolic inhibition assay have shown significant cytotoxicity against lymphocytes from patients with chronic B-cell lymphocytic leukemia (B-CLL). Yet the water soluble analogue, topotecan, which was inhibitory at > 1 microM in vitro, had no clinical activity in vivo. In the present study, we evaluated the in vitro cytotoxicities of SN-38, the active form of irinotecan, and two newer water soluble camptothecin derivatives 10,11-methylenedioxy-20(S)-camptothecin glycinate (MDCG) and 7-chloromethyl-10,11-methylenedioxy-20(S)-camptothecin glycinate (CMMDCG). These two glycinate esters are prodrugs for 10,11-methylenedioxy-20(S)-camptothecin (MDC) and 7-chloromethyl-10,11-methylenedioxy-20(S)-camptothecin (CMMDC), respectively. Effects on cellular metabolism, induction of apoptosis, and overall cell survival were used to evaluate chemosensitivity. We report that the relative cytotoxic potency for these compounds is MDC > or = CMMDC > or = SN-38 >> TPT > CPT-11, where MDC, CMMDC, and SN-38 were over an order of magnitude more cytotoxic than TPT and CPT-11. We also investigated potential mechanisms underlying the unexpected cytotoxicity of these camptothecin derivatives in B-CLL cells that are known to be arrested in G0/G1 of the cell cycle, and found that this class of compounds inhibited [3H]uridine incorporation. We therefore postulate that the inhibition of RNA rather than DNA synthesis may be responsible for the observed cytotoxicity in non-cycling B-CLL cells.