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.

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.

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.

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.

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.

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.

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).

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.

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.

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.

Protein structure determination using a database of interatomic distance probabilities

The accelerated pace of genomic sequencing has increased the demand for structural models of gene products. Improved quantitative methods are needed to study the many systems (e.g., macromolecular assemblies) for which data are scarce. Here, we describe a new molecular dynamics method for protein structure determination and molecular modeling. An energy function, or database potential, is derived from distributions of interatomic distances obtained from a database of known structures. X-ray crystal structures are refined by molecular dynamics with the new energy function replacing the Van der Waals potential. Compared to standard methods, this method improved the atomic positions, interatomic distances, and side-chain dihedral angles of structures randomized to mimic the early stages of refinement. The greatest enhancement in side-chain placement was observed for groups that are characteristically buried. More accurate calculated model phases will follow from improved interatomic distances. Details usually seen only in high-resolution refinements were improved, as is shown by an R-factor analysis. The improvements were greatest when refinements were carried out using X-ray data truncated at 3.5 A. The database potential should therefore be a valuable tool for determining X-ray structures, especially when only low-resolution data are available.

Stem cell transplantation for metastatic breast cancer: analysis of tumor contamination

The purpose of this study was to determine the efficacy, engraftment kinetics, effect of bone marrow tumor contamination, and safety of high-dose therapy and granulocyte-colony stimulating factor (G-CSF) mobilized peripheral blood progenitor cell (PBPC) support for patients with responding metastatic breast cancer. Forty two patients underwent G-CSF (10 microg/kg) stimulated PBPC harvest. PBPC and bone marrow aspirates were analyzed by histologic and immunocytochemical methods for tumor contamination. Thirty-seven patients received high-dose therapy consisting of cyclophosphamide 6 g/m2, thiotepa 500 mg/m2, and carboplatin 800 mg/m2 (CTCb) given as an infusion over 4 d followed by PBPC reinfusion and G-CSF (5 microg/kg) support. No transplant related deaths or grade 4 toxicity was recorded. CD34+ cells/kg infused was predictive of neutrophil and platelet recovery. With a median follow-up of 38 months, three year survival was 44% with relapse-free survival of 19%. Histological bone marrow involvement, found in 10 patients, was a negative prognostic factor and was associated with a median relapse-free survival of 3.5 months. Tumor contamination of PBPC by immunohistochemical staining was present in 22.5% of patients and found not to be correlated with decreased survival. G-CSF stimulated PBPC collection followed by a single course of high dose chemotherapy and stem cell infusion with G-CSF stimulated marrow recovery leads to rapid, reliable engraftment with low toxicity and promising outcome in women with responding metastatic breast cancer.

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.

Human DNA topoisomerase I: quantitative analysis of the effects of camptothecin analogs and the benzophenanthridine alkaloids nitidine and 6-ethoxydihydronitidine on DNA topoisomerase I-induced DNA strand breakage

Human DNA topoisomerase I (topo I) has been purified from normal placenta and from a recombinant baculovirus expression system. A new radiolabeled plasmid DNA assay has been used to quantitate the activity of the purified enzymes and to compare the ability of several types of topo I-targeted drugs to induce topo I-mediated DNA strand breaks. The 100-kDa recombinant enzyme form isolated from the baculovirus expression system is able to relax 2564 ng of supercoiled M-13 mp19 plasmid per minute per nanogram of enzyme. The addition of camptothecin (1 microM) to the reaction lowers the rate to 1282 ng per minute per nanogram of enzyme. The 100-kDa topo I from human placenta is able to relax 1092 ng of supercoiled plasmid per minute per nanogram of enzyme and the 68-kDa topo I form from placenta is able to relax 2069 ng of supercoiled plasmid per minute per nanogram of enzyme. Camptothecin (1 microM) decreases the relaxation rate of the placental enzymes about 50%. In the presence of several different types of topo I-targeted drugs, both the recombinant and placental enzymes are induced to cleave plasmid DNA. Quantitative DNA cleavage assays with radioactive plasmid DNA and 9-aminocamptothecin, topotecan, SN-38, 10, 11-methylenedioxycamptothecin, 7-ethyl-10, 11-methylenedioxycamptothecin, 7-chloromethyl-10, 11-methylenedioxycamptothecin, nitidine, and 6-ethoxy-5, 6-dihydronitidine indicate that the order of potency in inducing topo I-mediated DNA breakage is methylenedioxycamptothecin analogs > SN-38 > 9-aminocamptothecin > topotecan and camptothecin > nitidine compounds. The order of potency correlates with the half-lives of the topo I-DNA drug complex determined with radiolabeled DNA in 0.45 M NaCl at 30 degrees C. The half-life of the complex formed with 7-chloromethyl-10,11-methylenedioxycamptothecin is greater than 90 min whereas the half-life of the topo I-DNA complex with 6-ethoxy-5, 6-dihydronitidine is less than 15 s. The other drugs tested were found to have drug complex half-lives which fall between these two extremes.

Cytotoxic constituents from the roots of Tovomita brevistaminea

Two known xanthones, trapezifolixanthone and manglexanthone were isolated as cytotoxic constituents from the CHCl3 extract of the roots of Tovomita brevistaminea by bioassay-guided fractionation using the KB cell line. In addition, a new compound, tovophenone C, and two known compounds, tovophenones A and B which are benzophenones, were found to be inactive constituents in this investigation. The structure of the new isolate was determined by detailed analysis of spectroscopic parameters including its 1D and 2D NMR spectroscopy data.

Water soluble 20(S)-glycinate esters of 10,11-methylenedioxycamptothecins are highly active against human breast cancer xenografts

Water-soluble 20(S)-glycinate esters of two highly potent 10,11-methylenedioxy analogues of camptothecin (CPT) have been synthesized and evaluated for their ability to eradicate human breast cancer tumor xenografts. The glycinate ester moiety increases the water solubility of the 10,11-methylenedioxy analogues 4-16-fold. However, in contrast to CPT-11, a water-soluble CPT analogue that was recently approved for second line treatment of colorectal cancer, the 20(S)-glycinate esters do not require carboxylesterase for conversion to their active forms. The glycinate esters are hydrolyzed to their parent, free 20(S)-hydroxyl active analogues in phosphate buffer (pH 7.5) and in mouse and human plasma. The glycinate esters are also 20-40-fold less potent than CPT-11 in inhibiting human acetylcholinesterase. In vivo, we examined 20(S)-glycinate-10,11-methylenedioxycamptothecin, 20(S)-glycinate-7-chloromethyl-10,11-methylenedioxycamptothecin, and CPT-11. We found that the two 10,11-methylenedioxy analogues had antitumor activity against breast cancer xenografts that was comparable to that of CPT-11. Our results indicate that water-soluble 20(S)-glycinate esters of highly potent CPT analogues provide compounds that maintain biological activity, do not require interactions with carboxylesterases, and do not inhibit human acetylcholinesterase.

Acquisition of incidental information during instruction for a response-chain skill

We examined the acquisition of incidental information and observational learning of incidental information by adolescents with moderate intellectual disabilities during school-directed systematic instruction. Effectiveness of constant time-delay instruction for vocational-skill acquisition was evaluated within a multiple-probe design across six dyads. Dyadic instructional arrangements allowed the assessment of incidental information acquired through observation. The constant time-delay procedure was effective in teaching the target vocational skill. In addition, participants acquired and retained approximately 50% of the incidental information to which they were exposed during the consequent events of constant time-delay instruction either through direct verbal presentation or through observation of their peers' instruction.

Camptothecin and taxol: discovery to clinic

Camptothecin (CPT) is a pentacyclic alkaloid isolated from wood and bark of Camptotheca acuminata. Initially it was found to be highly active in a number of mouse in vivo cancer assays. Subsequently, CPT was found to uniquely inhibit an enzyme, topoisomerase I, which is involved in DNA replication. A number of CPT analogs are in advanced clinical trial, and two, Topotecan and CPT-11, have been approved for marketing by the FDA. taxol, a taxane alkaloid, was isolated from Taxus brevifolia. Taxol is a highly cytotoxic compound active in several mouse antitumor assays. It was subsequently found to uniquely inhibit tubulin, a protein involved in mitosis. After clinical evaluation, it has become the drug of choice for treatment of ovarian cancer.

New compounds with DNA strand-scission activity from the combined leaf and stem of Uvaria hamiltonii

Two flavanones, hamiltones A (1) and B (2), an aurone, hamiltrone (3), a chalcone, hamilcone (4), and a tetrahydroxanthene, hamilxanthene (5), were isolated from Uvaria hamiltonii extracts guided initially by fractionation based on DNA strand-scission and/or 9KB cytotoxicity assays. Compounds 2-5 have not been reported previously, while 1 is new as a natural product. Structural assignments were made based on extensive spectroscopic measurements. Compounds 1-3 were inactive in the 9KB cytotoxicity assay, with compounds 4 and 5 having weak activity. In the DNA strand-scission assay, 3 was the most active compound found in the DNA strand-scission assay, being 10 times more potent than 1 or 2. Compound 4 was only weakly active, and 5 was inactive.

Motions of calmodulin characterized using both Bragg and diffuse X-ray scattering

BACKGROUND

Calmodulin is a calcium-activated regulatory protein which can bind to many different targets. The protein resembles a highly flexible dumbbell, and bends in the middle as it binds. This and other motions must be understood to formulate a realistic model of calmodulin function.

RESULTS

Using the Bragg reflections from X-ray crystallography, a multiple-conformer refinement of a calmodulin-peptide complex shows anisotropic displacements, with high variations of dihedral angles in several nonhelical domains: the flexible linker; three of the four calcium-binding sites (including both of the N-terminal sites); and a turn connecting the C-terminal EF-hand calcium-binding domains. Three-dimensional maps of the large scale diffuse X-ray scattering data show isotropic liquid-like motions with an unusually small correlation length. Three-dimensional maps of the small scale diffuse streaks show highly coupled, anisotropic motions along the head-to-tail molecular packing direction in the unit cell. There is also weak coupling perpendicular to the head-to-tail packing direction, particularly across a cavity occupied by the disordered linker domain of the molecule.

CONCLUSIONS

Together, the Bragg and diffuse scattering present a self-consistent description of the motions in the flexible linker of calmodulin. The other mobile regions of the protein are also of great interest. In particular, the high variations in the calcium-binding sites are likely to influence how strongly they bind ions. This is especially important in the N-terminal sites, which regulate the activity of the molecule.

Novel 7-alkyl methylenedioxy-camptothecin derivatives exhibit increased cytotoxicity and induce persistent cleavable complexes both with purified mammalian topoisomerase I and in human colon carcinoma SW620 cells

An alkylating camptothecin (CPT) derivative, 7-chloromethyl-10,11-methylenedioxy-camptothecin (7-CM-MDO-CPT) was recently shown to produce irreversible topoisomerase I (top1) cleavage complexes by binding to the +1 base of the scissile strand of a top1 cleavage site. We demonstrate that 7-CM-EDO-CPT (7-chloromethyl-10,11-ethylenedioxy-camptothecin) also induces irreversible top1-DNA complexes. 7-CM-MDO-CPT, 7-CM-EDO-CPT, and the nonalkylating derivative 7-ethyl-10,11-methylenedioxy-camptothecin (7-E-MDO-CPT) also induced reversible top1 cleavable complexes, which were markedly more stable to salt-induced reversal than those induced by 7-ethyl-10-hyroxy-CPT, the active metabolite of CPT-11. This greater stability of the top1 cleavable complexes was contributed by the 7-alkyl and the 10,11-methylene- (or ethylene-) dioxy substitutions. Studies in SW620 cells showed that 7-E-MDO-CPT, 7-CM-MDO-CPT, and 7-CM-EDO-CPT are more potent inducers of cleavable complexes and more cytotoxic than CPT. The reversal of the cleavable complexes induced by 7-E-MDO-CPT, 7-CM-MDO-CPT, and 7-CM-EDO-CPT was markedly slower after drug removal than that for CPT, which is consistent with the data with purified top1. By contrast to CPT, 7-E-MDO-CPT, 7-CM-MDO-CPT, and 7-CM-EDO-CPT were cytotoxic irrespective of the presence of 10 microM aphidicolin. These results suggest that 7-E-MDO-CPT, 7-CM-MDO-CPT, and 7-CM-EDO-CPT are more potent top1 poisons than CPT and produce long lasting top1 cleavable complexes and greater cytotoxicity than CPT in cells.

Three-dimensional diffuse x-ray scattering from crystals of Staphylococcal nuclease

We have developed methods for obtaining and characterizing three-dimensional maps of the reciprocal-space distribution of diffuse x-ray scattering from protein crystals, and have used the methods to study the nature of disorder in crystals of Staphylococcal nuclease. Experimentally obtained maps are 99.5% complete in the reciprocal-space resolution range of 10 A-2.5 A, show symmetry consistent with the P41 space group of the unit cell, and are highly reproducible. Quantitative comparisons of the data with three-dimensional simulations imply liquid-like motions of the protein [Caspar, D. L. D., Clarage, J., Salunke, D. M. & Clarage, M. (1988) Nature (London) 332, 659-662], with a correlation length of 10 A and a root-mean-square displacement of 0.36 A.

Comparative molecular field analysis and molecular modeling studies of 20-(S)-camptothecin analogs as inhibitors of DNA topoisomerase I and anticancer/antitumor agents

Conformational studies and comparative molecular field analysis (CoMFA) were undertaken for a series of camptothecin (CPT) analogs to correlate topoisomerase I inhibition with the steric and electrostatic properties of 32 known compounds. The resulting CoMFA models have been used to make predictions on novel CPT derivatives. Using the newly derived MM3 parameters, a molecular database of the 32 CPT analogs was created. Various point atomic charges were generated and assigned to the MM3 minimized structures, which were used in partial least-squares analyses. Overall, CoMFA models with the greatest predictive validity were obtained when both the R- and S-isomers were included in the data set, and semiempirical charges were calculated for MM3 minimized low-energy lactone structures. A cross-validated R2 of 0.758 and a non-cross-validated R2 of 0.916 were obtained for MM3 minimized structures with PM3 ESP charges for the 32 CPT analogs. The derived QSAR equations were used to assign topoisomerase I inhibition values for compounds in this study and compounds not included in the original data set. Prior to its appearance in the literature, an IC50 of 103 nM was predicted for the 10,11-oxazole derivative. This CoMFA predicted value compared favorably with the recently reported value of 150 nM. The CoMFA model was also evaluated by predicting the activities of recently reported 11-aza CPT and trione derivatives. The predicted activity (IC50 = 249 nM) for 11-aza CPT compared well with the reported value of 383 nM.

Triterpenes from the combined leaf and stem of Lithospermum caroliniense

An investigation of the combined leaf and stem of Lithospermum caroliniense afforded two new pentacyclic triterpenoids based on the olean-12-ene and taraxast-12-ene skeletal types. The structures of these compounds were elucidated on the basis of spectral analysis as 1 alpha,3 beta,23-trihydroxyolean-12-ene-28-oic acid and 3 alpha,19 beta,21 alpha,23-tetrahydroxytaraxast-12-ene-28-oic acid.

Camptothecin and taxol: from discovery to clinic

Camptothecin (CPT) and taxol are secondary metabolites found in the stembark of Camptotheca acuminata, a native of China, and Taxus brevifolia, found in the northwest Pacific coastal region of the USA, respectively. The compounds were isolated through bioassay-guided fractionation of various extracts and through chromatographic fractions. Their unique and hitherto unknown structures were elucidated by nuclear magnetic resonance, mass spectrometry and X-ray analysis. Both compounds have unique mechanisms of antitumor activity; CPT uniquely inhibits an enzyme, topoisomerase I, involved in DNA replication, while taxol binds to a protein, tubulin, thus inhibiting cell division. Taxol has been called the best new anticancer agent developed from natural products, showing particular efficacy against ovarian cancer. CPT and analogs singly or combined with cisplatinum show efficacy against solid tumors, breast, lung, and colorectal, which hitherto have been unaffected by most cancer chemotherapeutic agents.

Two isoflavones from the bark of Petalostemon purpureus

Two new isoflavones, 6,7,8,3',4',5'-hexamethoxyisoflavone and 7,8,3',4',5'-pentamethoxyisoflavone, have been isolated and characterized from the combined root bark and stem bark of Petalostemon purpureus.

A new prenylated flavonol from the root of Petalostemon purpureus

A new prenylated flavonol, petalopurpurenol (1), and a known dihydroflavonol, petalostemumol (2), have been isolated by DNA scission-guided fractionation of the organic portion of a 20% MeOH/CHCl3/H2O partition of a 50% MeOH/CHCl3 extract of the roots of Petalostemon purpureus. Compound 2 displayed moderate activity in DNA-scission assay. Both compounds 1 and 2 were evaluated for cytotoxicity in a panel of human cancer cell lines. The structures of petalopurpurenol (1) and petalostemumol (2) were determined by spectroscopic analysis.

Two isoflavones from the bark of Petalostemon purpureus

Two new isoflavones, 6,7,8,3',4',5'-hexamethoxyisoflavone and 7,8,3',4',5'-pentamethoxyisoflavone, have been isolated and characterized from the combined root bark and stem bark of Petalostemon purpureus.

Two new aromatic constitutents from the rootwood of Aeschynomene mimosifolia

The rootwood of Aeschynomene mimosifolia Vatke (Leguminosae) has yielded a new neoflavonoid, mimosifoliol (1), and an unusual C16-styrylcycloheptenone derivative, mimosifolenone (2). The structures of these compounds were determined on the basis of spectral analysis. Compound 1 demonstrated weak activity in DNA-strand scission assay, while compound 2 was found to be inactive. Mimosifoliol (1) was inactive toward several human cell lines, while 2 was moderately active against the KB cell line.

Isolation and structure identification of an active DNA strand-scission agent, (+)-3,4-di-hydroxy-8,9-methylenedioxypterocarpan

A new pterocarpan, (+)-3,4-dihydroxy-8,9-methylenedioxypterocarpan [1], was isolated from the flowers of Petalostemon purpureus by a DNA strand-scission assay-guided fractionation procedure. Compound 1 demonstrated activity in a standard in vitro DNA strand-scission assay, and cytotoxicity toward a KB tumor cell line. Two other related pterocarpans [2, 3] isolated from same plant were found to be moderately active for KB cells, but were inactive in the DNA strand-scission assay. (+)-4-Hydroxy-3-methoxy-8,9-methylenedioxypterocarpan [2] has not been reported previously as a natural product, while (+)-maackiain [3] has been isolated only as an optically inactive racemate along with its optical antipode, the (-)-isomer.

Gummiferol, a cytotoxic polyacetylene from the leaves of Adenia gummifera

A new polyacetylenic diepoxide compound, gummiferol [1] was isolated from the leaves of Adenia gummifera by KB cytotoxicity-guided fractionation. Compound 1 exhibited significant activity against the KB human cell line and a broad cytotoxic spectrum against other human cancer cell lines. The structure of 1 was established primarily on the basis of its spectral data.

Antitrypanosomal activity of camptothecin analogs. Structure-activity correlations

African trypanosomes (Trypanosoma brucei species) are parasitic protozoa that cause lethal diseases in humans and cattle. Previous studies showed that camptothecin, a potent and specific inhibitor of DNA topoisomerase I, is cytotoxic to African trypanosomes and related pathogenic hemoflagellates (Bodley AL and Shapiro TA, Proc Natl Acad Sci USA 92: 3726-3730, 1995). In this study, a series of camptothecin analogs was tested against axenically cultured, bloodstream form, T. brucei. Modifications to the pentacyclic nucleus of camptothecin ablated antiparasitic activity. In contrast, activity could be increased by substituents added to the parent ring system (e.g. 10,11-methylenedioxy or ethylenedioxy groups; alkyl additions to carbon 7; or 9-amino or 9-chloro substituents). Cytotoxicity was correlated with the level of cleavable complexes in trypanosomes, implicating topoisomerase I as the intracellular target for these compounds. To obtain some indication of selective toxicity, ten compounds were also tested against L1210 mouse leukemia cells. The 9-substituted-10,11-methylenedioxy analogs caused a disproportionate increase in antiparasitic activity, compared with mammalian cell toxicity. These findings provide a basis for designing further structural modifications and for selecting camptothecin analogs to test in animal models of trypanosomiasis.

Interaction of an alkylating camptothecin derivative with a DNA base at topoisomerase I-DNA cleavage sites

DNA topoisomerase I (top1) is a ubiquitous nuclear enzyme. It is specifically inhibited by camptothecin, a natural product derived from the bark of the tree Camptotheca acuminata. Camptothecin and several of its derivatives are presently in clinical trial and exhibit remarkable anticancer activity. The present study is a further investigation of the molecular interactions between the drug and the enzyme-DNA complex. We utilized an alkylating camptothecin derivative, 7-chloromethyl-10,11-methylenedioxycamptothecin (7-ClMe-MDO-CPT), and compared its activity against calf thymus top1 in a DNA oligonucleotide containing a single top1 cleavage site with the activity of its nonalkylating analog, 7-ethyl-10,11-methylenedioxycamptothecin (7-Et-MDO-CPT). In the presence of top1, 7-ClMe-MDO-CPT produced a DNA fragment that migrated more slowly than the top1-cleaved DNA fragment observed with 7-Et-MDO-CPT. Top1 was unable to religate this fragment in the presence of high NaCl concentration or proteinase K at 50 degrees C. This fragment was resistant to piperidine treatment and was also formed with an oligonucleotide containing a 7-deazaguanine at the 5' terminus of the top1-cleaved DNA (base + 1). It was however cleaved by formic acid treatment followed by piperidine. These observations are consistent with alkylation of the +1 base (adenine or guanine) by 7-ClMe-MDO-CPT in the presence of top1 covalent complexes and provide direct evidence that camptothecins inhibit top1 by binding at the enzyme-DNA interface.

High-resolution macromolecular structure determination using CCD detectors and synchrotron radiation

BACKGROUND

Synchrotron radiation sources have made impressive contributions to macromolecular crystallography. The delay in development of appropriate X-ray detectors has, however, been a significant limitation to their efficient use. New technologies, based on charge-coupled devices (CCDs), provide capabilities for faster, more accurate, automated data collection.

RESULTS

A CCD-based X-ray detector has been developed for use in macromolecular crystallography and has been in operation for about one and a half years at the Cornell High Energy Synchrotron Source. It has been used for a variety of crystallographic projects, including a number of high-resolution structural studies. The statistical quality of the data, the detector's ease and efficiency of use, and the growing number of structural results illustrate the practical utility of this new detector system.

CONCLUSIONS

The new detector has enhanced capabilities for measuring diffraction patterns from crystals of macromolecules, especially at high resolution, when the X-ray intensities are weak. The survey of results described here ranges from virus crystallography to weakly diffracting small-molecule structure determination and demonstrates the potential of CCD detectors when combined with synchrotron radiation sources.