Showing papers by "Peter Wipf published in 2008"

An experimental survey of the transition between two-state and downhill protein folding scenarios

Abstract: A kinetic and thermodynamic survey of 35 WW domain sequences is used in combination with a model to discern the energetic requirements for the transition from two-state folding to downhill folding. The sequences used exhibit a 600-fold range of folding rates at the temperature of maximum folding rate. Very stable proteins can achieve complete downhill folding when the temperature is lowered sufficiently below the melting temperature, and then at even lower temperatures they become two-state folders again because of cold denaturation. Less stable proteins never achieve a sufficient bias to fold downhill because of the onset of cold denaturation. The model, considering both heat and cold denaturation, reveals that to achieve incipient downhill folding (barrier <3 RT) or downhill folding (no barrier), the WW domain average melting temperatures have to be ≥50°C for incipient downhill folding and ≥90°C for downhill folding.

Development of a 384-well colorimetric assay to quantify hydrogen peroxide generated by the redox cycling of compounds in the presence of reducing agents.

Abstract: We report here the development and optimization of a simple 384-well colorimetric assay to measure H(2)O(2) generated by the redox cycling of compounds incubated with reducing agents in high-throughput screening (HTS) assay buffers. The phenol red-horseradish peroxidase (HRP) assay readily detected H(2)O(2) either added exogenously or generated by the redox cycling of compounds in dithiothreitol (DTT). The generation of H(2)O(2) was dependent on the concentration of both the compound and DTT and was abolished by catalase. Although both DTT and tris(2-carboxyethyl) phosphine sustain the redox cycling generation of H(2)O(2) by a model quinolinedione, 6-chloro-7-(2-morpholin-4-yl-ethylamino)-quinoline-5,8-dione (NSC 663284; DA3003-1), other reducing agents such as beta-mercaptoethanol, glutathione, and cysteine do not. The assay is compatible with HTS. Once terminated, the assay signal was stable for at least 5 h, allowing for a reasonable throughput. The assay tolerated up to 20% dimethyl sulfoxide, allowing a wide range of compound concentrations to be tested. The assay signal window was robust and reproducible with average Z-factors of > or =0.8, and the redox cycling generation of H(2)O(2) by DA3003-1 in DTT exhibited an average 50% effective concentration of 0.830 +/- 0.068 microM. Five of the mitogen-activated protein kinase phosphatase (MKP) 1 inhibitors identified in an HTS were shown to generate H(2)O(2) in the presence of DTT, and their inhibition of MKP-1 activity was shown to be time dependent and was abolished or significantly reduced by either 100 U of catalase or by higher DTT levels. A cross-target query of the PubChem database with three structurally related pyrimidotriazinediones revealed active flags in 36-39% of the primary screening assays. Activity was confirmed against a number of targets containing active site cysteines, including protein tyrosine phosphatases, cathepsins, and caspases, as well as a number of cellular cytotoxicity assays. Rather than utilize resources to conduct a hit characterization effort involving several secondary assays, the phenol red-HRP assay provides a simple, rapid, sensitive, and inexpensive method to identify compounds that redox cycle in DTT or tris(2-carboxyethyl)phosphine to produce H(2)O(2) that may indirectly modulate target activity and represent promiscuous false-positives from a primary screen.

A mitochondria-targeted nitroxide/hemigramicidin S conjugate protects mouse embryonic cells against gamma irradiation

Abstract: Purpose To evaluate the in vitro radioprotective effect of the mitochondria-targeted hemigramicidin S–conjugated 4-amino-2,2,6,6-tetramethyl-piperidine- N -oxyl (hemi-GS-TEMPO) 5-125 in γ-irradiated mouse embryonic cells and adenovirus-12 SV40 hybrid virus transformed human bronchial epithelial cells BEAS-2B and explore the mechanisms involved in its radioprotective effect. Methods and Materials Cells were incubated with 5-125 before (10 minutes) or after (1 hour) γ-irradiation. Superoxide generation was determined by using dihydroethidium assay, and lipid oxidation was quantitated by using a fluorescence high-performance liquid chromatography–based Amplex Red assay. Apoptosis was characterized by evaluating the accumulation of cytochrome c in the cytosol and externalization of phosphatidylserine on the cell surface. Cell survival was measured by means of a clonogenic assay. Results Treatment (before and after irradiation) of cells with 5-125 at low concentrations (5, 10, and 20 μm) effectively suppressed γ-irradiation–induced superoxide generation, cardiolipin oxidation, and delayed irradiation–induced apoptosis, evaluated by using cytochrome c release and phosphatidylserine externalization. Importantly, treatment with 5-125 increased the clonogenic survival rate of γ-irradiated cells. In addition, 5-125 enhanced and prolonged γ-irradiation–induced G 2 /M phase arrest. Conclusions Radioprotection/mitigation by hemi-GS-TEMPO likely is caused by its ability to act as an electron scavenger and prevent superoxide generation, attenuate cardiolipin oxidation in mitochondria, and hence prevent the release of proapoptotic factors from mitochondria. Other mechanisms, including cell-cycle arrest at the G 2 /M phase, may contribute to the protection.

A cell-active inhibitor of mitogen-activated protein kinase phosphatases restores paclitaxel-induced apoptosis in dexamethasone-protected cancer cells

Abstract: Mitogen-activated protein kinase phosphatase (MKP)-1 is a dual-specificity phosphatase that negatively regulates the activity of mitogen-activated kinases and that is overexpressed in human tumors. Contemporary studies suggest that induction of MKP-1 during chemotherapy may limit the efficacy of clinically used antineoplastic agents. Thus, MKP-1 is a rational target to enhance anticancer drug activity, but suitable small-molecule inhibitors of MKP-1 are currently unavailable. Here, we have used a high-content, multiparameter fluorescence-based chemical complementation assay for MKP activity in intact mammalian cells to evaluate the cellular MKP-1 and MKP-3 inhibitory activities of four previously described, quinone-based, dual-specificity phosphatase inhibitors, that is, NSC 672121, NSC 95397, DA-3003-1 (NSC 663284), and JUN-1111. All compounds induced formation of reactive oxygen species in mammalian cells, but only one (NSC 95397) inhibited cellular MKP-1 and MKP-3 with an IC(50) of 13 mumol/L. Chemical induction of MKP-1 by dexamethasone protected cells from paclitaxel-induced apoptosis but had no effect on NSC 95397. NSC 95397 phenocopied the effects of MKP-1 small inhibitory RNA by reversing the cytoprotective effects of dexamethasone in paclitaxel-treated cells. Isobologram analysis revealed synergism between paclitaxel and NSC 95397 only in the presence of dexamethasone. The data show the power of a well-defined cellular assay for identifying cell-active inhibitors of MKPs and support the hypothesis that small-molecule inhibitors of MKP-1 may be useful as antineoplastic agents under conditions of high MKP-1 expression.

Rhodium(I)-catalyzed cycloisomerizations of bicyclobutanes.

Abstract: The selection of rhodium precatalyst and phosphine ligand determines the course of the cycloisomerization of N-allylated bicyclo[1.1.0]butylalkylamines. Cyclopropane-fused pyrrolidines and azepines are obtained with high levels of stereo- and regiocontrol. Novel azatricyclo[6.1.0.0(1,5)]nonanes are the result of a tandem cycloisomerization-ring closing metathesis sequence. Allylic ethers lead to furans and oxepanes.

Computational design, synthesis and biological evaluation of para-quinone-based inhibitors for redox regulation of the dual-specificity phosphatase Cdc25B.

Abstract: Quinoid inhibitors of Cdc25B were designed based on the Linear Combination of Atomic Potentials (LCAP) methodology. In contrast to a published hypothesis, the biological activities and hydrogen peroxide generation in reducing media of three synthetic models did not correlate with the quinone half-wave potential, E1/2.

Density functional theory calculation of 13C NMR shifts of diazaphenanthrene alkaloids: reinvestigation of the structure of samoquasine A.

Abstract: The 13C NMR shifts of 48 diazaphenanthrene-type alkaloids have been calculated at the B3LYP/6−311+G(2d,p) level of theory. The results support the structural reassignment of samoquasine A as 2.

Toward a Molecular Understanding of the Interaction of Dual Specificity Phosphatases with Substrates: Insights from Structure-Based Modeling and High Throughput Screening

Abstract: Dual-specificity phosphatases (DSPs) are important, but poorly understood, cell signaling enzymes that remove phosphate groups from tyrosine and serine/threonine residues on their substrate. Deregulation of DSPs has been implicated in cancer, obesity, diabetes, inflammation, and Alzheimer's disease. Due to their biological and biomedical significance, DSPs have increasingly become the subject of drug discovery high-throughput screening (HTS) and focused compound library development efforts. Progress in identifying selective and potent DSP inhibitors has, however, been restricted by the lack of sufficient structural data on inhibitor-bound DSPs. The shallow, almost flat, substrate binding sites in DSPs have been a major factor in hampering the rational design and the experimental development of active site inhibitors. Recent experimental and virtual HTS studies, as well as advances in molecular modeling, provide new insights into the potential mechanisms for substrate recognition and binding by this important class of enzymes. We present herein an overview of the progress, along with a brief description of applications to two types of DSPs: Cdc25 and MAP kinase phosphatase (MKP) family members. In particular, we focus on combined computational and experimental efforts for designing Cdc25B and MKP-1 inhibitors and understanding their mechanisms of interactions with their target proteins. These studies emphasize the utility of developing computational models and methods that meet the two major challenges currently faced in structure-based in silico design of lead compounds: the conformational flexibility of the target protein and the entropic contribution to the selection and stabilization of particular bound conformers.

Three-Dimensional Database Mining Identifies a Unique Chemotype that Unites Structurally Diverse Botulinum Neurotoxin Serotype A Inhibitors in a Three-Zone Pharmacophore

Abstract: A search query consisting of two aromatic centers and two cationic centers was defined based on previously identified small molecule inhibitors of the botulinum neurotoxin serotype A light chain (BoNT/A LC) and used to mine the National Cancer Institute Open Repository. Ten small molecule hits were identified, and upon testing, three demonstrated inhibitory activity. Of these, one was structurally unique, possessing a rigid diazachrysene scaffold. The steric limitations of the diazachrysene imposed a separation between the overlaps of previously identified inhibitors, revealing an extended binding mode. As a result, the pharmacophore for BoNT/A LC inhibition has been modified to encompass three zones. To demonstrate the utility of this model, a novel three-zone inhibitor was mined and its activity was confirmed.

Is Cdc25 a Druggable Target

Abstract: Proper control of cell cycle progression requires the functionality of a small family of activating phosphatases termed Cdc25, which have been implicated in cancer and Alzheimer's disease. These protein tyrosine phosphatases are therefore recognized as attractive molecular targets for small molecules. We review the rationale, approaches, progress and challenges for developing small molecule inhibitors of the Cdc25 family. A number of potential chemical probes are discussed and their characteristics are summarized.

Synthesis of hydroxylated bicyclic amino acids from L-tyrosine: octahydro-1H-indole carboxylates.

Abstract: A stereoselective approach to polyhydroxylated L-Choi derivatives has been developed. The oxidative cyclization of L-tyrosine was optimized to avoid partial racemization and to allow a more efficient scale-up.

Synthesis of desacetoxytubulysin h and analogs thereof

Abstract: Compounds of formula I, XVI and XXI possess potent cell growth inhibitory activity. These compounds are described have therapeutic utility, particularly in the treatment of cancer as well as conditions and disorders related to uncontrolled cell growth wherein the variables R1, R2, R3, R4, R5, X, Y and Z are described herein.

Exploring the Optical Activity Tensor by Anisotropic Rayleigh Optical Activity Scattering

Abstract: Rayleigh optical activity (RayOA) spectroscopy promises to provide an elegant and robust analytical method to probe molecular stereochemistry. A careful selection of RayOA variants such as right-angle depolarized ICP (incident circular polarization) or backscattering DCP1 (in-phase dual circular polarization) allows analysis of the anisotropic component of the scattered light. In this study, we show that calculated anisotropic Rayleigh optical activity quantities provide key advantages over isotropic chiroptical quantities (such as optical rotation and RayOA variants domi nated by isotropic invariants): 1) higher sensitivity for probing the chiroptical tensor G′, 2) reduced dependence on small geometry changes, and 3) much less stringent computational demand for predicting an accurate sign than for optical rotation. Moreover, the stereochemical information provided by anisotropic RayOA and its invariants can be used to develop chirality descriptors because of the apparent correlation between structure/stereochemistry and the sign and magnitude of the anisotropic Rayleigh optical activity quantities. © 2008 Wiley-VCH Verlag GmbH & Co. KGaA.

Tubulin-perturbing naphthoquinone spiroketals.

Abstract: Several natural and synthetic naphthoquinone spiroketals are potent inhibitors of the thioredoxin-thioredoxin reductase redox system. Based on the antimitotic and weak antitubulin actions noted for SR-7 ([8-(furan-3-ylmethoxy)-1-oxo-1,4-dihydronaphthalene-4-spiro-2'-naphtho[1'',8''-de][1',3'][dioxin]), a library of related compounds was screened for tubulin-perturbing properties. Two compounds, TH-169 (5'-hydroxy-4'H-spiro[1,3-dioxolane-2,1'-naphthalen]-4'-one) and TH-223 (5'-methoxy-4'H-spiro[1,3-dioxane-2,1'-naphthalen]-4'-one), had substantial effects on tubulin assembly and were antiproliferative at low micromolar concentrations. TH-169 was the most potent at blocking GTP-dependent polymerization of 10 mum tubulin in vitro with a remarkable 50% inhibitory concentration of ca. 400 nm. It had no effect on paclitaxel-induced microtubule assembly and did not cause microtubule hypernucleation. TH-169 failed to compete with colchicine for binding to beta-tubulin. The 50% antiproliferative concentration of TH-169 against human cancer cells was at or slightly below 1 mum. Flow cytometry showed that 1 mum TH-169 caused an increase in G(2)/M and hypodiploid cells. TH-169 eliminated the PC-3 cells' polyploid population and increased their expression of p21(WAF1) and Hsp70 in a concentration-dependent manner. The antiproliferative effect of TH-169 was irreversible and independent of changes in caspases, actin, tubulin, glyceraldehyde phosphate dehydrogenase or Bcl-x(S/L). This structurally simple naphthoquinone spiroketal represents a small molecule, tubulin-interactive agent with a novel apoptotic pathway and attractive biological function.

Use of mitochondria-targeted electron scavengers as anti-inflammatory agents

Abstract: Provided herein are methods for using mitochondria-targeted electron scavengers as anti-inflammatory agents. The mitochondria-targeted electron scavenger comprises a free radical-scavenging group covalently linked to a mitochondria-targeting group derived from a hemigramicidin moiety. The mitochondria-targeted electron scavenger can be used to treat medical conditions associated with acute or chronic inflammation.

Rhodium(I)-Catalyzed Cycloisomerizations of Bicyclobutanes.

Abstract: The selection of rhodium precatalyst and phosphine ligand determines the course of the cycloisomerization of N-allylated bicyclo[1.1.0]butylalkylamines. Cyclopropane-fused pyrrolidines and azepines are obtained with high levels of stereo- and regiocontrol. Novel azatricyclo[6.1.0.0(1,5)]nonanes are the result of a tandem cycloisomerization-ring closing metathesis sequence. Allylic ethers lead to furans and oxepanes.

Synthesis of Functionalized Isoindolinones: Addition of in situ Generated Organoalanes to Acyliminium Ions.

Abstract: Addition of in situ generated di- or trisubstituted alkenylalanes to N-acyliminium ions provides rapid access to functionalized isoindolinones. Subsequent ring closing metathesis leads to tricyclic products. These transformations proceed under mild conditions and allow for the convergent synthesis of biologically significant scaffolds from readily available starting materials.