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The judges evaluated the submissions for the McMaster University High-Throughput Data-Mining and Docking Competition based on 3 criteria: identification of active compounds, percent enrichment, and overview of the competition. Using these metrics, 4 of the participating groups found meaningful enrichment, and 3 groups made perceptive comments about the general nature of the competition.

Observations of strong solar wind proton flux correlations with ROSAT X-ray rates along with high spectral resolution Chandra observations of X-rays from the dark Moon show that soft X-ray emission mirrors the behavior of the solar wind. In this paper, based on an analysis of an X-ray event observed by XMM-Newton resulting from charge exchange of high charge state solar wind ions and contemporaneous neutral solar wind data, we argue that X-ray observations may be able to provide reliable advance warning, perhaps by as much as half a day, of dramatic increases in solar wind flux at Earth. Like neutral atom imaging, this provides the capability to monitor the solar wind remotely rather than in-situ., Comment: in press in Adv. Space Research, 7 pages, 6 eps figures, resolution reduced for Astro-ph submission, see http://lena.gsfc.nasa.gov for full version

We report on the discovery of X-ray emission from SN 1970G in M101, 35 years after its outburst, using deep X-ray imaging with the Chandra X-ray observatory. The Chandra ACIS spectrum shows that the emission is soft (, 4 pages, 2 Postscript figures, submitted to ApJL, uses emulateapj5.sty

Detailed observations of an intermittent ultraluminous X-ray source indicate that its emission is unlikely to be powered by mass accretion onto an intermediate-mass black hole as previously thought. See Letter p.500 Ultraluminous X-ray sources (ULXs), more luminous than known stellar processes but less so than active galactic nuclei, are generally thought to be powered by either intermediate-mass black holes or smaller, stellar-mass black holes radiating at higher rates. Analysis of the optical spectra of M 101 ULX-1, a variable source in the nearby spiral galaxy M 101, suggests that matters may be more complicated. The luminosity of the source at the time of discovery was within the range expected for a ULX harbouring an intermediate-mass black hole. But the optical spectra reported here are consistent with the presence of a stellar-mass black hole, probably with a mass of 20–30 solar masses. The authors suggest that M 101 ULX-1 is driven by a black hole accreting gas from the wind of a companion star, a mechanism that had previously been rejected on the grounds that it was thought too slow for the purpose.

Integrating biological and chemical information is one key task in drug discovery, and one approach to attaining this goal is via three-dimensional pharmacophore descriptors derived from protein binding sites. The SitePrint program generates, aligns, scores, and classifies three-dimensional pharmacophore descriptors, active site grids, and ligand surfaces. The descriptors are formed from molecular fragments that have been docked, minimized, filtered, and clustered in protein active sites. The descriptors have geometric coordinates derived from the fragment positions, and they capture the shape, electrostatics, locations, and angles of entry into pockets of the recognition sites: they also provide a direct link to databases of organic molecules. The descriptors have been shown to be robust with respect to small changes in protein structure observed when multiple compounds are cocrystallized in a protein. Five aligned thrombin cocrystals with an average core alpha-carbon RMSD of 0.7 A gave three-dimensional pharmacophore descriptors with an average RMSD of 1.1 A. On a larger test set, alignment and scoring of the descriptors using clique-based alignment, and a best first search strategy with an adapted forward-looking Ullmann heuristic was able to select the global minimum three-dimensional alignment in twenty-nine out of thirty cases in less than one CPU second on a workstation. A protein family based analysis was then performed to demonstrate the usefulness of the method in producing a correlation of active site pharmacophore descriptors to protein function. Each protein in a test set of thirty was assigned membership to a family based on computed active site similarity to the following families: kinases, nuclear receptors, the aspartyl, cysteine, serine, and metallo proteases. This method of classifying proteins is complementary to approaches based on sequence or fold homology. The values within protein families for correctly assigning membership of a protein to a family ranged from 25% to 80%.

t A new generation of ONLINE assays has been developed that offers improved performance and enhanced ease of use. This family of assays is being applied to both the COBAS INTEGRA and Roche/Hitachi line of analyzers. The four ONLINE DAT II assays that were evaluated included cocaine (benzoylecgonine) (BE), methadone (MDN), opiates (OP), and tetrahydrocannabinol (THC). The BE assay has a dual cutoff (150/300 ng/mL) with a dynamic range from 0 to 5000 ng/mL. The MDN assay has a cutoff of 300 ng/mL with a dynamic range from 0 to 2000 ng/mL. The opiates assay has a 300 ng/mL cutoff with a 0 to 2000 ng/mL range and a 2000 ng/mL cutoff with a 0 to 8000 ng/mL range. The THC assay has 20, 50, and 100 ng/mL cutoffs with 0 to 100, 0 to 300, and 0 to 300 ng/mL dynamic ranges, respectively. The ranges of the intra- assay precision (coefficients of variation for n = 20) run in the semiquantitative mode are 2.3-7.5% for BE, 2.0-3.8% for MDN, 1.9-4.2% for OP, and 3.9-5.2% for THC. The intra-assay qualitative precision for all of the assays as calculated from absorbance values is generally higher than that of the intra-assay semiquantitative precision at the cutoff. The qualitative precision ranges between 0.4% and 3.1%. The standard curve stability defined for the COBAS INTEGRA systems for these reagents ranges from 35 to 68 days. The clinical sensitivity and specificity were compared to the OnLine generation I and CEDIA | immunoassays, as well as gas chromatography-mass spectrometry (GC-MS). The results indicate that for each assay, the sensitivity and specificity were the same or greater when compared to the other two immunoassay technologies. The results of each assay also correlated very well (> 99%) when compared with GC-MS.

AMPA (alpha-amino-3-hydroxy-5-methyl-4-isooxazole) receptors, a major subtype of ionotropic glutamate receptors (iGluRs), mediate the majority of the fast communication between neurons, and the activity-dependent trafficking of AMPA receptors at synapses plays a role in mammalian learning and memory. Here we describe the design, synthesis, and evaluation of a photoreactive AMPA receptor antagonist that provides a means of "knocking out" AMPA receptors present on the surface of cells. The antagonist, 6-azido-7-nitro-1,4-dihydroquinoxaline-2,3-dione (ANQX), was designed by introducing a photoreactive azido group onto a quinoxalinedione inhibitor scaffold. Computational docking of ANQX to the AMPA receptor ligand-binding core predicted efficient binding to AMPA receptors. Glutamate-evoked currents were reversibly blocked at micromolar ANQX concentrations prior to photolysis and irreversibly blocked following photolysis. ANQX provides a means of directly evaluating the trafficking of native AMPA receptors with unparalleled spatiotemporal resolution.

As with other mixed morphology remnants, W44's projected center is bright in thermal X-rays. It has an obvious radio shell, but no discernable X-ray shell. X-ray bright knots dot W44's image. The Chandra data show that the remnant's hot, bright projected center is metal-rich and that the bright knots are regions of comparatively elevated elemental abundances. The neon abundance is elevated, suggesting that the center is rich in ejecta. Furthermore, some of the emitting iron atoms appear to be underionized with respect to the other ions, providing the first X-ray evidence for dust destruction in a supernova remnant. We use the Chandra data to test the following explanations for W44's X-ray bright center: 1.) entropy mixing from thermal conduction or bulk mixing, 2.) cloud evaporation, and 3.) a metallicity gradient, possibly due to dust destruction and ejecta enrichment. In these tests, we assume that the remnant has evolved beyond the adiabatic evolutionary stage, which explains the X-ray dimness of the shell. The entropy mixed model spectrum was found to be a good match to the Chandra spectrum. The bright knots have similar levels of ionization as the surrounding regions, challenging the evaporating clouds model. While both of these models are known to predict centrally bright X-ray morphologies, their predictions fall short of the observed brightness gradient. The resulting brightness gap can be largely filled in by emission from the extra metals in and near the remnant's projected center. The preponderance of evidence suggests that W44's remarkable morphology can be attributed to dust destruction and ejecta enrichment within an entropy mixed, adiabatic phase supernova remnant., Accepted for publication in the August 20, 2004 issue of ApJ. 22 pages (in well spaced layout), references, captions, and figures

A modified version of the DOCK program has been used to predict inhibitors for cytochrome P450cam and its L244A mutant. A library of azole compounds was designed in silico and screened for binding to wild-type P450cam. Lead compounds were synthesized and found to inhibit wild-type P450cam. To test our approach to designing ligands that discriminate between closely related sites, the azole library was DOCKed into both the active sites of wild-type P450cam and its L244A mutant. The L244A active site is predicted to be slightly larger than that of wild-type P450cam. Ligands predicted to have a high affinity for the mutant alone were synthesized and assayed with the recombinant enzymes. All of the compounds showed inhibition of the L244A enzyme (IC(50) = 6-40 microM), and the compounds that were predicted to be too large to bind to the wild-type showed poor inhibition (IC(50) > or = 1 mM). The binding mode was shown to be similar to that predicted by our modified version of DOCK by spectroscopic analysis. A discrepancy between the IC(50) values and spectroscopic K(s) values indicates that the spectroscopic binding constants do not accurately estimate inhibitory activity. This study, the first report of computer-assisted ligand (drug) design for P450 enzymes in which the coordination bond between imidazole and the heme is explicitly considered in structural modeling, opens a promising design avenue because azole compounds are widely used as P450 enzyme inhibitors and drugs.

Matrix metalloproteinases (MMPs) represent a potentially important class of therapeutic targets for the treatment of diseases such as cancer. Selective inhibition of MMPs will be required given the high sequence identity across the family and the discovery that individual MMPs also regulate the natural angiogenesis inhibitor angiostatin. In this study, we have used computational methods to model the selectivity for six thiadiazole urea inhibitors with stromelysin-1 and gelatinase-A, two homologous MMPs that have been implicated in breast cancer. From continuum Generalized Born molecular dynamics (GB-MD) and MM-GBSA analysis, we estimated ligand free energies of binding using 200 snapshots obtained from a short 40 ps simulation of the relevant protein-ligand complex. The MM-GBSA free energies, computed from the continuum GB-MD trajectories, show strong correlation with the experimental affinities (r(2) = 0.74); prior studies have employed explicit water MD simulations. Including estimates for changes in solute entropy in the binding calculations slightly diminishes the overall correlation with experiment (r2 = 0.71). Notably, in every case, the simulation results correctly predict that a given ligand will bind selectively to stromelysin-1 over gelatinase-A which is gratifying given the high degree of structural homology between the two proteins. The increased selectivity for stromelysin-1 appears to be driven by (1) increased favorable van der Waals interactions, (2) increased favorable Coulombic interactions, and (3) decreased unfavorable total electrostatic energies (Coulombic plus desolvation).

The calculation of ligand-nucleic acid binding free energies is investigated by including solvation effects computed with the generalized-Born model. Modifications of the solvation module in DOCK, including introduction of all-atom parameters and revision of coefficients in front of different terms, are shown to improve calculations involving nucleic acids. This computing scheme is capable of calculating binding energies, with reasonable accuracy, for a wide variety of DNA-ligand complexes, RNA-ligand complexes, and even for the formation of double-stranded DNA. This implementation of GB/SA is also shown to be capable of discriminating strong ligands from poor ligands for a series of RNA aptamers without sacrificing the high efficiency of the previous implementation. These results validate this approach to screening large databases against nucleic acid targets. © 2003 Wiley Periodicals, Inc. Biopolymers 73:192–204, 2004

We present an XMM-Newton spectrum of diffuse X-ray emission from within the solar system. The spectrum is dominated by probable C VI lines at 0.37 keV and 0.46 keV, an O VII line at 0.56 keV, O VIII lines at 0.65 keV and ~0.8 keV, Ne IX lines at ~0.92 keV, and Mg XI lines at ~1.35 keV. This spectrum is consistent with that expected from charge exchange emission between the highly ionized solar wind and either interstellar neutrals in the heliosphere or material from Earth's exosphere. The emission is clearly seen as a low-energy (E, 26 pages, 6 figures, ApJ accepted

Nanocrystalline materials have demonstrated very interesting changes in physical, chemical and mechanical properties at severely diminished length scales. This article focuses on the topic of nanocrystalline ceramic composites specifically designed for applications requiring improved fracture toughness. The difficulty in producing fully consolidated ceramic composites that retain a nanocrystalline structure is the main hurdle for thorough investigations in this area. This obstacle has been overcome in the current investigation through the use of a fast, comparably lower temperature, sintering technique e.g., Spark Plasma Sintering. Alumina based nanocomposites incorporating carbon nanotubes and additionally incorporating nanocrystalline niobium have yielded fracture toughness values that have exceeded that for pure nanocrystalline alumina by more that 300%. This introduces the question of whether this improvement is merely additive or evidence of a synergistic toughening mechanism involving ductile phase and fiber toughening.

M101 is a nearby face-on spiral galaxy which can be used to study the hot ISM in the MilkyWay. We have used a deep Chandra image of M101 to characterize the X-ray emission. The X-ray emission follows the optical light/star formation. The spectrum does not change significantly with radius or with surface brightness. A hard thermal component can be identified with similar emission in the Milky Way; a softer thermal component is likely a combination of several different types of sources.

Computations are now an integrated part of structural biology and are used in data gathering, data processing, and data storage as well as in a full spectrum of theoretical pursuits. In this review, we focus on areas of great promise and call attention to important issues of internal consistency and error analysis.

Direct hydroxide attack on the scissile carbonyl of the substrate has been suggested as a likely mechanism for esterase antibodies elicited by phosphonate haptens, which mimic the transition states for the alkaline hydrolysis of esters. 1 The unique amidase activity of esterase antibody 43C9 has been attributed to nucleophilic attack by an active-site histidine residue. 2 Yet, the active site of 43C9 is strikingly similar to those of other esterase antibodies, particularly 17E8. We have carried out quantum mechanical calculations, molecular dynamics simulations, and free energy calculations to assess the mechanism involving direct hydroxide attack for 43C9. Results support this mechanism and suggest that the mechanism is plausible for other antiphosphonate antibodies that catalyze the hydrolysis of (p-nitro)phenyl esters.

We have applied the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method (J. Srinivasan, T. E. Cheatham, P. Cieplak, P. A. Kollman, and D. A. Case, Journal of the American Chemical Society, 1998, Vol. 120, pp. 9401-9409) to study the interaction of an RNA aptamer with theophylline and its analogs. The MM-PBSA free energy analysis provides a reasonable absolute binding free energy for the RNA aptamer-theophylline complex formation. Energetic analysis reveals that the van der Waals interaction and the nonpolar contribution to solvation provide the basis for the favorable absolute free energy of complex. This trend is similar to other protein-ligand interactions studied previously. The MM-PBSA method also ranks the relative binding energies of five theophylline analogs approximately correctly, but not as well as the more conventional thermodynamic integration calculations, which were carried out to convert theophylline into its analogs. The comparison of MM-PBSA with TI suggests that the MM-PBSA method has some difficulties with the first-solvation-shell energetics.

Computations are now an integrated part of structural biology and are used in data gathering, data processing, and data storage as well as in a full spectrum of theoretical pursuits. In this review, we focus on areas of great promise and call attention to important issues of internal consistency and error analysis.

As part of a spectroscopic survey of supernova remnant candidates in M83 using the Gemini-South telescope and GMOS, we have discovered one object whose spectrum shows very broad lines at H$\alpha$, [O~I] 6300,6363, and [O~III] 4959,5007, similar to those from other objects classified as `late time supernovae.' Although six historical supernovae have been observed in M83 since 1923, none were seen at the location of this object. Hubble Space Telescope Wide Field Camera 3 images show a nearly unresolved emission source, while Chandra and ATCA data reveal a bright X-ray source and nonthermal radio source at the position. Objects in other galaxies showing similar spectra are only decades post-supernova, which raises the possibility that the supernova that created this object occurred during the last century but was missed. Using photometry of nearby stars from the HST data, we suggest the precursor was at least 17 $\rm M_{sun}$, and the presence of broad H$\alpha$ in the spectrum makes a type II supernova likely. The supernova must predate the 1983 VLA radio detection of the object. We suggest examination of archival images of M83 to search for evidence of the supernova event that gave rise to this object, and thus provide a precise age., Comment: 25 pages, 9 figures, accepted for ApJ

Classifying proteins into functionally distinct families based only on primary sequence information remains a difficult task. We describe here a method to generate a large data set of small molecule affinity fingerprints for a group of closely related enzymes, the papain family of cysteine proteases. Binding data was generated for a library of inhibitors based on the ability of each compound to block active-site labeling of the target proteases by a covalent activity based probe (ABP). Clustering algorithms were used to automatically classify a reference group of proteases into subfamilies based on their small molecule affinity fingerprints. This approach was also used to identify cysteine protease targets modified by the ABP in complex proteomes by direct comparison of target affinity fingerprints with those of the reference library of proteases. Finally, experimental data were used to guide the development of a computational method that predicts small molecule inhibitors based on reported crystal structures. This method could ultimately be used with large enzyme families to aid in the design of selective inhibitors of targets based on limited structural/function information.

X-ray binaries in the Milky Way are among the brightest objects on the X-ray sky. With the increasing sensitivity of recent missions, it is now possible to study X-ray binaries in nearby galaxies. We present data on six luminous sources in the nearby spiral galaxy, M101, obtained with the Chandra ACIS-S. Of these, five appear to be similar to ultraluminous sources in other galaxies, while the brightest source, P098, shows some unique characteristics. We present our interpretation of the data in terms of an optically thick outflow, and discuss implications., Accepted for publication in Astrophysical Journal (16 pages including 4 figures)

Macromolecular interactions are crucial in numerous biologic processes, yet few general principles are available that establish firm expectations for the strength of these interactions or the expected contribution of specific forces. The simplest principle would be a monotonic increase in interactions as the size of the interface grows. The exact relationship might be linear or nonlinear depending on the nature of the forces involved. Simple "linear-free energy" relationships based on atomic properties have been well documented, for example, additivity for the interaction of small molecules with solvent, and, recently, have been explored for ligand-receptor interactions. Horton and Lewis propose such additivity based on buried surface area for protein-protein complexes. We investigated macromolecular interactions and found that the highest-affinity complexes do not fulfill this simple expectation. Instead, binding free energies of the tightest macromolecular complexes are roughly constant, independent of interface size, with the notable exception of DNA duplexes. By comparing these results to an earlier study of protein-ligand interactions we find that: (1) The maximum affinity is approximately 1.5 kcal/mol per nonhydrogen atom or 120 cal/mol A(2) of buried surface area, comparable to results of our earlier work; (2) the lack of an increase in affinity with interface size is likely due to nonthermodynamic factors, such as functional and evolutionary constraints rather than some fundamental physical limitation. The implication of these results have some importance for molecular design because they suggest that: (1) The stability of any given complex can be increased significantly if desired; (2) small molecule inhibitors of macromolecular interactions are feasible; and (3) different functional classes of protein-protein complexes exhibit differences in maximal stability, perhaps in response to differing evolutionary pressures. These results are consistent with the widespread observation that proteins have not evolved to maximize thermodynamic stability, but are only marginally stable.

Genetic algorithms have properties which make them attractive in de novo drug design. Like other de novo design programs, genetic algorithms require a method to reduce the enormous search space of possible compounds. Most often this is done using information from known ligands. We have developed the ADAPT program, a genetic algorithm which uses molecular interactions evaluated with docking calculations as a fitness function to reduce the search space. ADAPT does not require information about known ligands. The program takes an initial set of compounds and iteratively builds new compounds based on the fitness scores of the previous set of compounds. We describe the particulars of the ADAPT algorithm and its application to three well-studied target systems. We also show that the strategies of enhanced local sampling and re-introducing diversity to the compound population during the design cycle provide better results than conventional genetic algorithm protocols.

In this study, we compare the calculated and experimental binding free energies for a combinatorial library of inhibitors of cathepsin D (CatD), an aspartyl protease. Using a molecular dynamics (MD)-based, continuum solvent method (MM-PBSA), we are able to reproduce the experimental binding affinity for a set of seven inhibitors with an average error of ca. 1 kcal/mol and a correlation coefficient of 0.98. By comparing the dynamical conformations of the inhibitors complexed with CatD with the initial conformations generated by CombiBuild (University of California, San Francisco, CA, 1995), we have found that the docking conformation observed in an X-ray structure of one peptide inhibitor bound to CatD (Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 6796-6800) is in good agreement with our MD simulation. However, the DOCK scoring function, based on intermolecular van der Waals and electrostatics, using a distance-dependent dielectric constant (J. Comput. Chem. 1992, 13, 505-524), poorly reproduces the trend of experimental binding affinity for these inhibitors. Finally, the use of PROFEC (J. Comput.-Aided Mol. Des. 1998, 12, 215-227) analysis allowed us to identify two possible substitutions to improve the binding of one of the better inhibitors to CatD. This study offers hope that current methods of estimating the free energy of binding are accurate enough to be used in a multistep virtual screening protocol.

There have been many predictions of the reinforcing effects of carbon nanotubes in various composite matrices but large improvements in properties have not yet been convincingly demonstrated. In the present study, we have successfully realized this possibility in reinforcing nanocrystalline alumina. Fully dense single-wall carbon nanotubes (SWCN)/Al2O3 nanocomposites with nanocrystalline alumina matrix have been fabricated at sintering temperatures as low as 1150°C by spark-plasma-sintering (SPS). A fracture toughness of 9.7 MPam1/2, nearly three times that of pure nanocrystalline alumina, has been achieved in the 10 vol.% SWCN/Al2O3 nanocomposite. Moreover, high-strain-rate superplasticity has been achieved in Al2O3/ZrO2/MgAl2O4 nanocomposite with truly nanocrystalline grain size of 100 nm. Compression superplastic tests were conducted in the temperature range of 1300–1450°C at strain rates 10-3-10-1 s-1. The results generated a stress exponent of ∼ 2 and an activation energy of ∼ 620 kJ/mol.

A deep (98.2 ks) Chandra Cycle-1 observation has revealed a wealth of discrete X-ray sources as well as diffuse emission in the nearby face-on spiral galaxy M101. From this rich dataset we have created a catalog of the 110 sources from the S3 chip detected with a significance of >3 sigma, corresponding to a flux of ~1.0E-16 ergs/cm/cm/s and a luminosity of 1.0E36 ergs/s for a distance to M101 of 7.2 Mpc. The sources display a distinct correlation with the spiral arms and include a variety of X-ray binaries, supersoft sources, supernova remnants, and other objects of which only ~27 are likely to be background sources. There are only a few sources in the interarm regions, and most of these have X-ray colors consistent with that of background AGNs. The derived log N-log S relation for the sources in M101 (background subtracted) has a slope of -0.80+/-0.05 over the range of 1.0E36 - 1.0E38 ergs/s. The nucleus is resolved into 2 nearly identical X-ray sources, each with a 0.5-2.0 keV flux of 4.0E37 ergs/s. One of these sources coincides with the optical nucleus, and the other coincides with a cluster of stars 110 pc to the south., 39 pages including 13 figures and 4 tables; ApJ, in press

Tryptases betaI and betaII were heterologously expressed and purified in yeast to functionally characterize the substrate specificity of each enzyme. Three positional scanning combinatorial tetrapeptide substrate libraries were used to determine the primary and extended substrate specificity of the proteases. Both enzymes have a strict primary preference for cleavage after the basic amino acids, lysine and arginine, with only a slight preference for lysine over arginine. betaI and betaII tryptase share similar extended substrate specificity, with preference for proline at P4, preference for arginine or lysine at P3, and P2 showing a slight preference for asparagine. Measurement of kinetic constants with multiple substrates designed for beta-tryptases reveal that selectivity is highly dependent on ground state substrate binding. Coupled with the functional determinants, structural determinants of tryptase substrate specificity were identified. Molecular docking of the preferred substrate sequence to the three-dimensional tetrameric tryptase structure reveals a novel extended substrate binding mode that involves interactions from two adjacent protomers, including P4 Thr-96', P3 Asp-60B' and Glu-217, and P1 Asp-189. Based on the determined substrate information, a mechanism-based tetrapeptide-chloromethylketone inhibitor was designed and shown to be a potent tryptase inhibitor. Finally, the cleavage sites of several physiologically relevant substrates of beta-tryptases show consistency with the specificity data presented here.

In our continuation of the structure-based design of anti-trypanosomatid drugs, parasite-selective adenosine analogues were identified as low micromolar inhibitors of glyceraldehyde-3-phosphate dehydrogenase (GAPDH). Crystal structures of Trypanosoma brucei, Trypanosoma cruzi, Leishmania mexicana, and human GAPDH's provided details of how the adenosyl moiety of NAD(+) interacts with the proteins, and this facilitated the understanding of the relative affinities of a series of adenosine analogues for the various GAPDH's. From exploration of modifications of the naphthalenemethyl and benzamide substituents of a lead compound, N(6)-(1-naphthalenemethyl)-2'-deoxy-2'-(3-methoxybenzamido)adenosine (6e), N(6)-(substituted-naphthalenemethyl)-2'-deoxy-2'-(substituted-benzamido)adenosine analogues were investigated. N(6)-(1-Naphthalenemethyl)-2'-deoxy-2'-(3,5-dimethoxybenzamido)adenosine (6m), N(6)-[1-(3-hydroxynaphthalene)methyl]-2'-deoxy-2'-(3,5-dimethoxybenzamido)adenosine (7m), N(6)-[1-(3-methoxynaphthalene)methyl]-2'-deoxy-2'-(3,5-dimethoxybenzamido)adenosine (9m), N(6)-(2-naphthalenemethyl)-2'-deoxy-2'-(3-methoxybenzamido)adenosine (11e), and N(6)-(2-naphthalenemethyl)-2'-deoxy-2'-(3,5-dimethoxybenzamido)adenosine (11m) demonstrated a 2- to 3-fold improvement over 6e and a 7100- to 25000-fold improvement over the adenosine template. IC(50)'s of these compounds were in the range 2-12 microM for T. brucei, T. cruzi, and L. mexicana GAPDH's, and these compounds did not inhibit mammalian GAPDH when tested at their solubility limit. To explore more thoroughly the structure-activity relationships of this class of compounds, a library of 240 N(6)-(substituted)-2'-deoxy-2'-(amido)adenosine analogues was generated using parallel solution-phase synthesis with N(6) and C2' substituents chosen on the basis of computational docking scores. This resulted in the identification of 40 additional compounds that inhibit parasite GAPDH's in the low micromolar range. We also explored adenosine analogues containing 5'-amido substituents and found that 2',5'-dideoxy-2'-(3,5-dimethoxybenzamido)-5'-(diphenylacetamido)adenosine (49) displays an IC(50) of 60-100 microM against the three parasite GAPDH's.

In this paper we describe the search strategies developed for docking flexible molecules to macomolecular sites that are incorporated into the widely distributed DOCK software, version 4.0. The search strategies include incremental construction and random conformation search and utilize the existing Coulombic and Lennard-Jones grid-based scoring function. The incremental construction strategy is tested with a panel of 15 crystallographic testcases, created from 12 unique complexes whose ligands vary in size and flexibility. For all testcases, at least one docked position is generated within 2 A of the crystallographic position. For 7 of 15 testcases, the top scoring position is also within 2 A of the crystallographic position. The algorithm is fast enough to successfully dock a few testcases within seconds and most within 100 s. The incremental construction and the random search strategy are evaluated as database docking techniques with a database of 51 molecules docked to two of the crystallographic testcases. Incremental construction outperforms random search and is fast enough to reliably rank the database of compounds within 15 s per molecule on an SGI R10000 cpu.

We report a simple method for measuring the accessible conformational space explored by an ensemble of protein structures. The method is useful for diverse ensembles derived from molecular dynamics trajectories, molecular modeling, and molecular structure determinations. It can be used to examine a wide range of time scales. The central tactic we use, which has been previously employed, is to replace the true mechanical degrees of freedom of a molecular system with the conformationally effective degrees of freedom as measured by the root-mean squared cartesian distances among all pairs of conformations. Each protein conformation is treated as a point in a high dimensional euclidean space. In this article, we model this space in a novel way by representing it as an N-dimensional hypercube, describable with only two parameters: the number of dimensions and the edge length. To validate this approach, we provide a number of elementary test cases and then use the N-cube method for measuring the size and shape of conformational space covered by molecular dynamics trajectories spanning 10 orders of magnitude in time. These calculations were performed on a small protein, the villin headpiece subdomain, exploring both the native state and the misfolded/folding regime. Distinct features include single, vibrationally averaged, substate minima on the 0.1-1-ps time scale, thermally averaged conformational states that persist for 1-100 ps and transitions between these local minima on nanosecond time scales. Large-scale refolding modes appear to become uncorrelated on the microsecond time scale. Associated length scales for these events are 0.2 A for the vibrational minima; 0.5 A for the conformational minima; and 1-2 A for the nanosecond events. We find that the conformational space that is dynamically accessible during folding of villin has enough volume for approximately 10(9) minima of the variety that persist for picoseconds. Molecular dynamics trajectories of the native protein and experimentally derived solution ensembles suggest the native state to be composed of approximately 10(2) of these thermally accessible minima. Thus, based on random exploration of accessible folding space alone, protein folding for a small protein is predicted to be a milliseconds time scale event. This time can be compared with the experimental folding time for villin of 10-100 micros. One possible explanation for the 10-100-fold discrepancy is that the slope of the "folding funnel" increases the rate 1-2 orders of magnitude above random exploration of substates.

We present a general approach to the design, docking, and virtual screening of multiple combinatorial libraries against a family of proteins. The method consists of three main stages: docking the scaffold, selecting the best substituents at each site of diversity, and comparing the resultant molecules within and between the libraries. The core "divide-and-conquer" algorithm for side-chain selection, developed from an earlier version (Sun et al., J Comp Aided Mol Design 1998;12:597-604), provides a way to explore large lists of substituents with linear rather than combinatorial time dependence. We have applied our method to three combinatorial libraries and three serine proteases: trypsin, chymotrypsin, and elastase. We show that the scaffold docking procedure, in conjunction with a novel vector-based orientation filter, reproduces crystallographic binding modes. In addition, the free-energy-based scoring procedure (Zou et al., J Am Chem Soc 1999;121:8033-8043) is able to reproduce experimental binding data for P1 mutants of macromolecular protease inhibitors. Finally, we show that our method discriminates between a peptide library and virtual libraries built on benzodiazepine and tetrahydroisoquinolinone scaffolds. Implications of the docking results for library design are explored.

A virtual library of macrocyclic polyketide molecules was generated and screened to identify novel, conformationally constrained potential motilin receptor agonists ("motilides"). A motilide pharmacophore model was generated from the potent 6,9-enol ether erythromycin and known derivatives from the literature. The pharmacophore for each molecular conformation was a point in a distance-volume space based on presentation of the putative binding moieties. Two methods, one fragment based method and the other reaction based, were explored for constructing the polyketide virtual library. First, a virtual library was assembled from monomeric fragments using the CHORTLES language. Second, the virtual library was assembled by the in silico application of all possible polyketide synthase enzyme reactions to generate the product library. Each library was converted to low-energy 3D conformations by distance geometry and standard minimization methods. The distance-volume metric was calculated for low-energy conformations of the members of the virtual polyketide library and screened against the enol ether pharmacophore. The goal was to identify novel macrocycles that satisfy the pharmacophore. We identified three conformationally constrained, novel polyketide series that have low-energy conformations satisfying the distance-volume constraints of the motilide pharmacophore.

Lysosomal disturbances may be a contributing factor to Alzheimer's disease. We used novel compounds to test if suppression of the lysosomal protease cathepsin D blocks production of known precursors to neurofibrillary tangles. Partial lysosomal dysfunction was induced in cultured hippocampal slices with a selective inhibitor of cathepsins B and L. This led within 48 h to hyperphosphorylated tau protein fragments recognized by antibodies against human tangles. Potent nonpeptidic cathepsin D inhibitors developed using combinatorial chemistry and structure-based design blocked production of the fragments in a dose-dependent fashion. Threshold was in the submicromolar range, with higher concentrations producing complete suppression. The effects were selective and not accompanied by pathophysiology. Comparable results were obtained with three structurally distinct inhibitors. These results support the hypothesis that cathepsin D links lysosomal dysfunction to the etiology of Alzheimer's disease and suggest a new approach to treating the disease.

Kinesin motor proteins use ATP hydrolysis for transport along microtubules in the cell. We sought to identify small organic ligands to inhibit kinesin's activity. Candidate molecules were identified by computational docking of commercially available compounds using the computer program DOCK. Compounds were docked at either of two sites, and a selection was tested for inhibition of microtubule-stimulated ATPase activity. Twenty-two submillimolar inhibitors were identified. Several inhibitors appeared to be competitive for microtubule binding and not for ATP binding, and three compounds showed 50% inhibition down to single-digit micromolar levels. Most inhibitors grouped into four distinct classes (fluoresceins, phenolphthaleins, anthraquinones, and naphthylene sulfonates). We measured the binding of one inhibitor, rose bengal lactone (RBL), to kinesin (dissociation constant 2.5 microM) by its increase in steady-state fluorescence anisotropy. The RBL binding site on kinesin was localized by fluorescent resonance energy transfer (FRET) using a donor fluorophore (coumarin) covalently attached at unique, surface-exposed cysteine residues engineered at positions 28, 149, 103, 220, or 330. RBL was found to bind in its original docked site: the pocket cradled by loop 8 and beta-strand 5 in kinesin's three-dimensional structure. These results confirm this region's role in microtubule binding and identify this pocket as a novel binding site for kinesin inhibition.

Alumina based ceramic nanocomposites were investigated with the objective of improving fracture toughness. Specific focus during processing was directed at the retention of nanocrystalline microstructures in the matrix of the composites while still achieving full density. Second phases were added to the alumina matrix to investigate the applicability of toughening mechanisms that have been developed earlier for microcrystalline ceramics. The use of spark plasma sintering technique allowed the retention of ultrafine grain size of alumina due to lowered sintering temperatures and shorter sintering times. Very attractive improvements in fracture toughness were noted in Al2O3/Nb, Al2O3/carbon nanotube, Al2O3/SiC whisker, and Al2O3/Nb/carbon nanotube composites. The results were analyzed in the context of effective toughening mechanisms in these nanocrystalline matrices.

Silicon nitride/silicon carbide nanocomposites and alumina-based nanocomposites were investigated in an effort to produce materials with high structural integrity and service properties. Bulk nano-nano composites of silicon nitride and silicon carbide were processed by crystallization of amorphous Si-C-N ceramics that were consolidated in-situ during pyrolysis of a polymer precursor. This material was developed for the purpose of examining the creep behavior of covalent ceramics when there is no oxide glassy phase at grain boundaries. Si3N4/SiC micro-nano composites were sintered by spark plasma sintering (SPS), aiming at better microstructural control and improved creep resistance. Composites of alumina with diamond, silicon carbide and metal (Nb) were developed by high pressure sintering and SPS. These composites maintain microstructures with a nanometric alumina matrix and are targeted for studying the toughening mechanisms and superplastic deformation mechanisms.

Most protozoan parasites, such as Leishmania, Plasmodium, Toxoplasma and Trypanosoma, rely on a salvage pathway for their supply of purine ribonucleotides (Wang, 1984). Inhibition of this pathway therefore presents an interesting approach in the fight against microbial infections. To explore the feasibility of this approach we have attempted to identify inhibitors of the essential purine salvage enzyme hypoxanthine-guanine-xanthine phosphoribosyl transferase (HGXPRTase) of the protozoan parasite Tritrichomonas foetus. This sexually transmitted parasite causes causes bovine trichomoniasis, which can lead to embryonic death and infertility in cows. T. foetus relies primarily on a single enzyme, HGXPRTase, to transfer ribose 5-phosphate from α-D-5-phosphoribosyl-1-pyrophosphate to the N9 nitrogen atom of hypoxanthine, guanine or xanthine (Wang et al., 1983). Selectivity with respect to the mammalian enzyme hypoxanthine-guanine-phosphoribosyl transferase (HGPRTase), that has 27% sequence identity with the parasite enzyme, is important to avoid serious side effects. Currently available inhibitors are purine analogues with affinities in the millimolar range (Jadhav et al., 1979). Here we report the use of the molecular docking program DOCK 3.5 (Kuntz et al., 1982; Meng et al., 1993) for the discovery of more potent, novel inhibitors of HGXPRTase that are selective with respect to the human enzyme (Somoza et al., 1998).

Spinal tuberculosis (TB) accounts for about 2% of all cases of TB. New methods of diagnosis such as magnetic resonance imaging (MRI) or percutaneous needle biopsy have emerged. Two distinct patterns of spinal TB can be identified, the classic form, called spondylodiscitis (SPD) in this article, and an increasingly common atypical form characterized by spondylitis without disk involvement (SPwD). We conducted a retrospective study of patients with spinal TB managed in the area of Paris, France, between 1980 and 1994 with the goal of defining the characteristics of spinal TB and comparing SPD to SPwD. The 103 consecutive patients included in our study had TB confirmed by bacteriologic and/or histologic studies of specimens from spinal or paraspinal lesions (93 patients) or from extraspinal skeletal lesions (10 patients). Sixty-eight percent of patients were foreign-born subjects from developing countries. None of our patients was HIV-positive. SPD accounted for 48% of cases and SPwD for 52%. Patients with SPwD were younger and more likely to be foreign-born and to have multiple skeletal TB lesions. Neurologic manifestations were observed in 50% of patients, with no differences between the SPD and SPwD groups. Of the 44 patients investigated by MRI, 6 had normal plain radiographs; MRI was consistently positive and demonstrated epidural involvement in 77% of cases. Bacteriologic and histologic yields were similar for surgical biopsy (n = 16) and for percutaneous needle aspiration and/or biopsy (n = 77). Cultures for Mycobacterium tuberculosis were positive in 83% of patients, and no strains were resistant to rifampin. Median duration of antituberculous chemotherapy was 14 months. Surgical treatment was performed in 24% of patients. There were 2 TB-related deaths. Our data suggest that SPwD may now be the most common pattern of spinal TB in foreign-born subjects in industrialized countries. The reasons for this remain to be elucidated.

We present a set of programs, DREAM+2 (Docking and Reaction programs using Efficient seArch Methods written in C++), for docking computationally generated ligands into macromolecular binding sites. DREAM++ is composed of three programs: ORIENT++, REACT++ and SEARCH++. The program ORIENT++ positions molecules in a binding site with the DOCK algorithm. Its output can be used as input to REACT++ and SEARCH+2. The program REACT++ performs user-specific chemical reactions on a docked molecule, so that reaction products can be evaluated for three dimensional complementarity with the macromolecular site. The program SEARCH++ performs an efficient conformation search on the reaction products using a hybrid backtrack and incremental construction algorithm. We have applied the programs to HIV protease-inhibitor complexes as test systems. We found that we can differentiate high-affinity ligands based on several measures: interaction energies, occupancy of protein subsites and the number of successfully docked conformations for each product. Encouraged by the results in the test case, we applied the programs to propose novel inhibitors of HIV protease. These inhibitors can be generated by organic reactions using commercially available reagents. They are alternatives to the inhibitors synthesized by Glaxo.

To demonstrate the contribution of magnetic resonance imaging to the elucidation of mechanisms involved in "osteonecrosis-like syndrome of the medial tibial plateau".A magnetic resonance study with sagittal and coronal sections was done in 13 patients (age range, 57-95 years) two weeks to four months into a painful syndrome meeting the definition of "osteonecrosis-like syndrome of the medial tibial plateau". Gadolinium injection was used in nine patients. Clinical symptoms resolved within a few weeks in all 13 cases.T1-weighted images without gadolinium showed diffuse low signal from the epiphysis (n = 12) containing an area of even lower signal seen either as a crescent-shaped subchondral image (n = 3/12) or as a linear image (n = 9/12). On postgadolinium images, the low signal was abolished except for a line of low signal parallel to the subchondral bone. T2-weighted images demonstrated diffuse high signal from the medial tibial plateau with persistence of the line of low signal (n = 8/12).Magnetic resonance imaging allows to analyze the anatomic lesion responsible for "osteonecrosis-like syndrome of the medial tibial plateau". Our magnetic resonance findings were similar to those seen in stress fractures at other sites.

A flexible ligand docking protocol based on a divide-and-conquer strategy is investigated. This approach first separates total search space into conformation and orientation space. It uses a grid-based method to sample the conformation of an unbound ligand and to select the low-energy conformers. Rigid docking is then carried out to locate the low-energy binding orientations for these conformers. These docking structures are subsequently subjected to structure refinement including molecular mechanics minimization, conformational scanning at the binding site and a short period of molecular dynamics-based simulated annealing. This approach has been applied to twelve ligand-protein complexes with three to sixteen rotatable bonds. The docked lowest-energy structures have root mean square deviations ranging from 0.64 A to 2.01 A with respect to the corresponding crystal structures. The effect of atomic charges and van der Waals parameters on the docking results, and the role of the dielectric constant in the conformation sampling are discussed in detail. A fragment-based docking approach that takes advantages of the divide-and-conquer strategy has also been explored and the results are compared with those produced by a whole molecule-based approach.

Solvation plays an important role in ligand-protein association and has a strong impact on comparisons of binding energies for dissimilar molecules. When databases of such molecules are screened for complementarity to receptors of known structure, as often occurs in structure-based inhibitor discovery, failure to consider ligand solvation often leads to putative ligands that are too highly charged or too large. To correct for the different charge states and sizes of the ligands, we calculated electrostatic and non-polar solvation free energies for molecules in a widely used molecular database, the Available Chemicals Directory (ACD). A modified Born equation treatment was used to calculate the electrostatic component of ligand solvation. The non-polar component of ligand solvation was calculated based on the surface area of the ligand and parameters derived from the hydration energies of apolar ligands. These solvation energies were subtracted from the ligand-receptor interaction energies. We tested the usefulness of these corrections by screening the ACD for molecules that complemented three proteins of known structure, using a molecular docking program. Correcting for ligand solvation improved the rankings of known ligands and discriminated against molecules with inappropriate charge states and sizes.