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The addition of TiO 2 improves the densification of amorphous silicon carbonitride powder, making possible the preparation of Si 3 N 4 /SiC/TiC 0.3 N 0.7 nano-ceramics with attractive mechanical properties and a high electrical conductivity.

An accurate and efficient energy model to compute free energies of ligand binding to proteins is essential to understanding protein−ligand interactions, particularly to structure-based drug design. A bottleneck to derive such an energy model is how to account for the solvent effect. A grid-based free energy model was proposed (Zou et al. J. Am. Chem. Soc. 1999, 121, 8033−43),1 based on the generalized-Born (GB/SA) model of solvation for small molecules (Still et al. J. Am. Chem. Soc. 1990, 112, 6127−9).2 Although the grid-based free energy model shows much improved results than the current DOCK force field energy model (Meng et al. J. Comput. Chem. 1992, 13, 505−24)3 by taking into account the solvent effect, the computational speed for the free energy model restricts the model from a direct drug screen of a huge compound database. Rather, the model is used for a second-step screening after a pre-screening by the force field method. Here, we present a fast algorithm, the pairwise free energy model, for li...

This article focuses on nanocrystalline-matrix ceramic composites specifically designed for applications requiring improved fracture toughness. While the models and theory of toughening mechanisms for microcrystalline composites are well developed, the same cannot be said for their nanocrystalline counterparts. The difficulty in producing fully consolidated ceramic composites that retain a nanocrystalline structure is the main hurdle to thorough investigations in this area. Thus, much of the research on so-called nanocomposites has been on materials with microcrystalline matrices and nanometric second phases. In this article, we present the general principles of toughness mechanisms in microcrystalline ceramic composites, and then extend these ideas to consider how they should apply to ceramics with nanocrystalline matrices. While work in this area is still quite limited, we review current research focused on the production and testing of composites with nanocrystalline matrices and second phases, and we recap the results of some promising fracture toughness reports.

Development of the new generation of therapeutics against the influenza viral coat protein neuraminidase is a response to the continuing threat of influenza epidemics. A variety of structurally similar compounds have been reported that vary greatly in their ability to inhibit neuraminidase, a critical enzyme that cleaves sialic acid and promotes virion release. To determine how neuraminidase exhibits this wide range of affinities with structurally similar compounds, molecular dynamic simulations, coupled with free energy calculations, were used to determine the binding components of a series of neuraminidase inhibitors. Using four cocrystal structures of neuraminidase-inhibitor complexes, we examined the structural and energetic components of ligand potency and selectivity. An in-depth energetic analysis, including internal energy, entropy, and nonbonded interactions, reveals that potency of ligand binding is governed by nonpolar contacts. Electrostatic components generally oppose binding, although two of the best inhibitors use electrostatic interactions to orient the ligand. This investigation suggests that the enhanced selectivity and potency of the better ligands may arise from an improved positioning of their ligand atoms in the active site due to polar and hydrophobic functionalities. Simulations that included crystal water molecules in the active site indicate that the more potent ligands make less use of water-mediated interactions.

Using spark plasma sintering (SPS), BaTiO3/Al2O3 nanocomposites were successfully consolidated to more than 99% of theoretical density at a sintering temperature as low as 1150 °C in only 3 min. The processing methods for these dense nanocomposites where the retained grain size of alumina matrix was in the nanometer level were developed. The maximum volume content of BaTiO3 in the nanocrystalline matrix for toughening was around 15 vol.%. A significant increase in fracture toughness up to 5.36 MPa1/2 has been achieved in the 7.5 vol.% BaTiO3/Al2O3 nanocomposite. The toughening mechanism might be related to ferroelastic domain switching of ferroelectric phase in these nanocomposites.

For a completely enumerated set of conformers of a macromolecule or for exhaustive lattice walks of model polymers it is straightforward to use Shannon information theory to deduce the information content of the ensemble. It is also practicable to develop numerical measures of the information content of sets of exact distance constraints applied to specific conformational ensembles. We examine the effects of experimental uncertainties by considering “noisy” constraints. The introduction of noise requires additional assumptions about noise distribution and conformational clustering protocols that make the problem of measuring information content more complex. We make use of a standard concept in communication theory, the “noise sphere,” to link uncertainty in measurements to information loss. Most of our numerical results are derived from two-dimensional lattice ensembles. Expressing results in terms of information per degree of freedom removes almost all of the chain length dependence. We also explore off-lattice polyalanine chains that yield surprisingly similar results.

▪ Abstract Molecular docking is an invaluable tool in modern drug discovery. This review focuses on methodological developments relevant to the field of molecular docking. The forces important in molecular recognition are reviewed and followed by a discussion of how different scoring functions account for these forces. More recent applications of computational chemistry tools involve library design and database screening. Last, we summarize several critical methodological issues that must be addressed in future developments.

A dense 3-mol%-yttria-stabilized tetragonal zirconia polycrystalline (3Y-TZP) toughening alumina matrix nanocomposite with a nanocrystalline (

The production factor, or broad band averaged cross-section, for solar wind charge-exchange with hydrogen producing emission in the ROSAT 1/4 keV (R12) band is $3.8\pm0.2\times10^{-20}$ count degree$^{-2}$ cm$^4$. This value is derived from a comparison of the Long-Term (background) Enhancements in the ROSAT All-Sky Survey with magnetohysdrodynamic simulations of the magnetosheath. This value is 1.8 to 4.5 times higher than values derived from limited atomic data, suggesting that those values may be missing a large number of faint lines. This production factor is important for deriving the exact amount of 1/4 keV band flux that is due to the Local Hot Bubble, for planning future observations in the 1/4 keV band, and for evaluating proposals for remote sensing of the magnetosheath. The same method cannot be applied to the 3/4 keV band as that band, being composed primarily of the oxygen lines, is far more sensitive to the detailed abundances and ionization balance in the solar wind. We also show, incidentally, that recent efforts to correlate XMM-Newton observing geometry with magnetosheath solar wind charge-exchange emission in the oxygen lines have been, quite literally, misguided. Simulations of the inner heliosphere show that broader efforts to correlate heliospheric solar wind charge-exchange with local solar wind parameters are unlikely to produce useful results., Comment: 19 pages, 16 figures, submitted to ApJ

The extraordinary mechanical, thermal and electrical properties of carbon nanotubes have prompted intense research into a wide range of applications in structural materials, electronics, chemical processing and energy management. Attempts have been made to develop advanced engineering materials with improved or novel properties through the incorporation of carbon nanotubes in selected matrices (polymers, metals and ceramics). But the use of carbon nanotubes to reinforce ceramic composites has not been very successful; for example, in alumina-based systems only a 24% increase in toughness has been obtained so far. Here we demonstrate their potential use in reinforcing nanocrystalline ceramics. We have fabricated fully dense nanocomposites of single-wall carbon nanotubes with nanocrystalline alumina (Al2O3) matrix at sintering temperatures as low as 1,150 degrees C by spark-plasma sintering. A fracture toughness of 9.7 MPa m 1/2, nearly three times that of pure nanocrystalline alumina, can be achieved.

Spark plasma sintering is a new process by which ceramics and composites can be consolidated very rapidly to full density. In the present study, piezoelectric Nd 2 Ti 2 O 7 second phase toughening nanocrystalline alumina composites with higher toughness were successfully developed at relatively low temperatures through this technique.

The human immunodeficiency virus (HIV) epidemic is an important medical problem. Although combination drug regimens have produced dramatic decreases in viral load, current therapies do not provide a cure for HIV infection. We have used structure-based design and combinatorial medicinal chemistry to identify potent and selective HIV-1 reverse transcriptase (RT) inhibitors that may work by a mechanism distinct from that of current HIV drugs. The most potent of these compounds (compound 4 , 2-naphthalenesulfonic acid, 4-hydroxy-7-[[[[5-hydroxy-6-[(4-cinnamylphenyl)azo]-7-sulfo-2-naphthalenyl]amino]carbonyl]amino]-3-[(4-cinnamylphenyl)azo], disodium salt) has an IC 50 of 90 nM for inhibition of polymerase chain extension, a K d of 40 nM for inhibition of DNA–RT binding, and an IC 50 of 25–100 nM for inhibition of RNaseH cleavage. The parent compound ( 1 ) was as effective against 10 nucleoside and non-nucleoside resistant HIV-1 RT mutants as it was against the wild-type enzyme. Compound 4 inhibited HIV-1 RT and murine leukemia virus (MLV) RT, but it did not inhibit T 4 DNA polymerase, T 7 DNA polymerase, or the Klenow fragment at concentrations up to 200 nM. Finally, compound 4 protected cells from HIV-1 infection at a concentration more than 40 times lower than the concentration at which it caused cellular toxicity.

We present the result of a Chandra ACIS observation of the pulsar PSR B1853+01 and its associated pulsar wind nebula (PWN), embedded within the supernova remnant W44. A hard band ACIS map cleanly distinguishes the PWN from the thermal emission of W44. The nebula is extended in the north-south direction, with an extent about half that of the radio emission. Morphological differences between the X-ray and radio images are apparent. Spectral fitting reveals a clear difference in spectral index between the hard emission from PSR B1853+01 (Gamma ~ 1.4) and the extended nebula (Gamma ~ 2.2). The more accurate values for the X-ray flux and spectral index are used refine estimates for PWN parameters, including magnetic field strength, the average Lorentz factor, gamma, of the particles in the wind, the magnetization parameter, sigma, and the ratio k of electrons to other particles., Comment: 10 pages, 3 figures, accepted by 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.

Inhibitors of urokinase-type plasminogen activator (uPA) were selected in vitro from two ecotin phage-display libraries to study the effect on binding of amino acid substitutions at critical positions 108, 110, 112, and 113 within the 100s loop (RNKL, respectively, in wild type ecotin). The first, a focused library, was the result of a computation-assisted approach using the three-dimensional structure of the ecotin-trypsin complex to guide the modeling of amino acid substitutions predicted to increase affinity for uPA. The second, a complete library, allowed for all substitutions at the above identified positions. The consensus sequences selected from the focused, and complete libraries were RRWS and R(R/N)QL, respectively. Inhibition constant determinations showed ecotin variants containing these sequences to be similarly potent (K i = 1–2 nm). These substitutions were combined with previously identified substitutions in another critical region of ecotin. One of these combinations (D70R/M84R/RRQL) is the tightest (K i = 50 pm) ecotin variant inhibitor of uPA. The blending of combinatorial methods and computer algorithms designed to predict stronger binders has allowed us to obtain protein derivatives that exhibit greatly increased affinity for a predetermined target. This technology can be applied to select for enhanced binding interactions at protein-protein interfaces and accelerate the process of protease inhibitor development.

Analysis of molecular dynamics trajectories for a small protein, the villin headpiece subdomain, shows that its internal dynamics can be modeled as a random walk on a bounded high-dimensional lattice where each lattice point corresponds to a protein conformation. The time evolution of the dynamics trajectory can be described as a three-stage process. The first stage, over a very short time scale of 10 fs, is consistent with an all-atoms ballistic flight with an average path length of 0.068 A. The apparent conformational displacement "velocity" of 680 m/s is of similar magnitude to free flight monatomic carbon gas at room temperature. The second stage is unobstructed random walk diffusion in a high-dimensional space for ∼300 fs, average displacement of 0.4 A. In the third stage, at longer times, "harmonic-like" barriers confine the conformational diffusion to a few large-amplitude modes. We use this description to develop a lattice model that can reproduce the time dependence of the root-mean-square displacement (rmsd) along the dynamics trajectory with surprisingly few parameters. The lattice model allows exploration of specific energy landscapes on the folding of the villin headpiece subdomain. For example, we test a simple funnel landscape with a Monte Carlo search in which displacement is biased toward a corner of the lattice space representing the native state. An energy difference of ∼15 kcal/mol between native and unfolded states is sufficient to give a reasonable folding time of 10 μs with two-state kinetics. To our knowledge, these are the first protein-folding simulations that successfully fold the protein using a model with explicit time representation and a stochastic search and without a native-state specific potential function.

Hierarchical structures consisting of small sub-wavelength features stacked atop larger structures have been demonstrated as an effective means of reducing the reflectance of surfaces. However, optical devices require different antireflective properties depending on the application, and general unifying guidelines on hierarchical structures' design to attain a desired antireflection spectral response are still lacking. The type of reflectivity (diffuse, specular, or total/hemispherical) and its angular- and spectral-dependence are all dictated by the structural parameters. Through computational and experimental studies, guidelines have been devised to modify these various aspects of reflectivity across the solar spectrum by proper selection of the features of hierarchical structures. In this wavelength regime, micrometer-scale substructures dictate the long-wavelength spectral response and effectively reduce specular reflectance, whereas nanometer-scale substructures dictate primarily the visible wavelength spectral response and reduce diffuse reflectance. Coupling structures having these two length scales into hierarchical arrays impressively reduces surfaces' hemispherical reflectance across a broad spectrum of wavelengths and angles. Such hierarchical structures in silicon are demonstrated having an average total reflectance across the solar spectrum of 1.1% (average weighted reflectance of 1% in the 280–2500 nm range of the AM 1.5 G spectrum) and specular reflectance

Selective Laser Melting (SLM) of metal powder bed layers, whereby 3D metal objects can be printed from a digital file with unprecedented design flexibility, is spurring manufacturing innovations in medical, automotive, aerospace and textile industries. Because SLM is based on raster-scanning a laser beam over each layer, the process is relatively slow compared to most traditional manufacturing methods (hours to days), thus limiting wider spread use. Here we demonstrate the use of a large area, photolithographic method for 3D metal printing, using an optically-addressable light valve (OALV) as the photomask, to print entire layers of metal powder at once. An optical sheet of multiplexed ~5 kW, 20 ms laser diode and ~1 MW, 7 ns Q-switched laser pulses are used to selectively melt each layer. The patterning of near infrared light is accomplished by imaging 470 nm light onto the transmissive OALV, which consists of polarization-selective nematic liquid crystal sandwiched between a photoconductor and transparent conductor for switching.

Most metal additive manufacturing approaches are based on powder-bed melting techniques such as laser selective melting or electron beam melting, which often yield uncontrolled microstructures with defects (e.g., pores or microcracks) and residual stresses. Here, we introduce a proof-of-concept prototype of a 3D metal freeform fabrication process by direct writing of metallic alloys in the semi-solid regime. This process is achieved through controlling the particular microstructure and the rheological behavior of semi-solid alloy slurries, which demonstrate a well suited viscosity and a shear thinning property to retain the shape upon printing. The ability to control the microstructure through this method yields a flexible manufacturing route to fabricating 3D metal parts with full density and complex geometries.

We present an optical/NIR imaging survey of the face-on spiral galaxy M83, using data from the Hubble Space Telescope Wide Field Camera 3 (WFC3). Seven fields are used to cover a large fraction of the inner disk, with observations in nine broadband and narrowband filters. In conjunction with a deep Chandra survey and other new radio and optical ground-based work, these data enable a broad range of science projects to be pursued. We provide an overview of the WFC3 data and processing and then delve into one topic, the population of young supernova remnants. We used a search method targeted toward soft X-ray sources to identify 26 new supernova remnants. Many compact emission nebulae detected in [Fe II] 1.644 micron align with known remnants and this diagnostic has also been used to identify many new remnants, some of which are hard to find with optical images. We include 37 previously identified supernova remnants that the data reveal to be, 39 pages, 8 figures. accepted for ApJ

Microlattices make marvelous materials Framework or lattice structures can be remarkably strong despite their very low density. Using a very precise technique known as projection microstereolithography, Zheng et al. fabricated octet microlattices from polymers, metals, and ceramics. The design of the lattices meant that the individual struts making up the materials did not bend under pressure. The materials were therefore exceptionally stiff, strong, and lightweight. Science , this issue p. 1373

Parasitic protozoa lack the ability to synthesize purine nucleotides de novo, relying instead on purine salvage enzymes for their survival. Guanine phosphoribosyltransferase (GPRT) from the protozoan parasite Giardia lamblia is a potential target for rational antiparasitic drug design, based on the experimental evidence, which indicates the lack of interconversion between adenine and guanine nucleotide pools. The present study is a continuation of our efforts to use three-dimensional structures of parasitic phosphoribosyltransferases (PRTs) to design novel antiparasitic agents. Two micromolar phthalimide-based GPRT inhibitors were identified by screening the in-house phthalimide library. A combination of structure-based scaffold selection using virtual library screening across the PRT gene family and solid phase library synthesis led to identification of smaller (molecular weight, K i values in the 23 to 25 μM range. These results represent significant progress toward the goal of designing potent inhibitors of purine salvage in Giardia parasites. As a second step in this process, altering the phthalimide moiety to optimize interactions in the guanine-binding pocket of GPRT is expected to lead to compounds with promising activity against G. lamblia PRT.

Using stellar luminosity functions derived from ROSAT data, the contributions of Galactic stars to the diffuse X-ray background are calculated for ROSAT PSPC energy bands. The model follows that of Guillout et al. (1996), but uses ROSAT rather than {\it Einstein} data to determine the intrinsic luminosity distributions. The model adequately predicts the numbers of stellar sources observed in deep ROSAT surveys. The contribution of unresolved stellar sources to the ROSAT All-Sky Survey at the Galactic poles is 6.85, 4.76, and 4.91 $\times$ counts s$^{-1}$ arcmin$^{-2}$ in bands R12 (1/4 keV), R45(3/4 keV), and R67(1.5 keV), respectively, which is equivalent to 4.66, 31.3 and 26.9 $\times10^{-14}$ ergs cm$^{-2}$ s$^{-1}$ deg$^{-2}$., 14 pages, 8 figures, accepted by ApJ

Using a deep Chandra AO-1 observation of the face-on spiral galaxy M101, we examine three of five previously optically-identified X-ray sources which are spatially correlated with optical supernova remnants (MF54, MF57, and MF83). The X-ray fluxes from these objects, if due to diffuse emission from the remnants, are bright enough to require a new class of objects, with the possible attribution by Wang to diffuse emission from hypernova remnants. Of the three, MF83 was considered the most likely candidate for such an object due to its size, nature, and close positional coincidence. However, we find that MF83 is clearly ruled out as a hypernova remnant by both its temporal variability and spectrum. The bright X-ray sources previously associated with MF54 and MF57 are seen by Chandra to be clearly offset from the optical positions of the supernova remnants by several arc seconds, confirming a result suggested by the previous work. MF54 does have a faint X-ray counterpart, however, with a luminosity and temperature consistent with a normal supernova remnant of its size. The most likely classifications of the sources are as X-ray binaries. Although counting statistics are limited, over the 0.3--5.0 keV spectral band the data are well fit by simple absorbed power laws with luminosities in the 10^38 to 10^39 ergs/s range. The power law indices are softer than those of Milky Way LMXB of similar luminosities, and are more consistent with those of the Large Magellanic Cloud. Both the high luminosity and the soft spectral shape favor these being accreting black hole binaries in high soft states., 10 pages, 4 figures, ApJ Accepted

Three observational constraints can be placed on a warm-hot intergalactic medium (WHIM) using \rosat PSPC pointed and survey data, the emission strength, the energy spectrum, and the fluctuation spectrum. The upper limit to the emission strength of the WHIM is 7.5 +/- 1.0 keV s^-1 cm^-2 sr^-1 keV^-1 in the 3/4 keV band, an unknown portion of which value may be due to our own Galactic halo. The spectral shape of the WHIM emission can be described as thermal emission with log T=6.42, although the true spectrum is more likely to come from a range of temperatures. The values of emission strength and spectral shape are in reasonable agreement with hydrodynamical cosmological models. The autocorrelation function in the 0.44 keV < E < 1.21 keV band range, w(theta), for the extragalactic soft X-ray background (SXRB) which includes both the WHIM and contributions due to point sources, is less than about 0.002 for 10 arcminutes < theta < 20 arcminutes in the 3/4 keV band. This value is lower than the Croft et al. (2000) cosmological model by a factor of about 5, but is still not inconsistent with cosmological models. It is also found that the normalization of the extragalactic power law component of the soft X-ray background spectrum must be 9.5 +/- 0.9 keV s^-1 cm^-2 sr^-1 keV^-1 to be consistent with the ROSAT All-Sky Survey., 5 pages, 2 figures, submitted to Astrophysical Journal Letters

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 ∼109 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 ∼102 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 μs. 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. Proteins 2001;42:495–511. © 2001 Wiley-Liss, Inc.

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 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. Proteins 2001;42:296–318. © 2000 Wiley-Liss, Inc.

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.

We present evidence for the impact of a supernova blast‐wave on a molecular cloud located inside the Local Bubble, in the area of interaction with the Sco‐Cen OB association.The evidence comes from the analysis of the line of sight toward the nearby (170 pc) star HD102065, located behind the tail of a cometary‐shaped, infrared cirrus‐cloud which we believe is only 70 pc away from the Sun. The analysis includes numerous transitions of atoms, ions and molecules, in absorption and in emission, in the UV, the optical and the sub‐millimeter.Several peculiar characteristics of the cloud like the spatial structure of its cold phase, the high negative velocities, the high abundance of atoms in excited states and the highly ionized species associated with the highest velocities, as well as the unusually high abundance of small dust particles, are interpreted as the result of the interaction with a supernova shock wave.This line of sight provides an ideal laboratory to study turbulent flows and mixing layers in the ISM.We present evidence for the impact of a supernova blast‐wave on a molecular cloud located inside the Local Bubble, in the area of interaction with the Sco‐Cen OB association.The evidence comes from the analysis of the line of sight toward the nearby (170 pc) star HD102065, located behind the tail of a cometary‐shaped, infrared cirrus‐cloud which we believe is only 70 pc away from the Sun. The analysis includes numerous transitions of atoms, ions and molecules, in absorption and in emission, in the UV, the optical and the sub‐millimeter.Several peculiar characteristics of the cloud like the spatial structure of its cold phase, the high negative velocities, the high abundance of atoms in excited states and the highly ionized species associated with the highest velocities, as well as the unusually high abundance of small dust particles, are interpreted as the result of the interaction with a supernova shock wave.This line of sight provides an ideal laboratory to study turbulent flows and mixing layers in the...

International audience; Physical importance of the charge-exchange process in the interaction of the cold neutral cloud with surrounding hot fully ionized plasma is investigated. A non-stationary one-dimensional two-component model is presented. It is assumed in the model that the cloud consists of atomic hydrogen. Plasma is assumed to be quasi-neutral and magnetic fields are ignored. We demonstrate distribution of gas-dynamic parameters for plasma and neutral components in the interaction region and investigate time evolution of the interaction interface from the beginning of the interaction between neutral gas and plasma to very large time-intervals.Charge-exchange of atoms with heavy ions is a possible source of the X-ray emission. The charge-exchange rate as function of distance and time is shown. This rate being scaled with the relative abundances of minor heavy ions and with corresponding ion-atom cross-sections can be used to estimate X-ray emissivity for different astrophysical objects

The soft X-ray background in the 0.1-1.0 keV band is known to be produced by at least three sources; the Local Hot Bubble (LHB), the extragalactic power law (EPL), and a seemingly galactic component that lies outside the bulk of the absorption that is due to the ISM of the galactic disk. This last component, which we call the Trans-Absorption Emission (TAE), has been modeled by a number of groups who have derived disparate measures of its temperature. The differences have arisen from differing assumptions about the structure of the emitting gas and unrecognized methodological difficulties. In particular, spectral fitting methods do not uniquely separate the TAE from the foreground emission that is due the LHB. This "degeneracy" can be resolved using the angular variation of the absorption of the TAE. We show that the TAE cannot be characterized by a single thermal component; no single-component model can be consistent with both the spectral energy distribution of the TAE emission and the angular variation due to absorption by the galactic disk. We use the angular anticorrelation of the ROSAT All-Sky Survey with the galactic absorption to separate local from distant emission components, and to fit the spectral energy distribution of the resulting distant emission. We find that the emission is best described by a two-thermal-component model with logT(sub S) = 6.06(sup +0.14, sub -0.12) and log T(sub H) = 6.42(sup +0.14, sub -0.12). This two-thermal-component TAE fits the ROSAT spectral energy distribution significantly better than single-component models, and is consistent with both angular variation and spectral constraints.

This paper presents a catalog of shadows in the 1/4 keV soft X-ray diffuse background 4 (SXRB) that were identified by a comparison between ROSAT All-Sky Survey maps and DIRB&corrected IRAS 100 micron maps. These "shadows" are the negative correlations between the surface brightness of the SXRB and the column density of the Galactic interstellar medium (ISIM) over limited angular regions (a few degrees in extent). We have compiled an extensive but not exhaustive set of 378 shadows in the polar regions of the Galaxy (Absolute value (beta) > and approximately equal 20 deg.), and determined their foreground and background X-ray intensities (relative to the absorbing features), and the respective hardness ratios of that emission. The portion of the sky that was examined to find these shadows was restricted in general to regions where the minimum column density is less than and approximately equal to 4 x 10(exp 20) H/square cm, i.e., relatively high Galactic latitudes, and to regions away from distinct extended features in the SXRB such as supernova remnants and superbubbles. The results for the foreground intensities agree well with the recent results of a general analysis of the local 1/4 KeV emission while the background intensities show additional. but not unexpected scatter. The results also confirm the existence of a gradient in the hardness of the local 1/4 keV emission along a Galactic center/ anticenter axis with a temperature that varies from 10(exp 6.13) K to 10(exp 6.02) K, respectively. The average temperature of the foreground component from this analysis is 10(exp 6.08) K, compared to 10(exp 6.06) K in the previous analysis. Likewise, the average temperature for the distant component for the current and previous analyses are 10(exp 6.06) K and 10(exp 6.02) K, respectively. Finally, the results for the 1/4 keV halo emission are compared to the observed fluxes at 3/4 keV, where the lack of correlation suggests that the Galactic halo's 1/4 keV and 3/4 keV fluxes are likely produced by separate emission regions.

All parasitic protozoa lack the ability to synthesize purine nucleotides de novo, relying instead on purine salvage enzymes for their survival. Hypoxanthine-guanine-xanthine phosphoribosyltransferase (HGXPRT) from the protozoan parasite Tritrichomonas foetus is a rational target for antiparasitic drug design because it is the primary enzyme the parasite uses to salvage purine bases from the host. The study presented here is a continuation of our efforts to use the X-ray structure of the T. foetus HGXPRT-GMP complex to design compounds that bind tightly to the purine pocket of HGXPRT. The goal of the current project was to improve the affinity and selectivity of previously identified HGXPRT inhibitor TF1 [4-(3-nitroanilino)phthalic anhydride]. A virtual library of substituted 4-phthalimidocarboxanilides was constructed using methods of structure-based drug design, and was implemented synthetically on solid support. Compound 20 [(4'-phthalimido)carboxamido-3-benzyloxybenzene] was then used as a secondary lead for the second round of combinatorial chemistry, producing a number of low-micromolar inhibitors of HGXPRT. One of these compounds, TF2 [(4'-phthalimido)carboxamido-3-(4-bromobenzyloxy)benzene], was further characterized as a competitive inhibitor of T. foetus HGXPRT with respect to guanine with a K(I) of 0.49 microM and a 30-fold selectivity over the human HGPRT. TF2 inhibited the growth of cultured T. foetus cells in a concentration-dependent manner with an ED(50) of 2.8 microM, and this inhibitory effect could be reversed by addition of exogenous hypoxanthine. These studies underscore the efficiency of combining structure-based drug design with combinatorial chemistry to produce effective species-specific enzyme inhibitors of medicinal importance.

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.

We explore the question of what are the best ligands for macromolecular targets. A survey of experimental data on a large number of the strongest-binding ligands indicates that the free energy of binding increases with the number of nonhydrogen atoms with an initial slope of ≈−1.5 kcal/mol (1 cal = 4.18 J) per atom. For ligands that contain more than 15 nonhydrogen atoms, the free energy of binding increases very little with relative molecular mass. This nonlinearity is largely ascribed to nonthermodynamic factors. An analysis of the dominant interactions suggests that van der Waals interactions and hydrophobic effects provide a reasonable basis for understanding binding affinities across the entire set of ligands. Interesting outliers that bind unusually strongly on a per atom basis include metal ions, covalently attached ligands, and a few well known complexes such as biotin–avidin.

Accounting for the effect of solvent on the strength of molecular interactions has been a long-standing problem for molecular calculations in general and for structure-based drug design in particular. Here, we explore the generalized-Born (GB/SA) model of solvation (Still, W. C.; Tempczyk, A.; Hawley, R. C.; Hendrickson, T. J. Am. Chem. Soc. 1990, 112, 6127−9) to calculate ligand−receptor binding energies. The GB/SA approach allows for the estimation of electrostatic, van der Waals, and hydrophobic contributions to the free energy of binding. The GB/SA formulation provides a good balance between computational speed and accuracy in these calculations. We have derived a formula to estimate the binding free energy. We have also developed a procedure to penalize any unoccupied embedded space that might form between the ligand and the receptor during the docking process. To improve the computational speed, the protein contribution to the electrostatic screening is precalculated and stored on a grid. Refinement...

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.

We have developed an automatic protein fingerprinting method for the evaluation of protein structural similarities based on secondary structure element compositions, spatial arrangements, lengths, and topologies. This method can rapidly identify proteins sharing structural homologies as we demonstrate with five test cases: the globins, the mammalian trypsinlike serine proteases, the immunoglobulins, the cupredoxins, and the actinlike ATPase domain-containing proteins. Principal components analysis of the similarity distance matrix calculated from an all-by-all comparison of 1,031 unique chains in the Protein Data Bank has produced a distribution of structures within a high-dimensional structural space. Fifty percent of the variance observed for this distribution is bounded by six axes, two of which encode structural variability within two large families, the immunoglobulins and the trypsinlike serine proteases. Many aspects of the spatial distribution remain stable upon reduction of the database to 140 proteins with minimal family overlap. The axes correlated with specific structural families are no longer observed. A clear hierarchy of organization is seen in the arrangement of protein structures in the universe. At the highest level, protein structures populate regions corresponding to the all-alpha, all-beta, and α/β superfamilies. Large protein families are arranged along family-specific axes, forming local densely populated regions within the space. The lowest level of organization is intrafamilial; homologous structures are ordered by variations in peripheral secondary structure elements or by conformational shifts in the tertiary structure. Proteins 1999;34:317–332. © 1999 Wiley-Liss, Inc.

Theophylline (oxidative phase I metabolism) is biotransformed by the liver at an increasingly delayed rate with advancing age. Hymecromone (phase II metabolism) does not display any dependence of glucuronidisation on age. The indocyanine green half-life and the galactose elimination capacity show a highly significant dependence on age. Drugs with flow-limited elimination or mainly oxidative phase I biotransformation should be administered with reduced dosage level while monitoring the serum concentration levels. Drugs that are transformed via phase II reactions usually do not require dosage adjustment.

We present a set of programs, DREAM++ (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 [1, 2]. Its output can be used as input to REACT++ and SEARCH++. The program REACT++ performs user-specified 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 [3, 4] and incremental construction [5, 6] 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 [7, 8].

Human growth hormone (hGH) binds to its receptor (hGHr) in a three-body interaction: one molecule of the hormone and two identical monomers of the receptor form a trimer. Curiously, the hormone-receptor interactions in the trimer are not equivalent and the formation of the complex occurs in a specific kinetic order (Cunningham BC, Ultsch M, De Vos AM, Mulkerrin MG, Clauser KR, Wells JA, 1991, Science 254:821-825). In this paper, we model the recognition of hGH to the hGHr using shape complementarity of the three-dimensional structures and macromolecular docking to explore possible binding modes between the receptor and hormone. The method, reported previously (Hendrix DK, Kuntz ID, 1998, Pacific symposium on biocomputing 1998, pp 1234-1244), is based upon matching complementary-shaped strategic sites on the molecular surface. We modify the procedure to examine three-body systems. We find that the order of binding seen experimentally is also essential to our model. We explore the use of mutational data available for hGH to guide our model. In addition to docking hGH to the hGHr, we further test our methodology by successfully reproducing 16 macromolecular complexes from X-ray crystal structures, including enzyme-inhibitor, antibody-antigen, protein dimer, and protein-DNA complexes.

One hundred and forty-five patients suffering from diseases requiring long-term treatment with high doses of corticosteroids (30 mg/day or greater of prednisolone) were recruited to the study. Patients had to be steroid naive on entry to the study (not more than 15 days of treatment with a corticosteroid within the previous 24 months). Patients were randomized to receive either 1 microgram/day alfacalcidol or placebo capsules for 12 months. Bone mineral density (BMD) of the lumbar spine was assessed by dual-photon absorptiometry on entry and after 3, 6 and 12 months' treatment. Safety was monitored by the recording of all adverse events reported by patients and the regular screening of blood samples for hematology and serum biochemistry. Of the 145 patients, 74 were randomized to alfacalcidol and 71 to placebo. The treatment groups were well matched at baseline with no significant differences in demographic, clinical or biochemical parameters. The mean equivalent dose of prednisolone at baseline was 46.6 mg/day and 46.3 mg/day for the alfacalcidol and placebo group respectively. From the 145 patients randomized to treatment, 71 (38 who received alfacalcidol and 33 who received placebo) provided BMD data both at baseline and at 3, 6 and 12 months. The percentage change in BMD after 6 months' treatment was -2.11% in the alfacalcidol group and -4.00% in the placebo group (p = 0.39). After 12 months the percentage change in BMD was +0.39% (CI: -4.28 to 4.81) in the alfacalcidol group and -5.67% (CI: -8.13 to -3.21) in the placebo group, this difference (6.06%, CI: 0.88 to 11.24) being statistically significant (p = 0.02). An intention to treat analysis also showed a significant difference between the two treatment groups in alfacalcidol's favor (3.81%, p = 0.01; CI: 0.92 to 6.70). There was no significant difference between the two treatment groups in the corticosteroid dose at any time point during the study. Serum calcium was measured throughout and there were no significant differences between the two treatment groups at any visit. This study suggests that alfacalcidol can prevent corticosteroid-induced bone loss from the lumbar spine. Long-term use of alfacalcidol was not associated with any significant adverse effects in this diverse group of patients.

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.

Severe idiopathic osteoporosis in middle-aged men is still poorly understood. The aim of this study was to assess the contribution of genetic factors in these patients. We studied 38 men (mean age +/- SD, 50 +/- 11 years) presenting with vertebral or peripheral bone fractures due to primary osteoporosis and 73 of their relatives divided into four subgroups: 19 brothers, 22 sisters, 13 sons, and 19 daughters. The control group comprised 199 age-matched subjects. In all subjects, we measured bone mineral density (BMD) and calculated the Z score at the lumbar spine (LS) and femoral neck (FN) based on the fitted BMD value in the controls. LS BMD values were lower in each of the four subgroups compared with the age-matched controls. The mean Z score for the overall group of 73 relatives was decreased compared with the age-matched controls (-1. 28 +/- 1.48 at the LS and -1.03 +/- 1.19 at the FN) and was not influenced by gender or by whether the relatives were siblings or children. An LS Z score-1) was found in 54.8% of the relatives of osteoporotic patients versus 17.4% of the control subjects (risk ratio, 3.2). Alcohol and tobacco abuse are well-known risk factors for osteoporosis in men. Among the 38 osteoporotic patients, 7 were heavy smokers (20 pack-years), 8 were both heavy smokers and drinkers (80 g/day for at least 10 years and gammaGT40 UI/l), and 23 had neither of these risk factors. BMD, Z score, and anthropometric data were the same in patients with and without risk factors. Decreases in LS and FN Z scores were similar in relatives of patients with and without risk factors. In conclusion, low BMD is observed in relatives of osteoporotic men with or without risk factors for osteoporosis, indicating that familial factors contribute to primary osteoporosis in middle-aged men.