Structure-based design of inhibitors of NS3 serine protease of hepatitis C virus

We have designed small focused combinatorial library of hexapeptide inhibitors of NS3 serine protease of the hepatitis C virus (HCV) by structure-based molecular design complemented by combinatorial optimisation of the individual residues. Rational residue substitutions were guided by the structure and properties of the binding pockets of the enzyme's active site. The inhibitors were derived from peptides known to inhibit the NS3 serine protease by using unusual amino acids and alpha-ketocysteine or difluoroaminobutyric acid, which are known to bind to the S1 pocket of the catalytic site. Inhibition constants (Ki) of the designed library of inhibitors were predicted from a QSAR model that correlated experimental Ki of known peptidic inhibitors of NS3 with the enthalpies of enzyme-inhibitor interaction computed via molecular mechanics and the solvent effect contribution to the binding affinity derived from the continuum model of solvation. The library of the optimised inhibitors contains promising drug candidates-water-soluble anionic hexapeptides with predicted Ki* in the picomolar range.     

Computer simulations of protein dynamics and thermodynamics

The computational challenges of producing realistic biomedical simulations are reviewed. Techniques for applying classical mechanics simulation methods to proteins and ways to solve Newton's equations are discussed. Two recent applications of these methods are examined. The first considers the rate at which molecular oxygen binds to myoglobin, an oxygen-storage protein found in muscle. The second application involves the thermodynamics of the binding of oxygen to hemoglobin, a protein that is the major component of red blood cells. The comparison of this biochemical event to one in which oxygen is bound to an unusual variant of hemoglobin illustrates many of the simulation methods commonly used in the pharmaceutical industry to aid in the drug discovery process     

Generalized-ensemble simulations of spin systems and protein systems

In complex systems such as spin systems and protein systems, conventional simulations in the canonical ensemble will get trapped in states of energy local minima. We employ the generalized-ensemble algorithms in order to overcome this multiple-minima problem. Three well-known generalized-ensemble algorithms, namely, multicanonical algorithm, simulated tempering, and replica-exchange method, are described. We then present three new generalized-ensemble algorithms based on the combinations of the three methods. Effectiveness of the new methods are tested with a Potts model and protein systems.     

Verisim: formal analysis of network simulations

Network protocols are often analyzed using simulations. We demonstrate how to extend such simulations to check propositions expressing safety properties of network event traces in an extended form of linear temporal logic. Our technique uses the INS simulator together with a component of the MaC system to provide a uniform framework. We demonstrate its effectiveness by analyzing simulations of the ad hoc on-demand distance vector (AODV) routing protocol for packet radio networks. Our analysis finds violations of significant properties and we discuss the faults that cause them. Novel aspects of our approach include modest integration costs with other simulation objectives such as performance evaluation, greatly increased flexibility in specifying properties to be checked and techniques for analyzing complex traces of alarms raised by the monitoring software     

Shape design sensitivity analysis and optimization of spatially rotating objects

Shape design sensitivity analysis (DSA) and optimization of spatially rotating objects is presented in this paper. Design sensitivity expressions are derived using a continuum DSA method for spatial objects rotating with angular velocity and angular acceleration, based on three definitions of the finite element mass matrix: consistent, lumped, and diagonalized. The design sensitivity expression derived using a diagonalized element mass matrix, which is consistent with the finite element analysis (FEA) method used in ANSYS, is implemented, although the method can work with other FEA codes, such as MSC/NASTRAN or ABAQUS. Since the continuum DSA method is used, sensitivity information can be computed outside the FEA codes by postprocessing finite element data. Rotating block and turbine blade examples are presented to validate the proposed DSA method. The turbine blade example is optimized using an integrated optimization module of the Design Sensitivity Analysis and Optimization (DSO) tool developed at the University of Iowa. The integrated module consists of ANSYS, MSC/NASTRAN, or ABAQUS for FEA; Design Optimization Tool (DOT) for nonlinear programming; and DSA and design model update programs developed in DSO.     

Stability of C60 chains: molecular dynamics simulations

A linearly aligned structure of three C60 fullerene, interconnected by two benzorods of same size, have been investigated under heat treatment. The overall structure resembles a section of a beaded string. Nine different lengths of benzorods have been considered, and the effect on the thermal stability have been investigated by means of molecular dynamics method. It has been found that the structure is thermally stable up to elevated temperatures, and the linear alignment of the structure is persistent, up to the temperature of decomposition.     

Identification of apolipoprotein C-III as a potential plasmatic biomarker associated with the resolution of hepatitis C virus infection

Understanding the virus-host interactions that lead to approximately 20% of patients with acute Hepatitis C Virus (HCV) infection to viral clearance is probably a key towards the development of more effective treatment and prevention strategies. Acute hepatitis C infection is usually asymptomatic and therefore rarely diagnosed. Nevertheless, HCV nucleic acid testing carried out on all blood donations detects donors who have resolved their HCV infection after seroconversion. Here we have used SELDI-TOF-MS technology to compare, at a proteomic level, plasma samples respectively from donors with HCV clearance, from donors with chronic HCV infection and from unexposed healthy donors (n?=?15 per group). A candidate marker of about 9.4?kDa was detected as differentially expressed in the three groups. After purification we identified by nanoLC-Q-TOF-MS/MS this candidate marker as Apolipoprotein C-III (ApoC-III). The identification was confirmed by western blot analysis. Levels of ApoC-III were then determined in the 45 plasma samples by immunoturbidimetric assay. ApoC-III was found to be higher in donors who had resolved their HCV infection than in donors with chronic infection, results which were consistent with SELDI-TOF-MS data. ApoC-III is the first reported candidate biomarker in plasma associated with the spontaneous resolution of HCV infection.     

Analysis of the domain interactions between the protease and helicase of NS3 in dengue and hepatitis C virus

Flaviviridae non-structural 3 protein (NS3) is a multifunctional enzyme, composed by a protease domain (NS3pro) and an RNA helicase domain (NS3hel). The activities present in NS3 have proved to be critical for viral replication. The replicative cycle of Flaviviridae requires coordinated regulation of all the activities present in the full-length NS3 protein, however, the exact nature of these interactions remains unclear. The present work aimed to determine common structural features between NS3 of dengue and hepatitis C viruses and to characterize residues involved in the regulation of the interdomain motions between NS3pro and NS3hel. Analysis of the root mean square (RMS) variation shows that NS3pro increases the stability of subdomain 1 of the RNA helicase. Moreover, the dynamic behaviour of the carboxy terminus of NS3hel, supports the hypothesis that, upon release of the carboxy-terminus from NS3pro, the residues involved in this interaction are folded back into the last alpha-helix. Using normal mode analysis, we characterized slow collective motions of NS3, and observed that the two lowest-frequency normal modes are enough to describe reorientations of NS3pro relative to NS3hel. These movements induced an increment in the exposure of the active site of NS3pro that can be important during the proteolytic processing of the viral polyprotein. The third low-frequency normal mode was correlated to subdomain reorientations of NS3hel, similar to those proposed during NTP hydrolysis and dsRNA unwinding. Based on these data, we support a dynamic model, in which the domain movements between NS3pro and NS3hel result in the regulation of its activities.     

Structural analysis of lead fullerene-based inhibitor bound to human immunodeficiency virus type 1 protease in solution from molecular dynamics simulations

Molecular dynamics (MD) simulations of the HIV-1 protease (HIVP) complexed with lead fullerene-based inhibitor (diphenyl C60 alcohol) in the three protonated states, unprotonated (Un-), monoprotonated (Mono-), and diprotonated (Di-) states at Asp25 and Asp25' were performed. As the X-ray structure of the investigated complex is not available, it was built up starting with the X-ray crystallographic structure of the HIVP complexed with non-peptide inhibitor (PDB code: 1AID) and that of the diphenyl C60 alcohol optimized using the integrated ONIOM molecular orbital calculations. The inhibitor was, then, introduced into the enzyme pocket using a molecular docking method. Change of the HIVP binding cavity for all three states were evaluated in terms of distance between the two catalytic residues, Asp25 and Asp25' as well as those between the catalytic residues and the flap regions. The torsional angles formed by the O-C-C-O of the two carboxyl groups of the catalytic dyad show the non-planar configuration with the most frequency at about -45 degrees for the Un-, 35 degrees and -95 degrees for the Mono- and 60 degrees for the Di-systems. At equilibrium, different orientations of the fullerene-based inhibitor in the three protonation states were observed. For the Di-state, the OH group of the inhibitor stably forms hydrogen bonds with the two aspartic residues. It turns to the flap region to form hydrogen bonding to the backbone N of Ile50' for the Un-state. In contrast, the OH group turns to locate between the catalytic and the flap region for the Mono-states. Beside the molecular orientation, the rotation of the OH group of the inhibitor in the Un-state was also detected. In terms of solvation, the carboxylate oxygens of the aspartic residues in the Un- and Mono-states were solvated by one to three water molecules while the OH group in these two states was coordinated by one water molecule. This is in contrast to the Di-state in which no water molecule is available in the radius of 5-6A around the oxygen atoms of the carboxylate groups of enzyme and of the OH group of the inhibitor. The simulated results lead to the conclusion that the active site of the HIVP complexed with the diphenyl C60 alcohol is the diprotonation states on Asp25 and Asp25'.     

Three-dimensional static analysis,of a spatially loaded planar rigid-jointed plexus frame

An exact matrix solution for the static analysis of a multi-storey and multi-column rectangular rigid-jointed plexus frame, subjected to a general spatial loading, is presented. Since the obtained closed-form formulae, giving all the structure redundants, include matrices of maximum dimensions mn × mn (where m = number of storeys and n = number of columns), the proposed methodology is more convenient compared to other existing methods, because it requires less memory space and computer coding. Also, a numerical application demonstrates the correctness and the potentialities of the method. In addition, this solution technique may become a useful guideline for the further investigation of three-dimensional frame structures.     

Numerical analysis and simulations of contact problem with wear

This paper presents a quasistatic problem of an elastic body in frictional contact with a moving foundation. The model takes into account wear of the contact surface of the body caused by the friction. We recall existence and uniqueness results obtained in Sofonea et al. (2017). The main aim of this paper is to present a fully discrete scheme for numerical approximation together with an error estimation of a solution to this problem. Finally, computational simulations are performed to illustrate the mathematical model.     

A noncausal framework for model-based feedback control of spatially developing perturbations in boundary-layer flow systems. Part II: numerical simulations using state feedback

We present numerical results illustrating the successful state feedback control of a spatially developing boundary-layer flow system. Control is applied using the noncausal framework developed in Part I of this study. After addressing some important regularization issues related to the proper treatment of the infinite-dimensional nature and semi-infinite spatial extent of the present system, we compute the state-feedback control gains according to the equations developed in Part I at several spanwise wavenumbers β. We then inverse transform the result to obtain spatial convolution kernels for determining the control feedback. The effectiveness of the controls computed using these feedback kernels, which are well resolved on the computational grid and spatially localized in the spanwise direction, is tested using direct numerical simulation of the boundary-layer flow system. A significant damping of the flow perturbation is observed, which is of the same order as the damping that arises when applying significantly more expensive iterative adjoint-based control optimization schemes.     

Discrete analysis method for random vibration of structures subjected to spatially correlated filtered white noises

Random vibration analysis of large-span space structures or high-rise structures which are subjected to spatially correlated filtered white noise excitations such as wind load and earthquake motion, has been a difficult problem in engineering computation. Based on the idea of the discrete analysis method of random vibration, this paper attempts to solve this problem. The formulae of calculating structural mean and mean square responses are given. As an example, the wind-induced vibration of a cable roof structure is analysed by using these formulae.     

Conformational analysis of compstatin analogues with molecular dynamics simulations in explicit water

The cyclic 13-residue peptide compstatin is a potential therapeutic agent against the unregulated activation of the complement system. A thorough knowledge of its structural and dynamical properties in solution may assist the design of improved complement inhibitors. NMR studies have suggested that the 5-8 segment of free compstatin folds into a critical for activity 5-8 beta turn and the rest of the peptide is mainly disordered. Earlier computational studies of compstatin analogues with a polar-hydrogen/generalized-Born approximation reproduced the 5-8 turn, but also indicated the formation of beta-hairpin or alpha-helical elements and the existence of interactions between certain charged or aromatic sidechains. However, these features are absent or partly present in the NMR spectra, due to extensive conformational averaging. In order to check the compstatin properties with a more rigorous model of the intra- and intermolecular interactions, we conduct here 98-ns all-atom/explicit-water simulations of three compstatin analogues with variable activity; a native analogue, the more active mutant V4W/H9A and the inactive mutant Q5G. The 5-8 beta-turn population is in good accord with NMR. For the systems studied here, the simulations suggest that the 5-8 turn population does not correlate strictly with activity, in agreement with earlier mutational studies. Furthermore, they show structural differences among the analogues outside the 5-8 region. The possible role of these differences in activity is discussed. The probability of beta-hairpin or alpha-helix elements is much smaller with respect to the polar-hydrogen/GB simulations, and the persistent Trp4-Trp7 or Asp6-Arg11 sidechain interactions of the earlier GB studies are not reproduced. The present simulations extend the NMR data and improve our understanding of the properties of compstatin and related analogues.     

Performance analysis of direct N-body algorithms for astrophysical simulations on distributed systems

We discuss the performance of direct summation codes used in the simulation of astrophysical stellar systems on highly distributed architectures. These codes compute the gravitational interaction among stars in an exact way and have an O(N²) scaling with the number of particles. They can be applied to a variety of astrophysical problems, like the evolution of star clusters, the dynamics of black holes, the formation of planetary systems, and cosmological simulations. The simulation of realistic star clusters with sufficiently high accuracy cannot be performed on a single workstation but may be possible on parallel computers or grids. We have implemented two parallel schemes for a direct N-body code and we study their performance on general purpose parallel computers and large computational grids. We present the results of timing analyzes conducted on the different architectures and compare them with the predictions from theoretical models. We conclude that the simulation of star clusters with up to a million particles will be possible on large distributed computers in the next decade. Simulating entire galaxies however will in addition require new hybrid methods to speedup the calculation.     

Exploring the P2 and P3 ligand binding features for hepatitis C virus NS3 protease using some 3D QSAR techniques

Several three-dimensional quantitative structure-activity relationship (3D-QSAR) models have been constructed using the comparative molecular field analysis (CoMFA), comparative molecular similarity indices analysis (CoMSIA), and catalyst pharmacophore feature building programs for a series of 26 truncated ketoacid inhibitors designed particularly for exploring the P2 and P3 binding pockets of HCV NS3 protease. The structures of these inhibitors were built from a structure template extracted from the crystal structure of HCV NS3 protease. The structures were aligned through docking each inhibitor into the NS3 active site using program GOLD. The best CoMSIA model was identified from the stepwise analysis results and the corresponding pharmacophore features derived were used for constructing a pharmacophore hypothesis by the catalyst program. Pharmacophore features obtained by CoMFA and CoMSIA are found to be in accord with each other and are both mapped onto the molecular 5K surface of NS3 active site. These pharmacophore features were also compared with those obtained by the catalyst program and mapped onto the same NS3 molecular surface. The pharmacophore building process was also performed for 20 boronic acid based NS3 inhibitors characterized by a long hydrophobic side chain attached at position P2. This latter pharmacophore hypothesis built by the catalyst program was also mapped onto the molecular surface of NS3 active site to define a second hydrophobic feature at position P2. The possibility of using the pharmacophore features mapped P2 and P3 binding pocket to design more potent depeptidized NS3 inhibitors was discussed.     

Fast analysis of source code in C and C++

Static analysis is a popular tool for detecting the vulnerabilities that cannot be found by means of ordinary testing. The main problem in the development of static analyzers is their low speed. Methods for accelerating such analyzers are described, which include incremental analysis, lazy analysis, and header file caching. These methods make it possible to considerably accelerate the detection of defects and to integrate the static analysis tools in the development environment. As a result, defects in a file edited in the Visual Studio development environment can be detected in 0.5 s or faster, which means that they can be practically detected after each keystroke. Therefore, critical vulnerabilities can be detected and corrected at the stage of coding.     

Modeling analysis of ant system with multiple tasks and its application to spatially adjacent cell state estimate

The problem of multi-cell tracking plays an important role in studying dynamic cell cycle behaviors. In this paper, a novel ant system with multiple tasks is modeled for jointly estimating the number of cells and individual states in cell image sequences. In our ant system, in addition to pure cooperative mechanism used in traditional ant colony optimization algorithm, we model and investigate another two types of ant working modes, namely, dual competitive mode and interactive mode with cooperation and competition to evaluate the tracking performance on spatially adjacent cells. For adjacent ant colonies, dual competitive mode encourages ant colonies with different tasks to work independently, whereas the interactive mode introduces a trade-off between cooperation and competition. In simulations of real cell image sequences, the multi-tasking ant system integrated with interactive mode yielded better tracking results than systems adopting pure cooperation or dual competition alone, both of which cause tracking failures by under-estimating and over-estimating the number of cells, respectively. Furthermore, the results suggest that our algorithm can automatically and accurately track numerous cells in various scenarios, and is competitive with state-of-the-art multi-cell tracking methods.     

冲突减弱型LEO多址协议性能仿真分析

针对PRMA-HS协议中系统阻塞概率较大的问题,引入微时隙概念,提出了具有冲突减弱功能的MPRMA-HS协议,通过对可用时隙的再划分,增加系统竞争时隙数量,以降低系统拥塞。建立了协议模型,利用平衡点分析法对协议的接入阻塞概率、系统丢包率和吞吐率进行了理论推导。通过计算机仿真给出了协议的性能曲线,并与PRMA-HS进行了对比。结果表明,MPRMA-HS协议所能支持的最大用户终端数比PRMA-HS协议提高11.9%,而接入阻塞概率和丢包率均小于PRMA-HS协议。