A multi-drug resistant HIV-1 protease is resistant to the dimerization inhibitory activity of TLF-PafF

Human immunodeficiency virus type-1 (HIV-1) protease, a homodimeric aspartyl protease, is a critical drug target in designing anti-retroviral drugs to treat HIV/AIDS. Multidrug-resistant (MDR) clinical isolate-769 HIV-1 protease (PDB ID: 3PJ6) has been shown to exhibit expanded active site cavity with wide-open conformation of flaps (Gly48–Gly52) due to the accumulation of multiple mutations. In this study, an HIV-1 protease dimerization inhibitor (PDI)–TLF-PafF, was evaluated against MDR769 HIV-1 protease using X-ray crystallography. It was hypothesized that co-crystallization of MDR769 HIV-1 protease in complex with TLF-PafF would yield either a monomeric or a disrupted dimeric structure. However, crystal structure of MDR769 I10V HIV-1 protease co-crystallized with TLF-PafF revealed an undisrupted dimeric protease structure (PDB ID: 4NKK) that is comparable to the crystal structure of its corresponding apo-protease (PDB ID: 3PJ6). In order to understand the binding profile of TLF-PafF as a PDI, docking analysis was performed using monomeric protease (prepared from the dimeric crystal structure, PDB ID: 4NKK) as docking receptor. Docking analysis revealed that TLF-PafF binds at the N and C termini (dimerization domain) in a clamp shape for the monomeric wild type receptor but not the MDR769 monomeric receptor. TLF-PafF preferentially showed higher binding affinity to the expanded active site cavity of MDR769 HIV-1 protease than to the termini. Irrespective of binding location, the binding affinity of TLF-PafF against wild type receptor (−6.7 kcal/mol) was found to be higher compared to its corresponding binding affinity against MDR receptor (−4.6 kcal/mol) suggesting that the MDR769 HIV-1 protease could be resistant to the PDI-activity of TLF-PafF, thus supporting the dimeric crystal structure (PDB ID: 4NKK).     

P1 and P1′ para-fluoro phenyl groups show enhanced binding and favorable predicted pharmacological properties: Structure-based virtual screening of extended lopinavir analogs against multi-drug resistant HIV-1 protease

Crystal structure of multidrug-resistant (MDR) clinical isolate 769, human immunodeficiency virus type-1 (HIV-1) protease in complex with lopinavir (LPV) (PDB ID: 1RV7) showed altered binding orientation of LPV in the expanded active site cavity, causing loss of contacts and decrease in potency. In the current study, with a goal to restore the lost contacts, three libraries of LPV analogs containing extended P1 and/or P1′ phenyl groups were designed and docked into the expanded active site cavity of the MDR769 HIV-1 protease. The compounds were then ranked based on three criteria: binding affinity, overall binding profile and predicted pharmacological properties. Among the twelve proposed extensions in different combinations, compound 14 (consists of para-fluoro phenyl group as both P1 and P1′ moieties) was identified as a lead with improved binding profile, binding affinity against the MDR protease and favorable predicted pharmacological properties comparable to those of LPV. The binding affinity of 14 against wild type (NL4-3) HIV-1 protease was comparable to that of LPV and was better than LPV against an ensemble of MDR HIV-1 protease variants. Thus, 14 shows enhanced binding affinity by restoring lost contacts in the expanded active site cavity of MDR769 HIV-1 protease variants suggesting that it may have higher potency compared to that of LPV and hence should be further synthesized and evaluated against NL4-3 as well as MDR variants of HIV-1.     

Structure based virtual screening-driven identification of monastrol as a potent urease inhibitor

Virtual screening uses computer based methods to discover new ligands on the basis of biological structures. Among all virtual screening methods structure based docking has received considerable attention. In an attempt to identify new ligands as urease inhibitors, structure-based virtual screening (SBVS) of an in-house database of 10,000 organic compounds was carried out. The X-ray crystallographic structure of Bacillus pasteurii (BP) in complex with acetohydroxamic acid (PDB Code 4UBP) was used as a protein structure. As a starting point, ~10,000 compounds of our in-house database were analyzed to check redundancy and the compounds found repeated were removed from the database. Finally 6993 compounds were docked into the active site of BP urease using GOLD and MOE-Dock software. A remarkable feature of this study was the identification of monastrol, a well-known KSP inhibitor already in clinical trials, as a novel urease inhibitor. The hits identified were further evaluated by molecular docking and on examination of the affinity predictions, twenty-seven analogs of monastrol were synthesized by a multicomponent Biginelli reaction followed by their in vitro screening as urease inhibitors. Finally twelve compounds were identified as new urease inhibitors. The excellent in vitro activity suggested that these compounds may serve as viable lead compounds for the treatment of urease related problems.     

Virtual screening of novel reversible inhibitors for marine alkaline protease MP

Marine alkaline protease (MP,² accession no. ACY25898) is produced by a marine bacterium strain isolated from Yellow Sea sediment in China. Previous research has shown that this protease is a cold-adapted enzyme with antioxidant activity that could be used as a detergent additive. Owing to its instability in the liquid state, MP's application in liquid detergents was limited. Therefore, the discovery of reversible MP inhibitors to stabilize the protease was imperative. Here, we used the X-ray structure of MP and recompiled AutoDock 4.2 with refined Zn²⁺ characters to screen the free chemical database ZINC. After completing the docking procedure, we applied strategies including the “initial filter”, consensus scoring and pharmocophore model to accelerate the process and improve the virtual screening success rate. The “initial filter” was built based on the docking results of boronic acid derivatives validated as reversible inhibitors of MP by our previous studies. Finally, ten compounds were purchased or synthetized to test their binding affinity for MP. Three of the compounds could reversibly inhibit MP with apparent K_i values of 0.8–1.2 mmol. These active compounds and their binding modes provide useful information for understanding the molecular mechanism of reversible MP inhibition. The results may also serve as the foundation for further screening and design of reversible MP inhibitors.     

最优支持向量机用于HIV-1蛋白酶抑制剂的QSAR建模

为了建立HIV蛋白酶抑制剂QSAR的优良模型,本文采用粒子群优化法搜索支持向量机的多参数复杂模型空间,以此形成最优支持向量机。通过与传统的梯度下降法、网格搜索法等模型选择方法的比较,采用并行计算的基于PSO算法的最优支持向量机法在模型精度及稳定性、搜索效率等方面都有优良的性能,实例测试也表明所建QSAR模型,有良好的泛化能力,所建模型对研究HIV药物有重要促进作用。     

Virtual screening of eighteen million compounds against dengue virus: Combined molecular docking and molecular dynamics simulations study

Dengue virus is a major issue of tropical and sub-tropical regions. Dengue virus has been the cause behind the major alarming epidemics in the history with mass causalities from the decades. Unavailability of on-shelf drugs for the prevention of further proliferation of virus inside the human body results in immense number of deaths each year. This issue necessitates the design of novel anti-dengue drug. The protease enzyme pathway is the critical target for drug design due to its significance in the replication, survival and other cellular activities of dengue virus. Therefore, approximately eighteen million compounds from the ZINC database have been virtually screened against nonstructural protein 3 (NS3). The incremental construction algorithm of Glide docking program has been used with its features high throughput virtual screening (HTVS), standard precision (SP), extra precision (XP) and in combination of Prime module, induced fit docking (IFD) approach has also been applied. Five top-ranked compounds were then selected from the IFD results with better predicted binding energies with the catalytic triad residues (His51, Asp75, and Ser135) that may act as potential inhibitors for the underlying target protease enzyme. The top-ranked compounds ZINC95518765, ZINC44921800, ZINC71917414, ZINC39500661, ZINC36681949 have shown the predicted binding energies of −7.55, −7.36, −8.04, −8.41, −9.18 kcal/mol, respectively, forming binding interactions with three catalytically important amino acids. Top-docking poses of compounds are then used in molecular dynamics (MD) simulations. In computational studies, our proposed compounds confirm promising results against all the four serotypes of dengue virus, strengthening the opportunity of these compounds to work as potential on-shelf drugs against dengue virus. Further experimentation on the proposed compounds can result in development of strong inhibitors.     

硫代氨基甲酸酯类衍生物抗HIV-1逆转录酶抑制活性的QSAR研究

采用以MLR为基学习器的Boosting算法模型,对79种硫代氨基甲酸酯类衍生物做抗HIV-1逆转录酶抑制活性的QSAR研究。以E-Dragon软件计算的7组描述符分别为自变量,以化合物的半数效应浓度EC_(50)值为因变量构成7个原始数据集,用PSO算法筛选变量并建立MLR模型。各描述符建立的MLR模型中仅有RDF描述符模型同时通过外部预测和内部验证,故确定以其建立关于硫代氨基甲酸酯类衍生物抗HIV-1逆转录酶抑制活性的Boosting-MLR预测模型。Boosting-MLR模型与MLR模型相比,训练结果的决定系数R~2分别为0.728和0.741,预测结果R~2则分别为0.718和0.667,表明其泛化能力明显增强。对Boosting-MLR模型进一步进行稳定性验证,证明其预测稳定性较高。     

Schlumberger IPO on the cards?

The financial press has been speculating that Schlumberger’s smart card division will be sold off in an IPO in the second half of 2003. The move would be an attempt to reduce the parent company’s debt which reached US$5 billion in 2002.This is a short news story only. Visit www.compseconline.com for the latest computer security industry news     

H-NOX domains display different tunnel systems for ligand migration

Soluble guanylate cyclase (sGC) displays a high affinity for its physiological ligand (NO), but the ability of O₂ binding is not identified even if the presence of a large excess O₂ in vivo. Therefore, discrimination against O₂ by sGC is essential for NO signaling. Recently, the heme domain of sGC was termed as a member of new conversed hemoprotein family, namely H-NOX domain. Various ligand binding properties of H-NOX domains were observed and some of them bind O₂ tightly, whereas others have a poor affinity for O₂ or even no measurable affinity for O₂ at all like sGC. Several crystal structures of H-NOX domains are available now in both NO-bound form (Ns H-NOX; PDBid 2O0C) and O₂-bound form (Tt N-NOX; PDBid 1U55). These structures provide an ideal data for elucidating the molecular detail of ligand discrimination in H-NOX domains. In this work, by employing the locally enhanced sampling molecular dynamics (LESMD) simulations, we compared the ligand migration pathways between Ns H-NOX and Tt H-NOX. Interestingly, although they are similar in fold, the different spatial distributions of ligands between Ns H-NOX and Tt H-NOX are explored and proposed for ligand discrimination. The residue at position M144 in Ns H-NOX plays a key role in controlling the ligand entry and escape. However, in Tt H-NOX, the same position is a hydrogen-bonding tyrosine for stabilizing the oxygen binding and its steric effects of blocking the ligand migration is remarkable.     

TIBO类衍生物抗HIV-1活性与电子结构关系的研究

应用分子力学MM＋方法，半经验量子化学MNDO计算了19个TIBO HIV－1逆转录酶抑制剂的优势构象和电子结构，得到了其抗HIV－1活性与电子结构的定量构效关系。结果表明：（1）TIBO类衍生物的体积越大、极性越小，即疏水性越大对抑制HIV－1活性越有利；（2）化合物中存在较大的正电区域，当C2原子连接吸电性基团时对药物的活性有利。     

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.     

Universal constructor to build a Tierran machine structure

In constructing an artificial life system with a high potential for evolution, one of the elements that we should design most carefully is the machine structure, i.e., the architecture of the system controlling the operations of a digital creature. This article proposes an approach to modify the machine structure of Tierra in order to obtain higher evolvability. The structure of the Tierran digital creature that we propose is stimulated by the self-reproducing model proposed by von Neumann, which allows self-reproduction in a simple architecture. A verification of a digital creatures structure was carried out through computer simulation. As a result, the capabilities of self-reproduction and parasitism were demonstrated.This work was presented in part at the 8th International Symposium on Artificial Life and Robotics, Oita, Japan, January 24–26, 2003     

血管紧张素转化酶二肽抑制剂的构效关系

从肽链的一级结构出发,以分子电边矢量（molecular eleetro—negativity edge vector,MEEV）为参数,36种血管紧张素转化酶二肽抑制剂为样本,构建了血管紧张素转化酶二肽抑制剂的构效关系模型。通过模型分析得出二肽肽键的“二、五、七”键抑制酶活的规律,即：（1）肽键的羧基和Zn形成二配体,而肽键的N原子和羧基氧形成H键以稳定这一基团;（2）与ACE酶中Arg（Arginine,精氨酸）正电荷盐键作用的羧酸根和第二氨基酸的氨基之间形成的五键结构单元对其降压效果起关键作用;（3）含芳香族氨基酸的二肽抑制剂中的肽键的氨基和苯环部分羟基端呈反式构型,它们相隔7个键位。这一结构有利于分子间氢键的形成及保证抑制剂能稳定地和酶结合、结果表明：本模型有方法简单,能避免因为数据量的过大而引起的统计误差的优点,有望对血管紧张素肽类药物的台成及药物活性预测提供帮助.     

Industry returns to double digit growth

Smart card manufacturer Schlumberger Smart Cards and Terminals has released its annual smart card analysis for 2002, with the upbeat message that shipment rates for microprocessor cards have surged back into double-digits with a 13% rise to 725 million units (Table 1). That followed a major drop in 2001, primarily caused by the collapse in demand for SIM cards for mobile phones.This is a short news story only. Visit www.compseconline.com for the latest computer security industry news     

FCMLab: A finite cell research toolbox for MATLAB

The recently introduced Finite Cell Method combines the fictitious domain idea with the benefits of high-order finite elements. Although previous publications demonstrated the method’s excellent applicability in various contexts, the implementation of a three-dimensional Finite Cell code is challenging. To lower the entry barrier, this work introduces the object-oriented MATLAB toolbox FCMLab allowing for an easy start into this research field and for rapid prototyping of new algorithmic ideas. The paper reviews the essentials of the methods applied and explains in detail the class structure of the framework. Furthermore, the usage of the toolbox is discussed by means of different two- and three-dimensional examples demonstrating all important features of FCMLab (http://fcmlab.cie.bgu.tum.de/).     

ViewMotions Rainbow: A new method to illustrate molecular motions in proteins

The biological functions of many enzymes are often coupled with significant conformational changes. The end states of these conformational changes can often be determined by X-ray crystallography. These X-ray structures are snapshots of the two extreme conformations in which the macromolecule exists, but the dynamic movements between the states are not easily visualized in a two-dimensional illustration. Here we have developed a new method to visualize macromolecular motions called a ViewMotions Rainbow diagram. These diagrams show the initial and final states overlaid along with approximately 30 intermediate structures calculated by linear interpolation of the backbone coordinates of the initial and final states. This group of structures is then spectrally colored from the initial structure in blue to the final structure in red. ViewMotions Rainbow diagrams provide the reader with a much easier way to understand the macromolecular motions using a single two-dimensional illustration. Since producing these diagrams requires a number of different software packages, we have setup the ViewMotions Web Server (http://viewmotions.bc.edu) to automatically generate these diagrams from two Protein Data Bank files or from the Database of Macromolecular Movements (http://molmovdb.org).