Discovery of LRRK2 inhibitors by using an ensemble of virtual screening methods

In this paper, we present the results of a ligand- and structure-based virtual screen targeting LRRK2, a kinase that has been implicated in Parkinson’s disease. For the ligand-based virtual screen, the structures of 12 competitor compounds were used as queries for a variety of 2D and 3D searches. The structure-based virtual screen relied on homology models of LRRK2, as no X-ray structure is currently available in the public domain. From the virtual screening, 662 compounds were purchased, of which 35 showed IC₅₀ values below 10 μM in wild-type and/or mutant LRRK2 (a hit rate of 5.3%). Of these 35 hits, four were deemed to have potential for medicinal chemistry follow-up.     

Toward the virtual screening of Cdc25A phosphatase inhibitors with the homology modeled protein structure

Cdc25 phosphatases have been considered as attractive drug targets for anticancer therapy due to the correlation of their overexpression with a wide variety of cancers. As a method for the discovery of novel inhibitors of Cdc25 phosphatases, we have evaluated the computer-aided drug design protocol involving the homology modeling of Cdc25A and virtual screening with the two docking tools: FlexX and the modified AutoDock program implementing the effects of ligand solvation in the scoring function. The homology modeling with the X-ray crystal structure of Cdc25B as a template provides a high-quality structure of Cdc25A that enables the structure-based inhibitor design. Of the two docking programs under consideration, AutoDock is found to be more accurate than FlexX in terms of scoring putative ligands. A detailed binding mode analysis of the known inhibitors shows that they can be stabilized in the active site of Cdc25A through the simultaneous establishment of the multiple hydrogen bonds and the hydrophobic interactions. The present study demonstrates the usefulness of the modified AutoDock program as a docking tool for virtual screening of new Cdc25 phosphatase inhibitors as well as for binding mode analysis to elucidate the activities of known inhibitors. Figure Structures and available IC50 values (in μM) of the twenty Cdc25 phosphatase inhibitors seeded in docking library     

A novel class of antagonists for the FFAs receptor GPR40

The free fatty acid receptor, GPR40, is implicated in the pathophysiology of type 2 diabetes, and is a new potential drug target for the treatment of type 2 diabetes. Its antagonist is thought to be not only a useful chemical probe for further exploring the function of GPR40 but also a lead structure for drug development. With virtual screening based on a homology model followed by a cell-based calcium mobilization assay, we found that sulfonamides are a new class of small organic antagonists for GPR40. One of the compounds, DC260126, dose-dependently inhibited GPR40-mediated Ca²⁺ elevations stimulated by linoleic acid, oleic acid, palmitoleic acid and lauric acid (IC₅₀: 6.28 ± 1.14, 5.96 ± 1.12, 7.07 ± 1.42, 4.58 ± 1.14 μM, respectively), reduced GTP-loading and ERK1/2 phosphorylation stimulated by linoleic acid in GPR40-CHO cells, suppressed palmitic acid potentiated glucose-stimulated insulin secretion, and negatively regulated GPR40 mRNA expression induced by oleic acid in Min6 cells.     

BDCGrid:基于Globus的生物信息高性能计算网格系统

随着分子生物信息数据量高速增长,生物信息学面临着大规模、高通量、密集型计算的巨大挑战。为有效利用计算机资源,缩短高通量生物信息计算程序执行时间,我们基于Globus Toolkit网格中间件,实现了一个支持高通量生物数据计算的网格系统(Biological Data Computing Grid,简称BDCGrid)。BDCGrid计算网格系统模型可以有效整合中小型生物信息学实验室计算机资源,大大缩短高通量生物信息计算程序执行时间,为相关研究人员利用现有计算机资源处理大规模、高通量生物信息计算任务提供一种新的途径。     

Modeling of mammalian olfactory receptors and docking of odorants

Olfactory receptors (ORs) belong to the superfamily of G protein-coupled receptors (GPCRs), the second largest class of genes after those related to immunity, and account for about 3 % of mammalian genomes. ORs are present in all multicellular organisms and represent more than half the GPCRs in mammalian species (e.g., the mouse OR repertoire contains >1,000 functional genes). ORs are mainly expressed in the olfactory epithelium where they detect odorant molecules, but they are also expressed in a number of other cells, such as sperm cells, although their functions in these cells remain mostly unknown. It has recently been reported that ORs are present in tumoral tissues where they are expressed at different levels than in healthy tissues. A specific OR is over-expressed in prostate cancer cells, and activation of this OR has been shown to inhibit the proliferation of these cells. Odorant stimulation of some of these receptors results in inhibition of cell proliferation. Even though their biological role has not yet been elucidated, these receptors might constitute new targets for diagnosis and therapeutics. It is important to understand the activation mechanism of these receptors at the molecular level, in particular to be able to predict which ligands are likely to activate a particular receptor (‘deorphanization’) or to design antagonists for a given receptor. In this review, we describe the in silico methodologies used to model the three-dimensional (3D) structure of ORs (in the more general framework of GPCR modeling) and to dock ligands into these 3D structures.     

木质素生物合成酶CCR基因的生物信息学分析

肉桂酰辅酶A还原酶(Cinnamoyl-CoA reductase,CCR)是催化木质素特异途径的第一个关键酶,是调节碳素流向木质素潜在的控制关节点,对木质素单体的生物合成起着重要作用。通过NCBI数据库收集来自裸子植物、单子叶植物及双子叶植物的35条CCR基因的完整信息,对35条CCR基因的cDNA及其编码的氨基酸序列的进化规律、理化性质、结构域、导肽、信号肽、跨膜结构域、亲/疏水性以及蛋白质结构等性状进行了生物信息学分析与预测,构建了CCR基因的系统发育树。分析结果表明,单子叶植物CCR基因中GC的含量明显高于双子叶植物;CCR基因编码的氨基酸序列存在9个保守区域;所编码氨基酸的理化性质基本一致,但单子叶、双子叶及裸子植物的CCR基因编码主要氨基酸的种类和含量存在着差异;CCR蛋白的N-端存在一个脱氢酶/差向异构酶/辅酶Ⅰ结合蛋白的结构域,无导肽、信号肽及跨膜结构域,属亲水性蛋白;进化树绘制以及同源建模结果表明,CCR基因的进化和植物的进化基本一致,CCR蛋白三级结构模型的空间结构稳定,建模结果可靠。分析结果对于深入研究CCR蛋白在木质素合成中的作用具有一定的理论指导意义。     

牙齿发育相关基因Osr2的生物信息学分析

目的：为生物学实验研究Osr2与牙齿发育的关系提供思路和参考。方法：本文运用生物信息学的同源比对、进化分析等方法,对Osr2及其编码蛋白的生物信息学特征进行分析。结果：结果显示Osr2蛋白质无信号肽,是非跨膜的疏水性蛋白,具有C2H2型、CHY型锌指结构域,是一类进化保守,高度同源的转录因子。结论：这一结果可为Osr2深入的结构与功能分析及利用提供进一步的信息与参考。     

牙齿发育相关基因Osr2 的生物信息学分析

目的:为生物学实验研究Osr2与牙齿发育的关系提供思路和参考.方法:本文运用生物信息学的同源比对、进化分析等方法,对Osr2及其编码蛋白的生物信息学特征进行分析.结果:结果显示Osr2蛋白质无信号肽,是非跨膜的疏水性蛋白,具有C2H2型、CHY型锌指结构域,是一类进化保守,高度同源的转录因子.结论:这一结果可为Osr2深入的结构与功能分析及利用提供进一步的信息与参考.     

Virtual screening identification of novel severe acute respiratory syndrome 3C-like protease inhibitors and in vitro confirmation

The 3C-like protease (3CL^pro) of severe acute respiratory syndrome associated coronavirus (SARS-CoV) is vital for SARS-CoV replication and is a promising drug target. Structure based virtual screening of 308 307 chemical compounds was performed using the computation tool Autodock 3.0.5 on a WISDOM Production Environment. The top 1468 ranked compounds with free binding energy ranging from −14.0 to −17.09 kcal mol⁻¹ were selected to check the hydrogen bond interaction with amino acid residues in the active site of 3CL^pro. Fifty-three compounds from 35 main groups were tested in an in vitro assay for inhibition of 3CL^pro expressed by Escherichia coli. Seven of the 53 compounds were selected; their IC₅₀ ranged from 38.57 ± 2.41 to 101.38 ± 3.27 μM. Two strong 3CL^pro inhibitors were further identified as competitive inhibitors of 3CL^pro with K_i values of 9.11 ± 1.6 and 9.93 ± 0.44 μM. Hydrophobic and hydrogen bond interactions of compound with amino acid residues in the active site of 3CL^pro were also identified.     

Discovery of a novel pyrazole series of group X secreted phospholipase A2 inhibitor (sPLA2X) via fragment based virtual screening

The discovery of potent novel pyrazole containing group X secreted phospholipase A2 inhibitors via structure based virtual screening is reported. Docking was applied on a large set of in-house fragment collection and pharmacophore feature matching was used to filter docking poses. The selected virtual screening hits was run in NMR screening, a potent pyrazole containing fragment hit was identified and confirmed by its complex X-ray structure and the following biochemical assay result. Expansion on the fragment hit has led to further improvement of potency while maintaining high ligand efficiency, thus supporting the further development of this chemical series.     

Structure-based identification of novel PPAR gamma ligands

Peroxisome proliferator-activated receptor γ (PPARγ) is a nuclear receptor with an important role in the glucose metabolism and a target for type 2 diabetes mellitus therapy. The recent findings relating the use of the receptor full agonist rosiglitazone and the incidence of myocardial infarction raised concerns regarding whether receptor activation can actually be useful for diabetes management. The discovery of MRL-24 and GQ-16, ligands that can partially activate PPARγ and prevent weight gain and fluid retention, showed that a submaximal receptor activation can be a goal in the development of new ligands for PPARγ. Additionally, two previously described receptor antagonists, SR-202 and BADGE, were also shown to improve insulin sensitivity and decrease TNF-α level, revealing that receptor antagonism may also be an approach to pursue. Here, we used a structure-based approach to screen the subset ‘Drugs-Now’ of ZINC database. Fifteen ligands were selected after visual inspection and tested for their ability to bind to PPARγ. A benzoimidazol acetate, a bromobenzyl-thio-tetrazol benzoate and a [[2-[(1,3-dioxoinden-2-ylidene)methyl]phenoxy]methyl]benzoate were identified as PPARγ ligands, with IC₅₀ values smaller than 10 μM. Molecular dynamic simulations showed that the residues H323, H449, Y327, Y473, K367 and S289 are key structural elements for the molecular recognition of these ligands and the polar arm of PPARγ binding pocket.     

Identification of novel inhibitors of methionyl-tRNA synthetase (MetRS) by virtual screening

Multiple inhibitors of the antibacterial target, Staphylococcus aureus MetRS, were identified by virtual screening. The process consisted of building a Catalyst^® pharmacophore from a ligand-S. aureus MetRS structure and using this pharmacophore to screen a commercial database. The top hits from this search were then docked into the S. aureus MetRS structure and this information was used to select compounds for testing. This resulted in a high hit rate of compounds that are in distinct structural classes from the known MetRS ligands.     

Development of selective and reversible pyrazoline based MAO-B inhibitors: virtual screening, synthesis and biological evaluation

In an effort to develop selective MAO (monoamine oxidase) B inhibitors, structure based virtual screening was initiated on an in-house library. Top 10 HITS were synthesized and evaluated for MAO (A and B) inhibitory activity, both against human and rat enzymes. All the compounds were found selective, reversible and active in nM range (100 times more potent than selegeline) towards MAO-B. Outstanding co-relation between predicted and experimental K_i values were observed.     

Structure-based virtual screening and biological evaluation of potent and selective ADAM12 inhibitors

We describe a series of potent and selective inhibitors of ADAM12 that were discovered using computational screening of a focused virtual library. The initial structure-based virtual screening selected 64 compounds from a 3D database of 67,062 molecules. Being evaluated by a cell-based ADAM12 activity assay, compounds 5, 11, 14, 16 were further identified as the potent and selective inhibitors of ADAM12 with low nanomolar IC₅₀ values. The mechanism underlying the potency and selectivity of a representative compound, 5, was investigated through molecular docking studies.     

Improved Isolation of Anti-rhTNF-α scFvs from Phage Display Library by Bioinformatics

Phage display technology has been widely used to isolate antibodies with specific properties. The objective of this study was to isolate anti-rhTNF-α scFvs from phage display library. However, the inserted genes of eluted phages were either incorrect or truncated. In order to address this issue, bioinformatics was applied to facilitate the screening of the eluted phages. The alignment of the sequencing results was performed with the software ClustalW. The gene of scFv (F6) was assembled by ligating together the identical VH and VL fragments and then analyzed by using program BLASTX. F6 was identified to share 80% sequence identity with a human anti-TNF-α scFv. Subsequently, the conformation of F6 binding to hTNF-α predicted by docking assay showed that F6 could bind to hTNF-α via the six CDRs. Finally, ELISA assay and Western blot analysis indicated that F6 might bind to rhTNF-α specifically. Biological assay demonstrated that F6 might neutralize rhTNF-α-induced cytotoxicity in L929 cells. In conclusion, F6 could be a candidate for further investigation, based on the experimental data and the prediction by bioinformatics. Wei Chen and Juan Zhang are contributed equally to this work.     

The use of virtual screening and differential scanning fluorimetry for the rapid identification of fragments active against MEK1

We report the analysis of an in-house fragment screening campaign for the oncology target MEK1. The application of virtual screening (VS) as a primary fragment screening approach, followed by biophysical validation using differential screening fluorimetry (DSF), with resultant binding mode determination by X-ray crystallography (X-ray), is presented as the most time and cost-effective combination of in silico and in vitro methods to identify fragments. We demonstrate the effectiveness of the VS–DSF workflow for the early identification of fragments to both ‘jump-start’ the drug discovery project and to complement biochemical screening data.