GPCR structure-based virtual screening approach for CB2 antagonist search

The potential for therapeutic specificity in regulating diseases has made cannabinoid (CB) receptors one of the most important G-protein-coupled receptor (GPCR) targets in search for new drugs. Considering the lack of related 3D experimental structures, we have established a structure-based virtual screening protocol to search for CB2 bioactive antagonists based on the 3D CB2 homology structure model. However, the existing homology-predicted 3D models often deviate from the native structure and therefore may incorrectly bias the in silico design. To overcome this problem, we have developed a 3D testing database query algorithm to examine the constructed 3D CB2 receptor structure model as well as the predicted binding pocket. In the present study, an antagonist-bound CB2 receptor complex model was initially generated using flexible docking simulation and then further optimized by molecular dynamic and mechanical (MD/MM) calculations. The refined 3D structural model of the CB2-ligand complex was then inspected by exploring the interactions between the receptor and ligands in order to predict the potential CB2 binding pocket for its antagonist. The ligand-receptor complex model and the predicted antagonist binding pockets were further processed and validated by FlexX-Pharm docking against a testing compound database that contains known antagonists. Furthermore, a consensus scoring (CScore) function algorithm was established to rank the binding interaction modes of a ligand on the CB2 receptor. Our results indicated that the known antagonists seeded in the testing database can be distinguished from a significant amount of randomly chosen molecules. Our studies demonstrated that the established GPCR structure-based virtual screening approach provided a new strategy with a high potential for in silico identifying novel CB2 antagonist leads based on the homology-generated 3D CB2 structure model.     

StructRank: a new approach for ligand-based virtual screening

Screening large libraries of chemical compounds against a biological target, typically a receptor or an enzyme, is a crucial step in the process of drug discovery. Virtual screening (VS) can be seen as a ranking problem which prefers as many actives as possible at the top of the ranking. As a standard, current Quantitative Structure-Activity Relationship (QSAR) models apply regression methods to predict the level of activity for each molecule and then sort them to establish the ranking. In this paper, we propose a top-k ranking algorithm (StructRank) based on Support Vector Machines to solve the early recognition problem directly. Empirically, we show that our ranking approach outperforms not only regression methods but another ranking approach recently proposed for QSAR ranking, RankSVM, in terms of actives found.     

Design of new plasmepsin inhibitors: a virtual high throughput screening approach on the EGEE grid

Though different species of the genus Plasmodium may be responsible for malaria, the variant caused by P. falciparum is often very dangerous and even fatal if untreated. Hemoglobin degradation is one of the key metabolic processes for the survival of the Plasmodium parasite in its host. Plasmepsins, a family of aspartic proteases encoded by the Plasmodium genome, play a prominent role in host hemoglobin cleavage. In this paper we demonstrate the use of virtual screening, in particular molecular docking, employed at a very large scale to identify novel inhibitors for plasmepsins II and IV. A large grid infrastructure, the EGEE grid, was used to address the problem of large computation resources required for docking hundreds of thousands of chemical compounds on different plasmepsin targets of P. falciparum. A large compound library of about 1 million chemical compounds was docked on 5 different targets of plasmepsins using two different docking software, namely FlexX and AutoDock. Several strategies were employed to analyze the results of this virtual screening approach including docking scores, ideal binding modes, and interactions to key residues of the protein. Three different classes of structures with thiourea, diphenylurea, and guanidino scaffolds were identified to be promising hits. While the identification of diphenylurea compounds is in accordance with the literature and thus provides a sort of "positive control", the identification of novel compounds with a guanidino scaffold proves that high throughput docking can be effectively used to identify novel potential inhibitors of P. falciparum plasmepsins. Thus, with the work presented here, we do not only demonstrate the relevance of computational grids in drug discovery but also identify several promising small molecules which have the potential to serve as candidate inhibitors for P. falciparum plasmepsins. With the use of the EGEE grid infrastructure for the virtual screening campaign against the malaria causing parasite P. falciparum we have demonstrated that resource sharing on an eScience infrastructure such as EGEE provides a new model for doing collaborative research to fight diseases of the poor.     

A novel search engine for virtual screening of very large databases

Virtual screening of large chemical databases using the structure of the receptor can be computationally very demanding. We present a novel strategy that combines exhaustive similarity searches directly in SMILES format with the docking of flexible ligands, whose 3D structure is generated on the fly from the SMILES representation. Our strategy makes use of the recently developed LINGO tools to extract implicit chemical information from SMILES strings and integrates LINGO similarities into a pseudo-evolutionary algorithm. The algorithm represents a combination of a fast target-independent similarity method with a slower but information richer target-focused method. A virtual search of FactorXa ligands provided 62% of the potential hits after docking only 6.5% of a database of nearly 1 million molecules. The set of solutions showed good diversity, indicating that the method shows good scaffold hopping capabilities.     

Similarity search profiles as a diagnostic tool for the analysis of virtual screening calculations

An analysis method termed similarity search profiling has been developed to evaluate fingerprint-based virtual screening calculations. The analysis is based on systematic similarity search calculations using multiple template compounds over the entire value range of a similarity coefficient. In graphical representations, numbers of correctly identified hits and other detected database compounds are separately monitored. The resulting profiles make it possible to determine whether a virtual screening trial can in principle succeed for a given compound class, search tool, similarity metric, and selection criterion. As a test case, we have analyzed virtual screening calculations using a recently designed fingerprint on 23 different biological activity classes in a compound source database containing approximately 1.3 million molecules. Based on our predefined selection criteria, we found that virtual screening analysis was successful for 19 of 23 compound classes. Profile analysis also makes it possible to determine compound class-specific similarity threshold values for similarity searching.     

A pseudo-ligand approach to virtual screening

A virtual screening method is presented that is grounded on a receptor-derived pharmacophore model termed "virtual ligand" or "pseudo-ligand". The model represents an idealized constellation of potential ligand sites that interact with residues of the binding pocket. For rapid virtual screening of compound libraries the potential pharmacophore points of the virtual ligand are encoded as an alignment-free correlation vector, avoiding spatial alignment of pharmacophore features between the pharmacophore query (i.e., the virtual ligand) and the candidate molecule. The method was successfully applied to retrieving factor Xa inhibitors from a Ugi three-component combinatorial library, and yielded high enrichment of actives in a retrospective search for cyclooxygenase-2 (COX-2) inhibitors. The approach provides a concept for "de-orphanizing" potential drug targets and identifying ligands for hitherto unexplored or allosteric binding pockets.     

Library fingerprints: a novel approach to the screening of virtual libraries

We propose a novel method to prioritize libraries for combinatorial synthesis and high-throughput screening that assesses the viability of a particular library on the basis of the aggregate physical-chemical properties of the compounds using a na?ve Bayesian classifier. This approach prioritizes collections of related compounds according to the aggregate values of their physical-chemical parameters in contrast to single-compound screening. The method is also shown to be useful in screening existing noncombinatorial libraries when the compounds in these libraries have been previously clustered according to their molecular graphs. We show that the method used here is comparable or superior to the single-compound virtual screening of combinatorial libraries and noncombinatorial libraries and is superior to the pairwise Tanimoto similarity searching of a collection of combinatorial libraries.     

Hydra: a self regenerating high performance computing grid for drug discovery

Computer aided drug design is progressing and playing an increasingly important role in drug discovery. Computational methods are being used to evaluate larger and larger numbers of real and virtual compounds. New methods based on molecular simulations that take protein and ligand flexibility into account also contribute to an ever increasing need for compute time. Computational grids are therefore becoming a critically important tool for modern drug discovery, but can be expensive to deploy and maintain. Here, we describe the low cost implementation of a 165 node, computational grid at Anadys Pharmaceuticals. The grid makes use of the excess computing capacity of desktop computers deployed throughout the company and of outdated desktop computers which populate a central computing grid. The performance of the grid grows automatically with the size of the company and with advances in computer technology. To ensure the uniformity of the nodes in the grid, all computers are running the Linux operating system. The desktop computers run Linux inside MS Windows using coLinux as virtualization software. HYDRA has been used to optimize computational models, for virtual screening and for lead optimization.     

An integrated approach to knowledge-driven structure-based virtual screening

In many practical applications of structure-based virtual screening (VS) ligands are already known. This circumstance requires that the obtained hits need to satisfy initial made expectations i.e., they have to fulfill a predefined binding pattern and/or lie within a predefined physico-chemical property range. Based on the RApid Index-based Screening Engine (RAISE) approach, we introduce cRAISE—a user-controllable structure-based VS method. It efficiently realizes pharmacophore-guided protein-ligand docking to assess the library content but thereby concentrates only on molecules that have a chance to fulfill the given binding pattern. In order to focus only on hits satisfying given molecular properties, library profiles can be utilized to simultaneously filter compounds. cRAISE was evaluated on a range of strict to rather relaxed hypotheses with respect to its capability to guide binding-mode predictions and VS runs. The results reveal insights into a guided VS process. If a pharmacophore model is chosen appropriately, a binding mode below 2 Å is successfully reproduced for 85 % of well-prepared structures, enrichment is increased up to median AUC of 73 %, and the selectivity of the screening process is significantly enhanced leading up to seven times accelerated runtimes. In general, cRAISE supports a versatile structure-based VS approach allowing to assess hypotheses about putative ligands on a large scale.     

A knowledge-based weighting approach to ligand-based virtual screening

On the basis of the recently introduced reduced graph concept of ErG (extending reduced graphs), a straightforward weighting approach to include additional (e.g., structural or SAR) knowledge into similarity searching procedures for virtual screening (wErG) is proposed. This simple procedure is exemplified with three data sets, for which interaction patterns available from X-ray structures of native or peptidomimetic ligands with their target protein are used to significantly improve retrieval rates of known actives from the MDL Drug Report database. The results are compared to those of other virtual screening techniques such as Daylight fingerprints, FTrees, UNITY, and various FlexX docking protocols. Here, it is shown that wErG exhibits a very good and stable performance independent of the target structure. On the basis of this (and the fact that ErG retrieves structurally more dissimilar compounds due to its potential to perform scaffold-hopping), the combination of wErG and FlexX is successfully explored. Overall, wErG is not only an easily applicable weighting procedure that efficiently identifies actives in large data sets but it is also straightforward to understand for both medicinal and computational chemists and can, therefore, be driven by several aspects of project-related knowledge (e.g., X-ray, NMR, SAR, and site-directed mutagenesis) in a very early stage of the hit identification process.     

NIPALSTREE: a new hierarchical clustering approach for large compound libraries and its application to virtual screening

A hierarchical clustering algorithm--NIPALSTREE--was developed that is able to analyze large data sets in high-dimensional space. The result can be displayed as a dendrogram. At each tree level the algorithm projects a data set via principle component analysis onto one dimension. The data set is sorted according to this one dimension and split at the median position. To avoid distortion of clusters at the median position, the algorithm identifies a potentially more suited split point left or right of the median. The procedure is recursively applied on the resulting subsets until the maximal distance between cluster members exceeds a user-defined threshold. The approach was validated in a retrospective screening study for angiotensin converting enzyme (ACE) inhibitors. The resulting clusters were assessed for their purity and enrichment in actives belonging to this ligand class. Enrichment was observed in individual branches of the dendrogram. In further retrospective virtual screening studies employing the MDL Drug Data Report (MDDR), COBRA, and the SPECS catalog, NIPALSTREE was compared with the hierarchical k-means clustering approach. Results show that both algorithms can be used in the context of virtual screening. Intersecting the result lists obtained with both algorithms improved enrichment factors while losing only few chemotypes.     

Similarity search profiling reveals effects of fingerprint scaling in virtual screening

Fingerprint scaling is a method to increase the performance of similarity search calculations. It is based on the detection of bit patterns in keyed fingerprints that are signatures of specific compound classes. Application of scaling factors to consensus bits that are mostly set on emphasizes signature bit patterns during similarity searching and has been shown to improve search results for different fingerprints. Similarity search profiling has recently been introduced as a method to analyze similarity search calculations. Profiles separately monitor correctly identified hits and other detected database compounds as a function of similarity threshold values and make it possible to estimate whether virtual screening calculations can be successful or to evaluate why they fail. This similarity search profile technique has been applied here to study fingerprint scaling in detail and better understand effects that are responsible for its performance. In particular, we have focused on the qualitative and quantitative analysis of similarity search profiles under scaling conditions. Therefore, we have carried out systematic similarity search calculations for 23 biological activity classes under scaling conditions over a wide range of scaling factors in a compound database containing approximately 1.3 million molecules and monitored these calculations in similarity search profiles. Analysis of these profiles confirmed increases in hit rates as a consequence of scaling and revealed that scaling influences similarity search calculations in different ways. Based on scaled similarity search profiles, compound sets could be divided into different categories. In a number of cases, increases in search performance under scaling conditions were due to a more significant relative increase in correctly identified hits than detected false-positives. This was also consistent with the finding that preferred similarity threshold values increased due to fingerprint scaling, which was well illustrated by similarity search profiling.     

Surveying FDA-approved drugs as new potential inhibitors of N-cadherin protein: a virtual screening approach

Since N-cadherin protein plays a remarkable role in cancer metastasis and tumor growth and progression, finding new effective inhibitors of this protein can be of high importance in cancer treatment. Nevertheless, few molecules have been introduced to inhibit N-cadherin protein to date. In this work, in order to find and present potent inhibitors, 3358 FDA-approved small molecules were docked against N-cadherin protein. All complexes with binding energy ??9 to ??8 kcal/mol were selected for protein-ligand interaction analysis. In the following, Tanimoto coefficient (T_c) was calculated for those molecules that established appropriate interactions with N-cadherin in order to compute the similarity score between them. Afterwards, molecular dynamics simulation and free energy calculations were done to estimate the stability and ability of the chosen ligands in complex with the target protein. Finally, seven small molecules among 3358 FDA-approved were suggested as potential inhibitors of N-cadherin protein.

     

Ligand-guided optimization of CXCR4 homology models for virtual screening using a multiple chemotype approach

CXCR4 is a G-protein coupled receptor for CXCL12 that plays an important role in human immunodeficiency virus infection, cancer growth and metastasization, immune cell trafficking and WHIM syndrome. In the absence of an X-ray crystal structure, theoretical modeling of the CXCR4 receptor remains an important tool for structure–function analysis and to guide the discovery of new antagonists with potential clinical use. In this study, the combination of experimental data and molecular modeling approaches allowed the development of optimized ligand-receptor models useful for elucidation of the molecular determinants of small molecule binding and functional antagonism. The ligand-guided homology modeling approach used in this study explicitly re-shaped the CXCR4 binding pocket in order to improve discrimination between known CXCR4 antagonists and random decoys. Refinement based on multiple test-sets with small compounds from single chemotypes provided the best early enrichment performance. These results provide an important tool for structure-based drug design and virtual ligand screening of new CXCR4 antagonists.     

Multiple ligand docking by Glide: implications for virtual second-site screening

Performance of Glide was evaluated in a sequential multiple ligand docking paradigm predicting the binding modes of 129 protein-ligand complexes crystallized with clusters of 2-6 cooperative ligands. Three sampling protocols (single precision-SP, extra precision-XP, and SP without scaling ligand atom radii-SP hard) combined with three different scoring functions (GlideScore, Emodel and Glide Energy) were tested. The effects of ligand number, docking order and druglikeness of ligands and closeness of the binding site were investigated. On average 36?% of all structures were reproduced with RMSDs lower than 2??. Correctly docked structures reached 50?% when docking druglike ligands into closed binding sites by the SP hard protocol. Cooperative binding to metabolic and transport proteins can dramatically alter pharmacokinetic parameters of drugs. Analyzing the cytochrome P450 subset the SP hard protocol with Emodel ranking reproduced two-thirds of the structures well. Multiple ligand binding is also exploited by the fragment linking approach in lead discovery settings. The HSP90 subset from real life fragment optimization programs revealed that Glide is able to reproduce the positions of multiple bound fragments if conserved water molecules are considered. These case studies assess the utility of Glide in sequential multiple docking applications.