Visual characterization and diversity quantification of chemical libraries: 2. Analysis and selection of size-independent, subspace-specific diversity indices.

High Throughput Screening (HTS) is a standard technique widely used to find hit compounds in drug discovery projects. The high costs associated with such experiments have highlighted the need to carefully design screening libraries in order to avoid wasting resources. Molecular diversity is an established concept that has been used to this end for many years. In this article, a new approach to quantify the molecular diversity of screening libraries is presented. The approach is based on the Delimited Reference Chemical Subspace (DRCS) methodology, a new method that can be used to delimit the densest subspace spanned by a reference library in a reduced 2D continuous space. A total of 22 diversity indices were implemented or adapted to this methodology, which is used here to remove outliers and obtain a relevant cell-based partition of the subspace. The behavior of these indices was assessed and compared in various extreme situations and with respect to a set of theoretical rules that a diversity function should satisfy when libraries of different sizes have to be compared. Some gold standard indices are found inappropriate in such a context, while none of the tested indices behave perfectly in all cases. Five DRCS-based indices accounting for different aspects of diversity were finally selected, and a simple framework is proposed to use them effectively. Various libraries have been profiled with respect to more specific subspaces, which further illustrate the interest of the method.

Visual characterization and diversity quantification of chemical libraries: 1. creation of delimited reference chemical subspaces.

High-throughput screening (HTS) is a well-established technology which can test up to several million compounds in a few weeks. Despite these appealing capabilities, available resources and high costs may limit the number of molecules screened, making diversity analysis a method of choice to design and prioritize screening libraries. With a constantly increasing number of molecules available for screening, chemical space has become a key concept for visualizing, analyzing, and comparing chemical libraries. In this first article, we present a new method to build delimited reference chemical subspaces (DRCS). A set of 16 million screening compounds from 73 chemical providers has been gathered, resulting in a database of 6.63 million standardized and unique molecules. These molecules have been used to create three DRCS using three different sets of chemical descriptors. A robust principal component analysis model for each space has been obtained, whereby molecules are projected in a reduced two-dimensional viewable space. The specificity of our approach is that each reduced space has been delimited by a representative contour encompassing a very large proportion of molecules and reflecting its overall shape. The methodology is illustrated by mapping and comparing various chemical libraries. Several tools used in these studies are made freely available, thus enabling any user to compute DRCS matching specific requirements.

Synthesis and biological evaluation of cis-locked vinylogous combretastatin-A4 analogues: derivatives with a cyclopropyl-vinyl or a cyclopropyl-amide bridge.

A series of novel combretastatin A4 analogues, in which the cis-olefinic bridge is replaced by a cyclopropyl-vinyl or a cyclopropyl-amide moiety, were synthesized and evaluated for inhibition of tubulin polymerization and antiproliferative activity. The derivative 9a with a (cis,E)-cyclopropyl-vinyl unit is the most promising compound. As expected, molecular docking of 9a has shown that only one of the cis-cyclopropyl enantiomers is a good ligand for tubulin.

Optimization and validation of a docking-scoring protocol; application to virtual screening for COX-2 inhibitors.

To exploit available structural information about the cyclooxygenase enzyme for the virtual screening of large chemical libraries, a docking-scoring protocol was tuned and validated. The screening accuracy was assessed using a series of known inhibitors and a set of diverse a priori inactive compounds that was seeded with known active ligands. The major parameters of the DOCK algorithm were investigated. A large improvement of the results was obtained on tweaking some of them. The generated complexes were rescored using six scoring functions. In this way, the striking importance of this step was demonstrated, as well as the good performances of DOCK energy and SCORE for this target. The results were further improved via a consensus approach. As a first application, a subset of a large compound library was screened using this protocol. Among the compounds that were selected for biological testing, a third of them turned out to have a significant enzyme inhibition.

Identification of New Nonsteroidal RORα Ligands; Related Structure-Activity Relationships and Docking Studies.

A high throughput screen was developed to identify novel, nonsteroidal RORα agonists. Among the validated hit compounds, the 4-(4-(benzyloxy)phenyl)-5-carbonyl-2-oxo-1,2,3,4-tetrahydropyrimidine scaffold was the most prominent. Among the numerous analogues tested, compounds 8 and 9 showed the highest activity. Key structure-activity relationships (SAR) were established, where benzyl and urea moieties were both identified as very important elements to maintain the activity. Most notably, the SAR were consistent with the binding mode of the compound 8 (S-isomer) in the RORα docking model that was developed in this program. As predicted by the model, the urea moiety is engaged in the formation of key hydrogen bonds with the backbone of Tyr380 and Asp382. The benzyl group is located in a wide hydrophobic pocket. The structural relationships reported in this letter will help in further optimization of this compound series and will provide novel synthetic probes helpful for elucidation of complex RORα physiopathology.

Mining collections of compounds with Screening Assistant 2.

BACKGROUND: High-throughput screening assays have become the starting point of many drug discovery programs for large pharmaceutical companies as well as academic organisations. Despite the increasing throughput of screening technologies, the almost infinite chemical space remains out of reach, calling for tools dedicated to the analysis and selection of the compound collections intended to be screened. RESULTS: We present Screening Assistant 2 (SA2), an open-source JAVA software dedicated to the storage and analysis of small to very large chemical libraries. SA2 stores unique molecules in a MySQL database, and encapsulates several chemoinformatics methods, among which: providers management, interactive visualisation, scaffold analysis, diverse subset creation, descriptors calculation, sub-structure / SMART search, similarity search and filtering. We illustrate the use of SA2 by analysing the composition of a database of 15 million compounds collected from 73 providers, in terms of scaffolds, frameworks, and undesired properties as defined by recently proposed HTS SMARTS filters. We also show how the software can be used to create diverse libraries based on existing ones. CONCLUSIONS: Screening Assistant 2 is a user-friendly, open-source software that can be used to manage collections of compounds and perform simple to advanced chemoinformatics analyses. Its modular design and growing documentation facilitate the addition of new functionalities, calling for contributions from the community. The software can be downloaded at http://sa2.sourceforge.net/.

Insights into chiral recognition mechanisms in supercritical fluid chromatography. II. Factors contributing to enantiomer separation on tris-(3,5-dimethylphenylcarbamate) of amylose and cellulose stationary phases.

In this second part of our work on enantioselective supercritical fluid chromatography (SFC), we investigate the factors participating in the chiral recognition process on tris-(3,5-dimethylphenylcarbamate) of amylose and cellulose chiral stationary phases (CSPs). 135 racemates with diverse structures were analysed under identical SFC conditions on both stationary phases. The possibility of identifying the differential interactions of an enantiomer pair within the chromatographic system is assessed using a modified version of the solvation parameter model and factorial discriminant analysis. It is illustrated that one relationship of intermolecular interactions is insufficient to express the enantioseparation of different groups of racemates. An innovative approach is used in unravelling the interactions taking part in the enantiorecognition process. Different intermolecular interactions participating in the enantiomeric separation are demonstrated between the two stationary phases.

Insights into chiral recognition mechanisms in supercritical fluid chromatography. I. Non-enantiospecific interactions contributing to the retention on tris-(3,5-dimethylphenylcarbamate) amylose and cellulose stationary phases.

In this series of papers, we use a systematic approach to investigate the factors responsible for enantio-recognition in supercritical fluid chromatography (SFC) on chiral stationary phases (CSPs). In this first part, the interactions contributing to the retentions of the achiral solutes are measured with a modified version of the solvation parameter model. Since stereospecific interactions were not accounted for in the classical linear solvation energy relationship using Abraham descriptors, we introduce two additional descriptors, flexibility and globularity, to rationally quantify the stereochemical properties that may significantly affect enantiomeric resolutions. Two polysaccharide stationary phases presenting identical bonded groups on different polysaccharide backbones, namely tris-(3,5-dimethylphenylcarbamate) on amylose and on cellulose, are compared using 230 achiral and structurally diverse solutes. The experimental results are evaluated based on statistics and the chemical intuition of the chromatographic systems.

Synthesis and structure-activity relationships of constrained heterocyclic analogues of combretastatin A4.

A series of combretastatin A4 (CA4) analogues with a lactam or lactone ring fused to the trimethoxyphenyl or the B-phenyl moiety were synthesized in an efficient and stereoselective manner by using a domino Heck-Suzuki-Miyaura coupling reaction. The vascular-disrupting potential of these conformationally restricted CA4 analogues was assessed by various in vitro assays: inhibition of tubulin polymerization, modification of endothelial cell morphology, and disruption of endothelial cell cords. Compounds were also evaluated for their growth inhibitory effects against murine and human tumor cells. B-ring-constrained derivatives that contain an oxindole ring (in contrast to compounds with a benzofuranone ring) as well as analogues bearing a six-membered lactone core fused to the trimethoxyphenyl ring are endowed with significant biological activity. The most potent compound of this series (oxindole 9 b) is of particular interest, as it combines chemical stability and a biological activity profile characteristic of a vascular-disrupting agent.

Reverse pharmacognosy: identifying biological properties for plants by means of their molecule constituents: application to meranzin.

Reverse pharmacognosy aims at finding biological targets for natural compounds by virtual or real screening and identifying natural resources that contain the active molecules. We report herein a study focused on the identification of biological properties of meranzin, a major component isolated from Limnocitrus littoralis (Miq.) Swingle. Selnergy, an IN SILICO biological profiling software, was used to identify putative binding targets of meranzin. Among the 400 screened proteins, 3 targets were selected: COX1, COX2 and PPARgamma. Binding tests were realised for these 3 protein candidates, as well as two negative controls. The predictions made by Selnergy were consistent with the experimental results, meaning that these 3 targets can be modulated by an extract containing this compound in a suitable concentration. These results demonstrate that reverse pharmacognosy and its inverse docking component is a powerful tool to identify biological properties for natural molecules and hence for plants containing these compounds.

Managing, profiling and analyzing a library of 2.6 million compounds gathered from 32 chemical providers.

The data for 3.8 million compounds from structural databases of 32 providers were gathered and stored in a single chemical database. Duplicates are removed using the IUPAC International Chemical Identifier. After this, 2.6 million compounds remain. Each database and the final one were studied in term of uniqueness, diversity, frameworks, 'drug-like' and 'lead-like' properties. This study also shows that there are more than 87 000 frameworks in the database. It contains 2.1 million 'drug-like' molecules among which, more than one million are 'lead-like'. This study has been carried out using 'ScreeningAssistant', a software dedicated to chemical databases management and screening sets generation. Compounds are stored in a MySQL database and all the operations on this database are carried out by Java code. The druglikeness and leadlikeness are estimated with 'in-house' scores using functions to estimate convenience to properties; unicity using the InChI code and diversity using molecular frameworks and fingerprints. The software has been conceived in order to facilitate the update of the database. 'ScreeningAssistant' is freely available under the GPL license.

Structure and thermodynamics of alpha-, beta-, and gamma-cyclodextrin dimers. Molecular dynamics studies of the solvent effect and free binding energies.

The alpha-, beta-, and gamma-cyclodextrin (CyDs) dimers were studied by molecular dynamics (MD) simulations in water as an explicit solvent. The relative stability of dimers and the involved molecular interactions were determined. Three possible starting orientations were considered for the dimers: head-to-head, head-to-tail, and tail-to-tail. MD simulations were performed over a period of 5 ns to ensure the stability of the system for both the CyD dimers and monomers. The MM-PBSA methodology was used to obtain the free binding energy of the dimers and to determine the most stable arrangement for each solvated CyD. In a vacuum, MD simulations provided the head-to-head orientation as the most stable orientation for the three CyDs, while in aqueous solution the, the head-to-tail orientation was found to be the most stable for the alpha-CyD dimer and the tail-to-tail orientation the most stable for the beta- and gamma-CyD dimers.

2D QSAR consensus prediction for high-throughput virtual screening. An application to COX-2 inhibition modeling and screening of the NCI database.

Using classification (SOM, LVQ, Binary, Decision Tree) and regression algorithms (PLS, BRANN, k-NN, Linear), this paper details the building of eight 2D-QSAR models from a 266 COX-2 inhibitor training set. The predictive performances of these eight models were subsequently compared using an 88 COX-2 inhibitor test set. Each ligand is described by 52 2D descriptors expressed as van der Waals Surface Areas (P_VSA) and its COX-2 binding IC50. One of our best predictive models is the neural network model (BRANN), which is able to select a subset, from the 88 ligand test set, that contains 94% COX-2 active inhibitors (pIC50>7.5) and detects 71% of all the actives. We then introduce a QSAR consensus prediction protocol that is shown to be more predictive than any single QSAR model: our C3 consensus approach is able to select a subset from the 88 ligand test set that contains 94% active inhibitors and 83% of all the actives. The 2D QSAR consensus protocol was finally applied to the high-throughput virtual screening of the NCI database, containing 193,477 organic compounds.

Rapid analysis of triterpenic acids by liquid chromatography using porous graphitic carbon and evaporative light scattering detection.

An original system which uses Porous Graphitic Carbon as support and a mixture of organic solvents as mobile phase is proposed for the analysis of triterpenic acids by liquid chromatography. The separation of betulinic acid, ursolic acid, oleanolic acid, and 18alpha- and 18beta-glycyrrhetinic acids was carried out within a short time and monitored by evaporative light scattering detection as universal detection method. Molecular modelling studies show that the main contribution to the selectivity comes from the electrostatic interaction characterised by the dipole moment of the products.