Fusing Docking Scoring Functions Improves the Virtual Screening Performance for Discovering Parkinson's Disease Dual Target Ligands.

BACKGROUND: Virtual methodologies have become essential components of the drug discovery pipeline. Specifically, structure-based drug design methodologies exploit the 3D structure of molecular targets to discover new drug candidates through molecular docking. Recently, dual target ligands of the Adenosine A2A Receptor and Monoamine Oxidase B enzyme have been proposed as effective therapies for the treatment of Parkinson's disease. METHODS: In this paper we propose a structure-based methodology, which is extensively validated, for the discovery of dual Adenosine A2A Receptor/Monoamine Oxidase B ligands. This methodology involves molecular docking studies against both receptors and the evaluation of different scoring functions fusion strategies for maximizing the initial virtual screening enrichment of known dual ligands. RESULTS: The developed methodology provides high values of enrichment of known ligands, which outperform that of the individual scoring functions. At the same time, the obtained ensemble can be translated in a sequence of steps that should be followed to maximize the enrichment of dual target Adenosine A2A Receptor antagonists and Monoamine Oxidase B inhibitors. CONCLUSION: Information relative to docking scores to both targets have to be combined for achieving high dual ligands enrichment. Combining the rankings derived from different scoring functions proved to be a valuable strategy for improving the enrichment relative to single scoring function in virtual screening experiments.

Chemoinformatics Profiling of the Chromone Nucleus as a MAO-B/A2AAR Dual Binding Scaffold.

BACKGROUND: In the context of the current drug discovery efforts to find disease modifying therapies for Parkinson's disease (PD) the current single target strategy has proved inefficient. Consequently, the search for multi-potent agents is attracting more and more attention due to the multiple pathogenetic factors implicated in PD. Multiple evidences points to the dual inhibition of the monoamine oxidase B (MAO-B), as well as adenosine A2A receptor (A2AAR) blockade, as a promising approach to prevent the neurodegeneration involved in PD. Currently, only two chemical scaffolds has been proposed as potential dual MAO-B inhibitors/A2AAR antagonists (caffeine derivatives and benzothiazinones). METHODS: In this study, we conduct a series of chemoinformatics analysis in order to evaluate and advance the potential of the chromone nucleus as a MAO-B/A2AAR dual binding scaffold. RESULTS: The information provided by SAR data mining analysis based on network similarity graphs and molecular docking studies support the suitability of the chromone nucleus as a potential MAOB/ A2AAR dual binding scaffold. Additionally, a virtual screening tool based on a group fusion similarity search approach was developed for the prioritization of potential MAO-B/A2AAR dual binder candidates. Among several data fusion schemes evaluated, the MEAN-SIM and MIN-RANK GFSS approaches demonstrated to be efficient virtual screening tools. Then, a combinatorial library potentially enriched with MAO-B/A2AAR dual binding chromone derivatives was assembled and sorted by using the MIN-RANK and then the MEAN-SIM GFSS VS approaches. CONCLUSION: The information and tools provided in this work represent valuable decision making elements in the search of novel chromone derivatives with a favorable dual binding profile as MAOB inhibitors and A2AAR antagonists with the potential to act as a disease-modifying therapeutic for Parkinson's disease.

Ligand-Based Virtual Screening Using Tailored Ensembles: A Prioritization Tool for Dual A2AAdenosine Receptor Antagonists / Monoamine Oxidase B Inhibitors.

BACKGROUND: Virtual Screening methodologies have emerged as efficient alternatives for the discovery of new drug candidates. At the same time, ensemble methods are nowadays frequently used to overcome the limitations of employing a single model in ligand-based drug design. However, many applications of ensemble methods to this area do not consider important aspects related to both virtual screening and the modeling process. During the application of ensemble methods to virtual screening the proper validation of the models in virtual screening conditions is often neglected. No analysis of the diversity of the ensemble members is performed frequently or no considerations regarding the applicability domain of the base models are being made. METHODS: In this research, we review basic concepts and definitions related to virtual screening. We comment recent applications of ensemble methods to ligand-based virtual screening and highlight their advantages and limitations. RESULTS: Next, we propose a method based on genetic algorithms optimization for the generation of virtual screening tailored ensembles which address the previously identified problems in the current applications of ensemble methods to virtual screening. CONCLUSION: Finally, the proposed methodology is successfully applied to the generation of ensemble models for the ligand-based virtual screening of dual target A2A adenosine receptor antagonists and MAO-B inhibitors as potential Parkinson's disease therapeutics.

Efficient and biologically relevant consensus strategy for Parkinson's disease gene prioritization.

BACKGROUND: The systemic information enclosed in microarray data encodes relevant clues to overcome the poorly understood combination of genetic and environmental factors in Parkinson's disease (PD), which represents the major obstacle to understand its pathogenesis and to develop disease-modifying therapeutics. While several gene prioritization approaches have been proposed, none dominate over the rest. Instead, hybrid approaches seem to outperform individual approaches. METHODS: A consensus strategy is proposed for PD related gene prioritization from mRNA microarray data based on the combination of three independent prioritization approaches: Limma, machine learning, and weighted gene co-expression networks. RESULTS: The consensus strategy outperformed the individual approaches in terms of statistical significance, overall enrichment and early recognition ability. In addition to a significant biological relevance, the set of 50 genes prioritized exhibited an excellent early recognition ability (6 of the top 10 genes are directly associated with PD). 40 % of the prioritized genes were previously associated with PD including well-known PD related genes such as SLC18A2, TH or DRD2. Eight genes (CCNH, DLK1, PCDH8, SLIT1, DLD, PBX1, INSM1, and BMI1) were found to be significantly associated to biological process affected in PD, representing potentially novel PD biomarkers or therapeutic targets. Additionally, several metrics of standard use in chemoinformatics are proposed to evaluate the early recognition ability of gene prioritization tools. CONCLUSIONS: The proposed consensus strategy represents an efficient and biologically relevant approach for gene prioritization tasks providing a valuable decision-making tool for the study of PD pathogenesis and the development of disease-modifying PD therapeutics.

Topological sub-structural molecular design (TOPS-MODE): a useful tool to explore key fragments of human A3 adenosine receptor ligands.

Adenosine regulates tissue function by activating four G-protein-coupled adenosine receptors (ARs). Selective agonists and antagonists for A3 ARs have been investigated for the treatment of a variety of immune disorders, cancer, brain, and heart ischemic conditions. We herein present a QSAR study based on a Topological sub-structural molecular design (TOPS-MODE) approach, intended to predict the A3 ARs of a diverse dataset of 124 (94 training set/ 30 prediction set) adenosine derivatives. The final model showed good fit and predictive capability, displaying 85.1 % of the experimental variance. The TOPS-MODE approach afforded a better understanding and interpretation of the developed model based on the useful information extracted from the analysis of the contribution of different molecular fragments to the affinity.

Combining QSAR classification models for predictive modeling of human monoamine oxidase inhibitors.

Due to their role in the metabolism of monoamine neurotransmitters, MAO-A and MAO-B present a significant pharmacological interest. For instance the inhibitors of human MAO-B are considered useful tools for the treatment of Parkinson Disease. Therefore, the rational design and synthesis of new MAOs inhibitors is considered of great importance for the development of new and more effective treatments of Parkinson Disease. In this work, Quantitative Structure Activity Relationships (QSAR) has been developed to predict the human MAO inhibitory activity and selectivity. The first step was the selection of a suitable dataset of heterocyclic compounds that include chromones, coumarins, chalcones, thiazolylhydrazones, etc. These compounds were previously synthesized in one of our laboratories, or elsewhere, and their activities measured by the same assays and for the same laboratory staff. Applying linear discriminant analysis to data derived from a variety of molecular representations and feature selection algorithms, reliable QSAR models were built which could be used to predict for test compounds the inhibitory activity and selectivity toward human MAO. This work also showed how several QSAR models can be combined to make better predictions. The final models exhibit significant statistics, interpretability, as well as displaying predictive power on an external validation set made up of chromone derivatives with unknown activity (that are being reported here for first time) synthesized by our group, and coumarins recently reported in the literature.

Topological sub-structural molecular design approach: radical scavenging activity.

In the last decades phenolic compounds have gained enormous interest because of their beneficial health effects such as anti-inflammatory, anticancer, or antiviral activities. The pharmacological effects of phenolic compounds are mainly due to their antioxidant activity and their inhibition of certain enzymes. This antoxidant activity is related to the structure and has been extensively reported throught SAR or QSAR models. These studies confirmed that the number and position of hydroxyl groups, the related glycosylation and other substitutions in the phenolic ring largely determined radical scavenging activity. Most of these models are based on certain families of chemicals (flavonoids, cinnamic acids, etc…) and the model by itself is not useful for other substances of a different family. In this study we developed a QSAR model for a heterogeneous group of substances with TOPS-MODE descriptors for an interpretation of the antioxidant activity of these compounds in the form of bond contributions. The model developed, able to describe more than 90% of the variance in the experimental activity, also has a good predictive ability and stability. The information extracted from the QSAR model revealed that the major driving forces for radical scavenging activity are hydrogen bond donation and polarity. With this work we have managed to unify the different families of antioxidants in a single model with sufficient capacity to make predictions of radical scavenging activity for unknown substances.

Two new parameters based on distances in a receiver operating characteristic chart for the selection of classification models.

There are several indices that provide an indication of different types on the performance of QSAR classification models, being the area under a Receiver Operating Characteristic (ROC) curve still the most powerful test to overall assess such performance. All ROC related parameters can be calculated for both the training and test sets, but, nevertheless, neither of them constitutes an absolute indicator of the classification performance by themselves. Moreover, one of the biggest drawbacks is the computing time needed to obtain the area under the ROC curve, which naturally slows down any calculation algorithm. The present study proposes two new parameters based on distances in a ROC curve for the selection of classification models with an appropriate balance in both training and test sets, namely the following: the ROC graph Euclidean distance (ROCED) and the ROC graph Euclidean distance corrected with Fitness Function (FIT(λ)) (ROCFIT). The behavior of these indices was observed through the study on the mutagenicity for four genotoxicity end points of a number of nonaromatic halogenated derivatives. It was found that the ROCED parameter gets a better balance between sensitivity and specificity for both the training and prediction sets than other indices such as the Matthews correlation coefficient, the Wilk's lambda, or parameters like the area under the ROC curve. However, when the ROCED parameter was used, the follow-on linear discriminant models showed the lower statistical significance. But the other parameter, ROCFIT, maintains the ROCED capabilities while improving the significance of the models due to the inclusion of FIT(λ).

Combining molecular docking and QSAR studies for modelling the antigyrase activity of cyclothialidine derivatives.

DNA gyrase is a well-established antibacterial target consisting of two subunits, GyrA and GyrB, in a heterodimer A(2)B(2), where GyrB catalyzes the hydrolysis of ATP. Cyclothialidine (Ro 09-1437) has been considered as a promising inhibitor whose modifications might lead to more potent compounds against the enzyme. We report here for the first time, QSAR studies regarding to ATPase inhibitors of DNA Gyrase. 1D, 2D and 3D descriptors from DRAGON software were used on a set of 42 cyclothialidine derivatives. Based on the core of the cyclothialidine GR122222X, different conformations were created by using OMEGA. FRED was used to dock these conformers in the cavity of the GyrB subunit to select the best conformations, paying special attention to the 12-membered ring. Three QSAR models were developed considering the dimension of the descriptors. The models were robust, predictive and good in statistical significance, over 70% of the experimental variance was explained. Interpretability of the models was possible by extracting the SAR(s) encoded by these predictive models. Analyzing the compound-enzyme interactions of the complexes obtained by docking allowed us to increase the reliability of the information obtained for the QSAR models.

QSAR models to predict mutagenicity of acrylates, methacrylates and alpha,beta-unsaturated carbonyl compounds.

OBJECTIVE: The purpose of this study is to develop a quantitative structure-activity relationship (QSAR) model that can distinguish mutagenic from non-mutagenic species with alpha,beta-unsaturated carbonyl moiety using two endpoints for this activity - Ames test and mammalian cell gene mutation test - and also to gather information about the molecular features that most contribute to eliminate the mutagenic effects of these chemicals. METHODS: Two data sets were used for modeling the two mutagenicity endpoints: (1) Ames test and (2) mammalian cells mutagenesis. The first one comprised 220 molecules, while the second one 48 substances, ranging from acrylates, methacrylates to alpha,beta-unsaturated carbonyl compounds. The QSAR models were developed by applying linear discriminant analysis (LDA) along with different sets of descriptors computed using the DRAGON software. RESULTS: For both endpoints, there was a concordance of 89% in the prediction and 97% confidentiality by combining the three models for the Ames test mutagenicity. We have also identified several structural alerts to assist the design of new monomers. SIGNIFICANCE: These individual models and especially their combination are attractive from the point of view of molecular modeling and could be used for the prediction and design of new monomers that do not pose a human health risk.

A topological substructural molecular design approach for predicting mutagenesis end-points of alpha, beta-unsaturated carbonyl compounds.

Chemically reactive, alpha, beta-unsaturated carbonyl compounds are common environmental pollutants able to produce a wide range of adverse effects, including, e.g. mutagenicity. This toxic property can often be related to chemical structure, in particular to specific molecular substructures or fragments (alerts), which can then be used in specialized software or expert systems for predictive purposes. In the past, there have been many attempts to predict the mutagenicity of alpha, beta-unsaturated carbonyl compounds through quantitative structure activity relationships (QSAR) but considering only one exclusive endpoint: the Ames test. Besides, even though those studies give a comprehensive understanding of the phenomenon, they do not provide substructural information that could be useful forward improving expert systems based on structural alerts (SAs). This work reports an evaluation of classification models to probe the mutagenic activity of alpha, beta-unsaturated carbonyl compounds over two endpoints--the Ames and mammalian cell gene mutation tests--based on linear discriminant analysis along with the topological Substructure molecular design (TOPS-MODE) approach. The obtained results showed the better ability of the TOPS-MODE approach in flagging structural alerts for the mutagenicity of these compounds compared to the expert system TOXTREE. Thus, the application of the present QSAR models can aid toxicologists in risk assessment and in prioritizing testing, as well as in the improvement of expert systems, such as the TOXTREE software, where SAs are implemented.

QSPR modelling with the topological substructural molecular design approach: beta-cyclodextrin complexation.

This study aims at developing a quantitative structure-property relationship (QSPR) model for predicting complexation with beta-cyclodextrins (beta-CD) based on a large variety of organic compounds. Molecular descriptors were computed following the TOPological Substructural MOlecular DEsign (TOPS-MODE) approach and correlated with beta-CD complex stability constants by linear multivariate data analysis. This strategy afforded a final QSPR model that was able to explain around 86% of the variance in the experimental activity, along with showing good internal cross-validation statistics, and also good predictivity on external data. Topological substructural information influencing the complexation with beta-CD was extracted from the QSPR model. This revealed that the major driving forces for complexation are hydrophobicity and van der Waals interactions. Therefore, the presence of hydrophobic groups (hydrocarbon chains, aryl groups, etc.) and voluminous species (Cl, Br, I, etc.) in the molecules renders easy their complexity with beta-CDs. To our knowledge, this is the first time a correlation between TOPS-MODE descriptors and complexing abilities of beta-CDs has been reported.

Applications of 2D descriptors in drug design: a DRAGON tale.

In order to minimize expensive drug failures, is essential to determine potential activity, toxicity and ADME problems as early as possible. In view of the large libraries of compounds now being handled by combinatorial chemistry and high-throughput screening, identification of potential drug is advisable even before synthesis using computational techniques such as QSAR modeling. A great number of in silico approaches to activity/toxicity prediction have been described in the literature, using molecular 0D, 1D, 2D and 3D descriptors. Also these descriptors have been implemented in available computational tools such as DRAGON, SYBYL and CODESSA for it easy use. However, many of them only have been used to explain a few prediction problems. This review attempts to summarize present knowledge related to the computational biological activity prediction based in 2D molecular descriptors implemented in the DRAGON software. These applications rely on new computational techniques such as virtual combinatorial synthesis, virtual computational screening or inverse. Several topological molecular descriptors applications are described, ranging from simple topological indices to topological indices derived from matrices weighted with atomic and bond properties. Their advantages, limitations and its possibilities in drug design are also discussed.

Quantitative structure carcinogenicity relationship for detecting structural alerts in nitroso-compounds: species: rat; sex: male; route of administration: water.

In this work, Quantitative Structure-Activity Relationship (QSAR) modelling was used as a tool for predicting the carcinogenic potency of a set of 39 nitroso-compounds, which have been bioassayed in male rats by using the oral route of administration. The optimum QSAR model provided evidence of good fit and performance of predicitivity from training set. It was able to account for about 84% of the variance in the experimental activity and exhibited high values of the determination coefficients of cross validations, leave one out and bootstrapping (q(2)(LOO)=78.53 and q(2)(Boot)=74.97). Such a model was based on spectral moments weighted with Gasteiger-Marsilli atomic charges, polarizability and hydrophobicity, as well as with Abraham indexes, specifically the summation solute hydrogen bond basicity and the combined dipolarity/polarizability. This is the first study to have explored the possibility of combining Abraham solute descriptors with spectral moments. A reasonable interpretation of these molecular descriptors from a toxicological point of view was achieved by means of taking into account bond contributions. The set of relationships so derived revealed the importance of the length of the alkyl chains for determining carcinogenic potential of the chemicals analysed, and were able to explain the difference between mono-substituted and di-substituted nitrosoureas as well as to discriminate between isomeric structures with hydroxyl-alkyl and alkyl substituents in different positions. Moreover, they allowed the recognition of structural alerts in classical structures of two potent nitrosamines, consistent with their biotransformation. These results indicate that this new approach has the potential for improving carcinogenicity predictions based on the identification of structural alerts.

QSAR modeling of the rodent carcinogenicity of nitrocompounds.

Chemical carcinogenicity is of primary interest, because it drives much of the current regulatory actions regarding new and existing chemicals, and its conventional experimental test takes around three years to design, conduct, and interpret as well as the costs of hundreds of millions of dollars, millions of skilled personnel hours, and several animal lives. Both academia and private companies are actively trying to develop alternative methods, such as QSAR models. This paper reports a QSAR study for predicting carcinogenic potency of nitrocompounds bioassayed in female rats. Several different theoretical molecular descriptors, calculated only on the basis of knowledge of the molecular structure and an efficient variable selection procedure, such as Genetic Algorithm, led to models with satisfactory predictive ability. But the best-final QSAR model is based on the GEometry, Topology, and Atom-Weights AssemblY (GETAWAY) descriptors capturing a reasonable interpretation. In fact, structural features such as molecular shape-linear, branched, cyclic, and polycyclic--and bond length are some of the key factors flagging the carcinogenicity of this set of nitrocompounds. This QSAR model, after removal of one identified nitrocompound outlier, is able to explain around 86% of the variance in the experimental activity and manifest good predictive ability as indicated by the higher q(2)s of cross- and external-validations, which demonstrate the practical value of the final QSAR model for screening and priority testing. This model can be applied to nitrochemicals different from the studied nitrocompounds (even those not yet synthesized) as it is based on theoretical molecular descriptors that might be easily and rapidly calculated.

Quantitative structure carcinogenicity relationship for detecting structural alerts in nitroso-compounds.

Prevention of environmentally induced cancers is a major health problem of which solutions depend on the rapid and accurate screening of potential chemical hazards. Lately, theoretical approaches such as the one proposed here - Quantitative Structure-Activity Relationship (QSAR) - are increasingly used for assessing the risks of environmental chemicals, since they can markedly reduce costs, avoid animal testing, and speed up policy decisions. This paper reports a QSAR study based on the Topological Substructural Molecular Design (TOPS-MODE) approach, aiming at predicting the rodent carcinogenicity of a set of nitroso-compounds selected from the Carcinogenic Potency Data Base (CPDB). The set comprises nitrosoureas (14 chemicals), N-nitrosamines (18 chemicals) C-nitroso-compounds (1 chemical), nitrosourethane (1 chemical) and nitrosoguanidine (1 chemical), which have been bioassayed in male rat using gavage as the route of administration. Here we are especially concerned in gathering the role of both parameters on the carcinogenic activity of this family of compounds. First, the regression model was derived, upon removal of one identified nitrosamine outlier, and was able to account for more than 84% of the variance in the experimental activity. Second, the TOPS-MODE approach afforded the bond contributions -- expressed as fragment contributions to the carcinogenic activity -- that can be interpreted and provide tools for better understanding the mechanisms of carcinogenesis. Finally, and most importantly, we demonstrate the potentialities of this approach towards the recognition of structural alerts for carcinogenicity predictions.

Probing the anticancer activity of nucleoside analogues: a QSAR model approach using an internally consistent training set.

The cancer research community has begun to address the in silico modeling approaches, such as quantitative structure-activity relationships (QSAR), as an important alternative tool for screening potential anticancer drugs. With the compilation of a large dataset of nucleosides synthesized in our laboratories, or elsewhere, and tested in a single cytotoxic assay under the same experimental conditions, we recognized a unique opportunity to attempt to build predictive QSAR models. Here, we report a systematic evaluation of classification models to probe anticancer activity, based on linear discriminant analysis along with 2D-molecular descriptors. This strategy afforded a final QSAR model with very good overall accuracy and predictability on external data. Finally, we search for similarities between the natural nucleosides, present in RNA/DNA, and the active nucleosides well-predicted by the model. The structural information then gathered and the QSAR model per se shall aid in the future design of novel potent anticancer nucleosides.

QSAR studies using radial distribution function for predicting A1 adenosine receptors agonists.

The radial distribution function (RDF) approach has been applied to the study of the A(1) adenosine receptors agonist effect of 32 adenosine analogues. A model able to describe more than 79% of the variance in the experimental activity was developed with the use of the mentioned approach. In contrast, none of the three different approaches, including the use of 2D autocorrelations, BCUT and 3D-MORSE descriptors were able to explain more than 72% of the variance in the mentioned property with the same number of variables in the equation. In addition, we established a comparison with other models reported by us for this receptor subtype using this data set, and the RDF descriptors continue getting the best results.

Quantitative structure activity relationships as useful tools for the design of new adenosine receptor ligands. 1. Agonist.

In order to minimize expensive drug failures it is essential to determine the potential biological activity of new candidates as early as possible. In view of the large libraries of nucleoside analogues that are now being handled in organic synthesis, the identification of a drugs biological activity is advisable even before synthesis and this can be achieved using predictive biological activity methods. In this sense, computer aided rational drug design strategies like Quantitative Structure Activity Relationships (QSAR) or docking approaches have emerged as promising tools. Although a large number of in silico approaches have been described in the literature for the prediction of different biological activities, the use of traditional QSAR applications in the development of new agonist molecules with affinity toward adenosine receptors is scarce. This review attempts to summarize the current level of knowledge concerning computational affinity predictions for adenosine receptors using QSAR models based on knowledge of the agonist ligands. Several computational protocols and different 2D and 3D descriptors have been described in the literature for these targets, but more effort is still required in this area.

2D autocorrelation modelling of the inhibitory activity of cytokinin-derived cyclin-dependent kinase inhibitors.

The inhibitory activity towards p34(cdc2)/cyclin b kinase (CBK) enzyme of 30 cytokinin-derived compounds has been successfully modelled using 2D spatial autocorrelation vectors. Predictive linear and non-linear models were obtained by forward stepwise multi-linear regression analysis (MRA) and artificial neural network (ANN) approaches respectively. A variable selection routine that selected relevant non-linear information from the data set was employed prior to networks training. The best ANN with three input variables was able to explain about 87% data variance in comparison with 80% by the linear equation using the same number of descriptors. Similarly, the neural network had higher predictive power. The MRA model showed a linear dependence between the inhibitory activities and the spatial distributions of masses, electronegativities and van der Waals volumes on the inhibitors molecules. Meanwhile, ANN model evidenced the occurrence of non-linear relationships between the inhibitory activity and the mass distribution at different topological distance on the cytokinin-derived compounds. Furthermore, inhibitors were well distributed regarding its activity levels in a Kohonen self-organizing map (SOM) built using the input variables of the best neural network.