East Lansing, MI, United States
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Esposito E.X.,32 University Drive | Stouch T.R.,Junction Solutions | Wymore T.,Oak Ridge National Laboratory | Madura J.D.,Duquesne University
Chemical Research in Toxicology | Year: 2014

The inactivation of acetylcholinesterase (AChE) by organophosphorus agent (OP) compounds is a serious problem regardless of how the individual was exposed. The reactivation of OP-inactivated AChE is dependent on the OP conjugate, and commonly a specific oxime is better at reactivating a specific OP conjugate than several diverse OP conjugates. The presented research explores the physicochemical properties needed for the reactivation of OP-inactivated AChE. Four different OPs, cyclosarin, sarin, tabun, and VX, were analyzed using the same set of oxime reactivators. A trial descriptor pool of semiempirical, traditional, and molecular interaction field descriptors was used to construct an ensemble of QSAR models for each OP-conjugate pair. Based on the molecular information and the cross-validation ability, individual QSAR models were selected to be part of an OP-conjugate consensus model. The OP-conjugate specific models provide important insight into the physicochemical properties required to reactivate the OP conjugates of interest. The reactivation of AChE inactivated with either cyclosarin or tabun requires the oxime therapeutic to possess an overall polar-positive surface area. Oxime therapeutics for the reactivation of sarin-inactivated AChE are conformationally dependent while oxime reverse therapeutics for VX require a compact region with a highly hydrophilic region and two positively charged pyridine rings. © 2013 American Chemical Society.

Su B.-H.,National Taiwan University | Slien M.-Y.,National Taiwan University | Esposito E.X.,32 University Drive | Esposito E.X.,Chem21 Group Inc. | And 3 more authors.
Journal of Chemical Information and Modeling | Year: 2010

Blockage of the human ether-a-go-go related gene (hERG) potassium ion channel is a major factor related to cardiotoxicity. Hence, drugs binding to this channel have become an important biological end point in side effects screening. A set of 250 structurally diverse compounds screened for hERG activity from the literature was assembled using a set of reliability filters. This data set was used to construct a set of two- state hERG QSAR models. The descriptor pool used to construct the models consisted of 4D-fingerprints generated from the thermodynamic distribution of conformer states available to a molecule, 204 traditional 2D descriptors and 76 3D VolSurf-like descriptors computed using the Molecular Operating Environment (MOE) software. One model is a continuous partial least-squares (PLS) QSAR hERG binding model. Another related model is an optimized binary classification QSAR model that classifies compounds as active or inactive. This binary model achieves 91% accuracy over a large range of molecular diversity spanning the training set. Two external test sets were constructed. One test set is the condensed PubChem bioassay database containing 876 compounds, and the other test set consists of 106 additional compounds found in the literature. Both of the test sets were used to validate the binary QSAR model. The binary QSAR model permits a structural interpretation of possible sources for hERG activity. In particular, the presence of a polar negative group at a distance of 6-8 A from a hydrogen bond donor in a compound is predicted to be a quite structure- specific pharmacophore that increases hERG blockage. Since a data set of high chemical diversity was used to construct the binary model, it is applicable for performing general virtual hERG screening. © 2010 American Chemical Society.

Esposito E.X.,32 University Drive | Esposito E.X.,The Chem21 Group Inc. | Hopfinger A.J.,The Chem21 Group Inc. | Hopfinger A.J.,University of New Mexico | And 4 more authors.
Toxicology and Applied Pharmacology | Year: 2015

Carbon nanotubes have become widely used in a variety of applications including biosensors and drug carriers. Therefore, the issue of carbon nanotube toxicity is increasingly an area of focus and concern. While previous studies have focused on the gross mechanisms of action relating to nanomaterials interacting with biological entities, this study proposes detailed mechanisms of action, relating to nanotoxicity, for a series of decorated (functionalized) carbon nanotube complexes based on previously reported QSAR models. Possible mechanisms of nanotoxicity for six endpoints (bovine serum albumin, carbonic anhydrase, chymotrypsin, hemoglobin along with cell viability and nitrogen oxide production) have been extracted from the corresponding optimized QSAR models. The molecular features relevant to each of the endpoint respective mechanism of action for the decorated nanotubes are also discussed. Based on the molecular information contained within the optimal QSAR models for each nanotoxicity endpoint, either the decorator attached to the nanotube is directly responsible for the expression of a particular activity, irrespective of the decorator's 3D-geometry and independent of the nanotube, or those decorators having structures that place the functional groups of the decorators as far as possible from the nanotube surface most strongly influence the biological activity. These molecular descriptors are further used to hypothesize specific interactions involved in the expression of each of the six biological endpoints. © 2015 Elsevier Inc.

Tseng Y.J.,National Taiwan University | Hopfinger A.J.,University of New Mexico | Hopfinger A.J.,Chem21 Group Inc. | Esposito E.X.,Chem21 Group Inc. | Esposito E.X.,32 University Drive
Journal of Computer-Aided Molecular Design | Year: 2012

The usefulness and utility of QSAR modeling depends heavily on the ability to estimate the values of molecular descriptors relevant to the endpoints of interest followed by an optimized selection of descriptors to form the best QSAR models from a representative set of the endpoints of interest. The performance of a QSAR model is directly related to its molecular descriptors. QSAR modeling, specifically model construction and optimization, has benefited from its ability to borrow from other unrelated fields, yet the molecular descriptors that form QSAR models have remained basically unchanged in both form and preferred usage. There are many types of endpoints that require multiple classes of descriptors (descriptors that encode 1D through multi-dimensional, 4D and above, content) needed to most fully capture the molecular features and interactions that contribute to the endpoint. The advantages of QSAR models constructed from multiple, and different, descriptor classes have been demonstrated in the exploration of markedly different, and principally biological systems and endpoints. Multiple examples of such QSAR applications using different descriptor sets are described and that examined. The take-home-message is that a major part of the future of QSAR analysis, and its application to modeling biological potency, ADME-Tox properties, general use in virtual screening applications, as well as its expanding use into new fields for building QSPR models, lies in developing strategies that combine and use 1D through nD molecular descriptors. © 2011 Springer Science+Business Media B.V.

Shao C.-Y.,National Taiwan University | Chen S.-Z.,National Taiwan University | Su B.-H.,National Taiwan University | Tseng Y.J.,National Taiwan University | And 4 more authors.
Journal of Chemical Information and Modeling | Year: 2013

Little attention has been given to the selection of trial descriptor sets when designing a QSAR analysis even though a great number of descriptor classes, and often a greater number of descriptors within a given class, are now available. This paper reports an effort to explore interrelationships between QSAR models and descriptor sets. Zhou and co-workers (Zhou et al., Nano Lett.2008, 8 (3), 859-865) designed, synthesized, and tested a combinatorial library of 80 surface modified, that is decorated, multi-walled carbon nanotubes for their composite nanotoxicity using six endpoints all based on a common 0 to 100 activity scale. Each of the six endpoints for the 29 most nanotoxic decorated nanotubes were incorporated as the training set for this study. The study reported here includes trial descriptor sets for all possible combinations of MOE, VolSurf, and 4D-fingerprints (FP) descriptor classes, as well as including and excluding explicit spatial contributions from the nanotube. Optimized QSAR models were constructed from these multiple trial descriptor sets. It was found that (a) both the form and quality of the best QSAR models for each of the endpoints are distinct and (b) some endpoints are quite dependent upon 4D-FP descriptors of the entire nanotube-decorator complex. However, other endpoints yielded equally good models only using decorator descriptors with and without the decorator-only 4D-FP descriptors. Lastly, and most importantly, the quality, significance, and interpretation of a QSAR model were found to be critically dependent on the trial descriptor sets used within a given QSAR endpoint study. © 2012 American Chemical Society.

Chang C.-Y.,National Taiwan University | Hsu M.-T.,National Taiwan University | Esposito E.X.,32 University Drive | Tseng Y.J.,National Taiwan University
Journal of Chemical Information and Modeling | Year: 2013

The traditional biological assay is very time-consuming, and thus the ability to quickly screen large numbers of compounds against a specific biological target is appealing. To speed up the biological evaluation of compounds, high-throughput screening is widely used in the fields of biomedical, biological information, and drug discovery. The research presented in this study focuses on the use of support vector machines, a machine learning method, various classes of molecular descriptors, and different sampling techniques to overcome overfitting to classify compounds for cytotoxicity with respect to the Jurkat cell line. The cell cytotoxicity data set is imbalanced (a few active compounds and very many inactive compounds), and the ability of the predictive modeling methods is adversely affected in these situations. Commonly imbalanced data sets are overfit with respect to the dominant classified end point; in this study the models routinely overfit toward inactive (noncytotoxic) compounds when the imbalance was substantial. Support vector machine (SVM) models were used to probe the proficiency of different classes of molecular descriptors and oversampling ratios. The SVM models were constructed from 4D-FPs, MOE (1D, 2D, and 21/2D), noNP+MOE, and CATS2D trial descriptors pools and compared to the predictive abilities of CATS2D-based random forest models. Compared to previous results in the literature, the SVM models built from oversampled data sets exhibited better predictive abilities for the training and external test sets. © 2013 American Chemical Society.

Su B.-H.,National Taiwan University | Tu Y.-S.,National Taiwan University | Esposito E.X.,32 University Drive | Tseng Y.J.,National Taiwan University
Journal of Chemical Information and Modeling | Year: 2012

The inclusion and accessibility of different methodologies to explore chemical data sets has been beneficial to the field of predictive modeling, specifically in the chemical sciences in the field of Quantitative Structure-Activity Relationship (QSAR) modeling. This study discusses using contemporary protocols and QSAR modeling methods to properly model two biomolecular systems that have historically not performed well using traditional and three-dimensional QSAR methodologies. Herein, we explore, analyze, and discuss the creation of a classification human Ether-a-go-go Related Gene (hERG) potassium channel model and a continuous Tetrahymena pyriformis (T. pyriformis) model using Support Vector Machine (SVM) and Support Vector Regression (SVR), respectively. The models are constructed with three types of molecular descriptors that capture the gross physicochemical features of the compounds: (i) 2D, 2 1/2D, and 3D physical features, (ii) VolSurf-like molecular interaction fields, and (iii) 4D-Fingerprints. The best hERG SVM model achieved 89% accuracy and the three-best SVM models were able to screen a Pubchem data set with an accuracy of 97%. The best T. pyriformis model had an R 2 value of 0.924 for the training set and was able to predict the continuous end points for two test sets with R 2 values of 0.832 and 0.620, respectively. The studies presented within demonstrate the predictive ability (classification and continuous end points) of QSAR models constructed from curated data sets, biologically relevant molecular descriptors, and Support Vector Machines and Support Vector Regression. The ability of these protocols and methodologies to accommodate large data sets (several thousands compounds) that are chemically diverse - and in the case of classification modeling unbalanced (one experimental outcome dominates the data set) - allows scientists to further explore a remarkable amount of biological and chemical information. © 2012 American Chemical Society.

Dunbar J.B.,University of Michigan | Smith R.D.,University of Michigan | Damm-Ganamet K.L.,University of Michigan | Ahmed A.,University of Michigan | And 9 more authors.
Journal of Chemical Information and Modeling | Year: 2013

A major goal in drug design is the improvement of computational methods for docking and scoring. The Community Structure Activity Resource (CSAR) has collected several data sets from industry and added in-house data sets that may be used for this purpose (www.csardock.org). CSAR has currently obtained data from Abbott, GlaxoSmithKline, and Vertex and is working on obtaining data from several others. Combined with our in-house projects, we are providing a data set consisting of 6 protein targets, 647 compounds with biological affinities, and 82 crystal structures. Multiple congeneric series are available for several targets with a few representative crystal structures of each of the series. These series generally contain a few inactive compounds, usually not available in the literature, to provide an upper bound to the affinity range. The affinity ranges are typically 3-4 orders of magnitude per series. For our in-house projects, we have had compounds synthesized for biological testing. Affinities were measured by Thermofluor, Octet RED, and isothermal titration calorimetry for the most soluble. This allows the direct comparison of the biological affinities for those compounds, providing a measure of the variance in the experimental affinity. It appears that there can be considerable variance in the absolute value of the affinity, making the prediction of the absolute value ill-defined. However, the relative rankings within the methods are much better, and this fits with the observation that predicting relative ranking is a more tractable problem computationally. For those in-house compounds, we also have measured the following physical properties: logD, logP, thermodynamic solubility, and pKa. This data set also provides a substantial decoy set for each target consisting of diverse conformations covering the entire active site for all of the 58 CSAR-quality crystal structures. The CSAR data sets (CSAR-NRC HiQ and the 2012 release) provide substantial, publically available, curated data sets for use in parametrizing and validating docking and scoring methods. © 2013 American Chemical Society.

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