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Biomedical subjects

Xiaoyang Xia

Publications and source records attributed to Xiaoyang Xia.

3 recordsLinked to original sources

Classification of kinase inhibitors using a Bayesian model.

The use of Bayesian statistics to model both general (multifamily) and specific (single-target) kinase inhibitors is investigated. The approach demonstrates an alternative to current computational methods applied to heterogeneous structure/activity data sets. This approach operates rapidly and is readily modifiable as required. A generalized model generated using inhibitor data from multiple kinase classes shows meaningful enrichment for several specific kinase targets. Such an approach can be used to prioritize compounds for screening or to optimally select compounds from third-party data collections. The observed benefit of the approach is finding compounds that are not structurally related to known actives, or novel targets for which there is not enough information to build a specific kinase model. The general kinase model described was built from a basis of mostly tyrosine kinase inhibitors, with some serine/threonine inhibitors; all the test cases used in prediction were also on tyrosine kinase targets. Confirming the applicability of this technique to other kinase families will be determined once those biological assays become available.

Artificial Intelligence↗

Solubility prediction by recursive partitioning.

PURPOSE: To build and test a computational model for predicting small molecule solubility, to improve the cost-effectiveness of the selection of vendor compounds suitable for nuclear magnetic resonance (NMR) screening. METHODS: A simple recursive partitioning decision tree-based classification model was generated utilizing "off-the-shelf" commercial software from Accelrys Inc., with a training set of 1992 compounds based on a series of calculated topologic and physical properties. The predictive ability of the decision tree was then assessed by employing it to classify a test set of 2851 vendor compounds, and the classification was subsequently used to guide the purchase of 686 compounds for the purpose of NMR screening. RESULTS: When the decision tree was used to guide purchasing, the percentage of "acceptable" compounds suitable for NMR screening doubled compared with the use of a simple cLogP cutoff, improving the successful selection rate from 25% to 50%. CONCLUSIONS: A simple recursive partitioning decision tree may successfully be used to improve cost-effectiveness by reducing the wastage associated with the unnecessary purchase of vendor compounds unsuitable for NMR screening because of insolubility.

Computer Simulation↗

High-throughput logP measurement using parallel liquid chromatography/ultraviolet/mass spectrometry and sample-pooling.

A novel approach to high-throughput logP measurement based on liquid chromatography/ultraviolet/mass spectrometry (LC/UV/MS) is proposed. The logP value is determined by correlation with the logk value, where k is the capacity factor k = (t(r)-t(0))/t(0), with the logP value using a defined set of standards. Since the analyte retention time (t(r)) is determined from the appropriate extracted ion chromatogram (EIC), there are no interferences from impurities and this allows the pooling of multiple compounds into one injection. To ensure the accuracy and instrument robustness in a routine high-throughput environment, a simple and MS-friendly mobile phase consisting of 20 mM ammonium carbonate (pH 8.0) for basic compounds or 20 mM ammonium formate (pH 1.0) for acidic compounds, both in combination with methanol at a ratio of 45:55, is used. This approach has been successfully used on single as well as parallel multi-channel LC/UV/MS systems to screen small to large sets of lead compounds and their analogs. A high-throughput capability to analyze over 1000 compounds per day has been achieved.

Animals↗