New horizons in mouse immunoinformatics: reliable in silico prediction of mouse class I histocompatibility major complex peptide binding affinity

Quantitative structure-activity relationship (QSAR) analysis is a main cornerstone of modern informatic disciplines. Predictive computational models, based on QSAR technology, of peptide-major histocompatibility complex (MHC) binding affinity have now become a vital component of modern day computational immunovaccinology. Historically, such approaches have been built around semi-qualitative, classification methods, but these are now giving way to quantitative regression methods. The additive method, an established immunoinformatics technique for the quantitative prediction of peptide-protein affinity, was used here to identify the sequence dependence of peptide binding specificity for three mouse class I MHC alleles: H2-D(b), H2-K(b) and H2-K(k). As we show, in terms of reliability the resulting models represent a significant advance on existing methods. They can be used for the accurate prediction of T-cell epitopes and are freely available online ( http://www.jenner.ac.uk/MHCPred).     

Prediction of peptide binding to a major histocompatibility complex class I molecule based on docking simulation

Binding between major histocompatibility complex (MHC) class I molecules and immunogenic epitopes is one of the most important processes for cell-mediated immunity. Consequently, computational prediction of amino acid sequences of MHC class I binding peptides from a given sequence may lead to important biomedical advances. In this study, an efficient structure-based method for predicting peptide binding to MHC class I molecules was developed, in which the binding free energy of the peptide was evaluated by two individual docking simulations. An original penalty function and restriction of degrees of freedom were determined by analysis of 361 published X-ray structures of the complex and were then introduced into the docking simulations. To validate the method, calculations using a 50-amino acid sequence as a prediction target were performed. In 27 calculations, the binding free energy of the known peptide was within the top 5 of 166 peptides generated from the 50-amino acid sequence. Finally, demonstrative calculations using a whole sequence of a protein as a prediction target were performed. These data clearly demonstrate high potential of this method for predicting peptide binding to MHC class I molecules.     

Reflectance near-infrared spectroscopic method with a chemometric technique using partial least squares multivariate calibration for simultaneous determination of chondroitin, glucosamine, and ascorbic acid

A reflectance near-infrared (RNIR) spectroscopy method was developed for simultaneous determination of chondroitin (CH), glucosamine (GO), and ascorbic acid (AS) in capsule powder. A simple preparation of the sample was done by grinding, sieving, and compression of the powder sample for improving RNIR spectra. Partial least squares (PLS-1 and PLS-2) was successfully applied to quantify the three components in the studied mixture using information included in RNIR spectra in the 4240-9780 cm(-1) range. The calibration model was developed with the three drug concentrations ranging from 50 to 150% of the labeled amount. The calibration models using pure standards were evaluated by internal validation, cross-validation, and external validation using synthetic and pharmaceutical preparations. The proposed method was applied for analysis of two pharmaceutical products. Both pharmaceutical products had the same active principle and similar excipients, but with different nominal concentration values. The results of the proposed method were compared with the results of a pharmacopoeial method for the same pharmaceutical products. No significant differences between the results were found. The standard error of prediction was 0.004 for CH, 0.003 for GO, and 0.005 for AS. The correlation coefficient was 0.9998 for CH, 0.9999 for GO, and 0.9997 for AS. The highly accurate and precise RNIR method can be used for QC of pharmaceutical products.     

Predicting class I major histocompatibility complex (MHC) binders using multivariate statistics: comparison of discriminant analysis and multiple linear regression

The accurate in silico identification of T-cell epitopes is a critical step in the development of peptide-based vaccines, reagents, and diagnostics. It has a direct impact on the success of subsequent experimental work. Epitopes arise as a consequence of complex proteolytic processing within the cell. Prior to being recognized by T cells, an epitope is presented on the cell surface as a complex with a major histocompatibility complex (MHC) protein. A prerequisite therefore for T-cell recognition is that an epitope is also a good MHC binder. Thus, T-cell epitope prediction overlaps strongly with the prediction of MHC binding. In the present study, we compare discriminant analysis and multiple linear regression as algorithmic engines for the definition of quantitative matrices for binding affinity prediction. We apply these methods to peptides which bind the well-studied human MHC allele HLA-A*0201. A matrix which results from combining results of the two methods proved powerfully predictive under cross-validation. The new matrix was also tested on an external set of 160 binders to HLA-A*0201; it was able to recognize 135 (84%) of them.     

Boosted regression trees, multivariate adaptive regression splines and their two-step combinations with multiple linear regression or partial least squares to predict blood-brain barrier passage: a case study

The use of some unconventional non-linear modeling techniques, i.e. classification and regression trees and multivariate adaptive regression splines-based methods, was explored to model the blood-brain barrier (BBB) passage of drugs and drug-like molecules. The data set contains BBB passage values for 299 structural and pharmacological diverse drugs, originating from a structured knowledge-based database. Models were built using boosted regression trees (BRT) and multivariate adaptive regression splines (MARS), as well as their respective combinations with stepwise multiple linear regression (MLR) and partial least squares (PLS) regression in two-step approaches. The best models were obtained using combinations of MARS with either stepwise MLR or PLS. It could be concluded that the use of combinations of a linear with a non-linear modeling technique results in some improved properties compared to the individual linear and non-linear models and that, when the use of such a combination is appropriate, combinations using MARS as non-linear technique should be preferred over those with BRT, due to some serious drawbacks of the BRT approaches.     

Development of a generic flow-injection analysis method for compounds with a secondary amine or amide function, using an experimental design approach: Part II. Selection and evaluation of the chemical reaction parameters

A second part in the development of a generic flow injection analysis (FIA) method to determine compounds with a secondary amine or amide in their structure is described. This part consists in the selection and evaluation of the chemical reaction conditions. Sodium hypochlorite first converts the secondary amine or the amide to a primary amine. The latter reacts with o-phthalaldehyde (OPA) and a thiol (N-acetylcysteine (NAC)) to form a derivative which can be measured fluorimetrically. To investigate the influence of the different chemical reaction parameters on the peak height for a set of 31 pharmaceutical compounds, a quarter-fraction factorial design for six factors at two levels (2^6-2-resolution IV, 16 experiments) was executed. Effects on the responses were calculated for each compound. Parallel coordinate geometry (PCG) plots and principal component analysis (PCA) were also applied on the measured responses as aids in the interpretation of the results.