Automated benchmarking of peptide-MHC class I binding predictions

Motivation: Numerous in silico methods predicting peptide binding to major histocompatibility complex (MHC) class I molecules have been developed over the last decades. However, the multitude of available prediction tools makes it non-trivial for the end-user to select which tool to use for a given task. To provide a solid basis on which to compare different prediction tools, we here describe a framework for the automated benchmarking of peptide-MHC class I binding prediction tools. The framework runs weekly benchmarks on data that are newly entered into the Immune Epitope Database (IEDB), giving the public access to frequent, up-to-date performance evaluations of all participating tools. To overcome potential selection bias in the data included in the IEDB, a strategy was implemented that suggests a set of peptides for which different prediction methods give divergent predictions as to their binding capability. Upon experimental binding validation, these peptides entered the benchmark study. Results: The benchmark has run for 15 weeks and includes evaluation of 44 datasets covering 17 MHC alleles and more than 4000 peptide-MHC binding measurements. Inspection of the results allows the end-user to make educated selections between participating tools. Of the four participating servers, NetMHCpan performed the best, followed by ANN, SMM and finally ARB. Availability and implementation: Up-to-date performance evaluations of each server can be found online at http://tools.iedb.org/auto-bench/mhci/weekly. All prediction tool developers are invited to participate in the benchmark. Sign-up instructions are available at http://tools.iedb.org/auto-bench/mhci/join.Fil: Trolle, Thomas. Technical University of Denmark; DinamarcaFil: Metushi, Imir G.. La Jolla Institute for Allergy and Immunology; Estados UnidosFil: Greenbaum, Jason A.. La Jolla Institute for Allergy and Immunology; Estados UnidosFil: Kim, Yohan. La Jolla Institute for Allergy and Immunology; Estados UnidosFil: Sidney, John. La Jolla Institute for Allergy and Immunology; Estados UnidosFil: Lund, Ole. Technical University of Denmark; DinamarcaFil: Sette, Alessandro. La Jolla Institute for Allergy and Immunology; Estados UnidosFil: Peters, Bjoern. La Jolla Institute for Allergy and Immunology; Estados UnidosFil: Nielsen, Morten. Technical University of Denmark; Dinamarca. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; Argentin

Investigation of the Mechanism of Idiosyncratic Drug-induced Liver Injury

Idiosyncratic drug reactions represent a special problem because of their unpredictable nature, and idiosyncratic drug-induced liver injury (IDILI) is a major reason for drug withdrawal. Our objective was to investigate the mechanism of IDILI caused by isoniazid and amodiaquine. Isoniazid-induced liver injury was believed to be due to bioactivation of N-acetylhydrazine, a metabolite of isoniazid; however, that conclusion was based on a rat model with characteristics very different from isoniazid-induced IDILI in patients. I found that isoniazid is directly bioactivated and covalently binds to hepatic proteins; furthermore, mice are a better model for human isoniazid metabolism than rats. We found that mild isoniazid-induced liver injury in patients is associated with an increase in Th17 cells and IL-10-producing T cells. I also found anti-isoniazid antibodies in the serum of patients with isoniazid-induced liver failure. These results suggest that isoniazid-induced IDILI is immune-mediated rather than metabolic idiosyncrasy as previously believed. Treatment of mice with isoniazid failed to lead to significant liver injury. We postulated that this was because of immune tolerance; however, attempts to develop an animal model using mice with impaired immune tolerance were unsuccessful. Treatment of mice with amodiaquine resulted in mild liver injury that resolved despite continued treatment similar to the more common type of IDILI observed in humans. In this model, liver injury is immune-mediated with the initial injury mediated by natural killer cells, while the resolution of liver injury appears to involve the adaptive immune system because resolution was slower in Rag-/- mice. In summary, my studies have resulted a change in what is considered to be the mechanism of isoniazid-induced IDILI. We have developed an animal model of mild immune-mediated amodiaquine-induced liver injury, but we failed to develop a valid animal model of severe IDILI, most likely because the dominant immune response in the liver is tolerance.Ph

Assessment and Comparison of Vitreous Humor as an Alternative Matrix for Forensic Toxicology Screening by GC-MS.

Alternative specimens have been occasionally considered as substitutes for whole blood for postmortem toxicology testing. We studied the applicability of vitreous humor, and evaluated whether it would be suitable to replace (or augment) whole blood for routine drug screening. Results showed that from 51 autopsy cases, we were able to identify an aggregate of 209 findings in whole blood compared with 169 in vitreous. The total number of compounds identified was 71 for whole blood and 60 for vitreous humor. Quantitative analysis showed that whole-blood concentrations of trazodone were several fold higher than vitreous humor concentrations (1.42 ± 0.57 vs. 0.15 ± 0.05 mg/L, respectively) and similar results were also obtained for diazepam (0.37 ± 0.06 vs. 0.13 ± 0.01, respectively). For other drugs such as oxycodone, hydrocodone and doxylamine, a trend suggesting higher concentrations in vitreous humor vs. whole blood was observed; however, this was not significant. Our results are consistent with the limited work of other investigators, and suggest that vitreous humor could be an appropriate matrix for drug screening in postmortem toxicology

Evaluation of the Waters MassTrak LC-MS/MS Assay for Tacrolimus and a Comparison to the Abbott Architect Immunoassay.

BackgroundTacrolimus (Prograf, Advagraf, and FK-506) is the most commonly prescribed calcineurin inhibitor after kidney and liver transplantation. The use of tacrolimus (in conjunction with other drugs) has successfully contributed to the maintenance of solid organ allografts; however, it also exhibits toxic side effects. Therapeutic drug monitoring of tacrolimus is used as an aid to achieve drug concentrations within a narrow therapeutic window.MethodsThe Waters MassTrak Immunosuppressants assay (LC-MS/MS) for the quantification of tacrolimus in whole blood was evaluated for precision, linearity, lower limit of quantification, matrix effects, and accuracy. A method comparison with the Abbott Architect Tacrolimus immunoassay was also performed.ResultsThe mean concentration (nanograms per milliliter) and coefficient of variation for low, mid, and high patient pools were 0.6% ± 19.9%, 16.0% ± 5.4%, and 31.2% ± 5.8%, respectively. The MassTrak assay was linear from 0.5 to 30.0 ng/mL. Although the MassTrak and Architect assays correlated well (R = 0.97) for patient samples, the MassTrak assay displayed an average negative bias of 18.5% versus Architect (range of 0.0%-36.7%). Analysis of a certified tacrolimus reference material in human whole blood [European Reference Materials (ERM)-DA110a, LGC Standards] on both platforms failed to completely explain the observed difference for patient samples.ConclusionsTwo widely used assays for therapeutic drug monitoring of tacrolimus are not in agreement with one another. Care should be exercised when interpreting results generated on these 2 assay platforms

Evaluation of the Waters MassTrak LC-MS/MS Assay for Tacrolimus and a Comparison to the Abbott Architect Immunoassay.

BackgroundTacrolimus (Prograf, Advagraf, and FK-506) is the most commonly prescribed calcineurin inhibitor after kidney and liver transplantation. The use of tacrolimus (in conjunction with other drugs) has successfully contributed to the maintenance of solid organ allografts; however, it also exhibits toxic side effects. Therapeutic drug monitoring of tacrolimus is used as an aid to achieve drug concentrations within a narrow therapeutic window.MethodsThe Waters MassTrak Immunosuppressants assay (LC-MS/MS) for the quantification of tacrolimus in whole blood was evaluated for precision, linearity, lower limit of quantification, matrix effects, and accuracy. A method comparison with the Abbott Architect Tacrolimus immunoassay was also performed.ResultsThe mean concentration (nanograms per milliliter) and coefficient of variation for low, mid, and high patient pools were 0.6% ± 19.9%, 16.0% ± 5.4%, and 31.2% ± 5.8%, respectively. The MassTrak assay was linear from 0.5 to 30.0 ng/mL. Although the MassTrak and Architect assays correlated well (R = 0.97) for patient samples, the MassTrak assay displayed an average negative bias of 18.5% versus Architect (range of 0.0%-36.7%). Analysis of a certified tacrolimus reference material in human whole blood [European Reference Materials (ERM)-DA110a, LGC Standards] on both platforms failed to completely explain the observed difference for patient samples.ConclusionsTwo widely used assays for therapeutic drug monitoring of tacrolimus are not in agreement with one another. Care should be exercised when interpreting results generated on these 2 assay platforms

Titanium(IV) Complexes of Disulfide-Linked Schiff Bases

With the goal of preparing Ti­(IV) complexes bearing a sulfur-based redox function of possible use in electrocatalytic oxidations of alcohols at electrode surfaces, a series of seven 2,2′-dithiodianiline Schiff-base derivatives, including two new variations, were tested in reactions with Ti­(OR)₄ (R = ⁱPr, ^tBu). Instead of the expected dimetallic products of general formula [LTi­(OR)₂]₂, mononuclear species LTi­(OR)₂ were obtained, confirmed by crystallographic determinations to have an unprecedented, symmetrical, and macrocyclic arrangement with four-point binding to the metal center and with the disulfide moieties remaining uncoordinated. Cyclic voltammetry performed in CH₂Cl₂ displayed oxidations at potentials useful for fuel cells (+1.1–1.5 V vs Ag/AgCl), but despite the uncoordinated disulfide moieties, the complexes were reticent to engage in reduction processes

Direct Oxidation and Covalent Binding of Isoniazid to Rodent Liver and Human Hepatic Microsomes: Humans Are More Like Mice than Rats

Isoniazid (INH) is associated with serious liver injury and autoimmunity. Classic studies in rats indicated that a reactive metabolite of acetylhydrazine is responsible for the covalent binding and toxicity of INH. Studies in rabbits suggested that hydrazine might be the toxic species. However, these models involved acute toxicity with high doses of INH, and INH-induced liver injury in humans has very different features than such animal models. In this study, we demonstrated that a reactive metabolite of INH itself can covalently bind in the liver of mice and also to human liver microsomes. Covalent binding also occurred in rats, but it was much less than that in mice. We were able to trap the reactive metabolite of INH with <i>N</i>-α-acetyl-l-lysine in incubations with human liver microsomes. This suggests that the reactive intermediate of INH that leads to covalent binding is a diazohydroxide rather than a radical or carbocation because those reactive metabolites would be too reactive to trap in this way. Treatment of mice or rats with INH for up to 5 weeks did not produce severe liver injury. The alanine transaminase assay (ALT) is inhibited by INH, and other assays such as glutamate and sorbitol dehydrogenase (SDH) were better biomarkers of INH-induced liver injury. High doses of INH (200 and 400 mg/kg/day) for one week produced steatosis in rats and an increase in SDH, which suggests that it can cause mitochondrial injury. However, steatosis was not observed when INH was given at lower doses for longer periods of time to either mice or rats. We propose that covalent binding of the parent drug can contribute to INH-induced hepatotoxicity and autoimmunity. We also propose that these are immune-mediated reactions, and there are clinical data to support these hypotheses