Carfilzomib alters the HLA-presented peptidome of myeloma cells and impairs presentation of peptides with aromatic C-termini.

Recent studies suggest that multiple myeloma is an immunogenic disease, which might be effectively targeted by antigen-specific T-cell immunotherapy. As standard of care in myeloma includes proteasome inhibitor therapy, it is of great importance to characterize the effects of this treatment on HLA-restricted antigen presentation and implement only robustly presented targets for immunotherapeutic intervention. Here, we present a study that longitudinally and semi-quantitatively maps the effects of the proteasome inhibitor carfilzomib on HLA-restricted antigen presentation. The relative presentation levels of 4780 different HLA ligands were quantified in an in vitro model employing carfilzomib treatment of MM.1S and U266 myeloma cells, which revealed significant modulation of a substantial fraction of the HLA-presented peptidome. Strikingly, we detected selective down-modulation of HLA ligands with aromatic C-terminal anchor amino acids. This particularly manifested as a marked reduction in the presentation of HLA ligands through the HLA allotypes A*23:01 and A*24:02 on MM.1S cells. These findings implicate that carfilzomib mediates a direct, peptide motif-specific inhibitory effect on HLA ligand processing and presentation. As a substantial proportion of HLA allotypes present peptides with aromatic C-termini, our results may have broad implications for the implementation of antigen-specific treatment approaches in patients undergoing carfilzomib treatment.

Reentrant condensation of proteins in solution induced by multivalent counterions.

Negatively charged globular proteins in solution undergo a condensation upon adding trivalent counterions between two critical concentrations C and C, C

Development of a fluorescence-based assay for screening of modulators of human organic anion transporter 1B3 (OATP1B3).

The organic anion transporting protein 1B3 (OATP1B3), formerly termed OATP8, is responsible for uptake and subsequent elimination of multiple amphipathic drugs by the liver. In silico methods for the prediction of transport rates for drugs and drug-like molecules might provide an important tool in drug development. Most prediction methods however require a large training set of in vitro experimental data in order to yield reliable results. To obtain these data, we have developed a fluorescence-based assay that allows screening a relatively high number of substances for their transporter affinity. HEK293 cells overexpressing OATP1B3 (HEK-OATP8) [Y. Cui, J. Konig, D. Keppler, Vectorial transport by double-transfected cells expressing the human uptake transporter SLC21A8 and the apical export pump ABCC2, Mol. Pharmacol. 60 (2001) 934-943.] were tested for transport of Fluo-3. Fluo-3 uptake could be seen in a concentration-dependent manner. Uptake can be inhibited completely by the addition of the known OATP1B3-inhibitor rifampicin proving that Fluo-3 is transported by OATP1B3. To verify the suitability of the system to identify modulators of OATP1B3, we tested known substrates for competitively inhibiting the Fluo-3 transport by giving them simultaneously with a 2muM Fluo-3-solution to the cells. The transport of Fluo-3 was decreased by all test substrates in a concentration dependent manner.

Novel formulation of nonlocal electrostatics.

The accurate modeling of the dielectric properties of water is crucial for many applications in physics, computational chemistry, and molecular biology. This becomes possible in the framework of nonlocal electrostatics, for which we propose a novel formulation allowing for numerical solutions for the nontrivial molecular geometries arising in the applications mentioned before. Our approach is based on the introduction of a secondary field psi, which acts as the potential for the rotation free part of the dielectric displacement field D. For many relevant models, the dielectric function of the medium can be expressed as the Green's function of a local differential operator. In this case, the resulting coupled Poisson (-Boltzmann) equations for psi and the electrostatic potential phi reduce to a system of coupled partial differential equations. The approach is illustrated by its application to simple geometries.

BioMiner--modeling, analyzing, and visualizing biochemical pathways and networks.

MOTIVATION: Understanding the biochemistry of a newly sequenced organism is an essential task for post-genomic analysis. Since, however, genome and array data grow much faster than biochemical information, it is necessary to infer reactions by comparative analysis. No integrated and easy to use software tool for this purpose exists as yet. RESULTS: We present a new software system--BioMiner--for analyzing and visualizing biochemical pathways and networks. BioMiner is based on a new comprehensive, extensible and reusable data model--BioCore--which can be used to model biochemical pathways and networks. As a first application we present PathFinder, a new tool predicting biochemical pathways by comparing groups of related organisms based on sequence similarity. We successfully tested PathFinder with a number of experiments, e.g. the well studied glycolysis in bacteria. Additionally, an application called PathViewer for the visualization of metabolic networks is presented. PathViewer is the first application we are aware of which supports the graphical comparison of metabolic networks of different organisms. AVAILABILITY: http://www.zbi.uni-saarland.de/chair/projects/BioMiner SUPPLEMENTARY INFORMATION: Additional information on experimental results can be found on our web site.

BALL--rapid software prototyping in computational molecular biology. Biochemicals Algorithms Library.

MOTIVATION: Rapid software prototyping can significantly reduce development times in the field of computational molecular biology and molecular modeling. Biochemical Algorithms Library (BALL) is an application framework in C++ that has been specifically designed for this purpose. RESULTS: BALL provides an extensive set of data structures as well as classes for molecular mechanics, advanced solvation methods, comparison and analysis of protein structures, file import/export, and visualization. BALL has been carefully designed to be robust, easy to use, and open to extensions. Especially its extensibility which results from an object-oriented and generic programming approach distinguishes it from other software packages. BALL is well suited to serve as a public repository for reliable data structures and algorithms. We show in an example that the implementation of complex methods is greatly simplified when using the data structures and functionality provided by BALL.