Identifying Drug Effects via Pathway Alterations using an Integer Linear Programming Optimization Formulation on Phosphoproteomic Data

Understanding the mechanisms of cell function and drug action is a major endeavor in the pharmaceutical industry. Drug effects are governed by the intrinsic properties of the drug (i.e., selectivity and potency) and the specific signaling transduction network of the host (i.e., normal vs. diseased cells). Here, we describe an unbiased, phosphoproteomicbased approach to identify drug effects by monitoring drug-induced topology alterations. With the proposed method, drug effects are investigated under several conditions on a cell-type specific signaling network. First, starting with a generic pathway made of logical gates, we build a cell-type specific map by constraining it to fit 13 key phopshoprotein signals under 55 experimental cases. Fitting is performed via a formulation as an Integer Linear Program (ILP) and solution by standard ILP solvers; a procedure that drastically outperforms previous fitting schemes. Then, knowing the cell topology, we monitor the same key phopshoprotein signals under the presence of drug and cytokines and we re-optimize the specific map to reveal the drug-induced topology alterations. To prove our case, we make a pathway map for the hepatocytic cell line HepG2 and we evaluate the effects of 4 drugs: 3 selective inhibitors for the Epidermal Growth Factor Receptor (EGFR) and a non selective drug. We confirm effects easily predictable from the drugs’ main target (i.e. EGFR inhibitors blocks the EGFR pathway) but we also uncover unanticipated effects due to either drug promiscuity or the cell’s specific topology. An interesting finding is that the selective EGFR inhibitor Gefitinib is able to inhibit signaling downstream the Interleukin-1alpha (IL-1α) pathway; an effect that cannot be extracted from binding affinity based approaches. Our method represents an unbiased approach to identify drug effects on a small to medium size pathways and is scalable to larger topologies with any type of signaling perturbations (small molecules, 3 RNAi etc). The method is a step towards a better picture of drug effects in pathways, the cornerstone in identifying the mechanisms of drug efficacy and toxicity

A new approach for the fabrication of microscale lipid bilayers at glass pipets : application to quantitative passive permeation visualization

A new method of planar bilayer lipid membrane (BLM) formation is presented that allows stable, solvent-free lipid bilayers exhibiting high seal resistances to be formed rapidly, easily and reproducibly. Using these bilayers the passive permeation of a series of carboxylic acids is investigated, to determine quantitatively the trend in permeability with lipophilicity of the acid. BLMs are formed at the tip openings of pulled theta pipets, and the rate of permeation of each carboxylic acid across the bilayer, from within the pipet into the bulk solution is determined. This is achieved through spatially-resolved measurements of the pH change that occurs upon the permeation of the weak acid, visualized using a pH-sensitive fluorophore with a confocal laser scanning microscope. The extracted fluorescence profiles are matched to finite element method (FEM) simulations, to allow the associated permeation coefficient for each weak acid to be determined with high accuracy, since this is the only adjustable parameter used to fit the experimental data. For bilayers formed in this way, the weak acids show increasing permeability with lipophilicity. Furthermore, the arrangement allows the effect of a trans-membrane electric field on permeation to be explored. For both propanoic and hexanoic acid it is found that an applied electric field enhances molecular transport, which is attributed to the formation of pores within the membrane

Passive membrane permeability: beyond the standard solubility-diffusion model

The spontaneous diffusion of solutes through lipid bilayers is still a challenge for theoretical predictions. Since permeation processes remain beyond the capabilities of unbiased molecular dynamics simulations, an alternative strategy is currently adopted to gain insight into their mechanism and time scale. This is based on a monodimensional description of the translocation process only in terms of the position of the solute along the normal to the lipid bilayer, which is formally expressed in the solubility-diffusion model. Actually, a role of orientational and conformational motions has been pointed out, and the use of advanced simulation techniques has been proposed to take into account their effect. Here, we discuss the limitations of the standard solubility-diffusion approach and propose a more general description of membrane translocation as a diffusion process on a free energy surface, which is a function of the translational and rotational degrees of freedom of the molecule. Simple expressions for the permeability coefficient are obtained under suitable conditions. For fast solute reorientation, the classical solubility-diffusion equation is recovered. Under the assumption that well-defined minima can be identified on the free energy landscape, a mechanistic interpretation of the permeability coefficient in terms of all possible permeation paths is given

A role for Rhesus factor Rhcg in renal ammonium excretion and male fertility.

The kidney has an important role in the regulation of acid-base homeostasis. Renal ammonium production and excretion are essential for net acid excretion under basal conditions and during metabolic acidosis. Ammonium is secreted into the urine by the collecting duct, a distal nephron segment where ammonium transport is believed to occur by non-ionic NH(3) diffusion coupled to H(+) secretion. Here we show that this process is largely dependent on the Rhesus factor Rhcg. Mice lacking Rhcg have abnormal urinary acidification due to impaired ammonium excretion on acid loading-a feature of distal renal tubular acidosis. In vitro microperfused collecting ducts of Rhcg(-/-) acid-loaded mice show reduced apical permeability to NH(3) and impaired transepithelial NH(3) transport. Furthermore, Rhcg is localized in epididymal epithelial cells and is required for normal fertility and epididymal fluid pH. We anticipate a critical role for Rhcg in ammonium handling and pH homeostasis both in the kidney and the male reproductive tract.Journal ArticleResearch Support, Non-U.S. Gov'tinfo:eu-repo/semantics/publishe