A Translational Systems Pharmacology Model for Aß Kinetics in Mouse, Monkey, and Human.

A mechanistic model of amyloid beta production, degradation, and distribution was constructed for mouse, monkey, and human, calibrated and externally verified across multiple datasets. Simulations of single-dose avagacestat treatment demonstrate that the Aß42 brain inhibition may exceed that in cerebrospinal fluid (CSF). The dose that achieves 50% CSF Aß40 inhibition for humans (both healthy and with Alzheimer's disease (AD)) is about 1 mpk, one order of magnitude lower than for mouse (10 mpk), mainly because of differences in pharmacokinetics. The predicted maximal percent of brain Aß42 inhibition after single-dose avagacestat is higher for AD subjects (about 60%) than for healthy individuals (about 45%). The probability of achieving a normal physiological level for Aß42 in brain (1 nM) during multiple avagacestat dosing can be increased by using a dosing regimen that achieves higher exposure. The proposed model allows prediction of brain pharmacodynamics for different species given differing dosing regimens.

A Mathematical Modeling Approach to Understanding the Effect of Anti-Interleukin Therapy on Eosinophils.

Emerging T-helper type 2 (Th2 ) cytokine-based asthma therapies, such as tralokinumab, lebrikizumab (anti-interleukin (IL)-13), and mepolizumab (anti-IL-5), have shown differences in their blood eosinophil (EOS) response. To better understand these effects, we developed a mathematical model of EOS dynamics. For the anti-IL-13 therapies, lebrikizumab and tralokinumab, the model predicted an increase of 30% and 10% in total and activated EOS in the blood, respectively, and a decrease in the total and activated EOS in the airways. The model predicted a rapid decrease in total and activated EOS levels in blood and airways for the anti-IL-5 therapy mepolizumab. All model-based predictions were consistent with published clinical observations. The modeling approach provided insights into EOS response after treatment with Th2 -targeted therapies, and supports the hypothesis that an increase in blood EOS after anti-IL-13 therapy is part of the pharmacological action of these therapies.

A systems pharmacology perspective on the clinical development of Fatty Acid amide hydrolase inhibitors for pain.

The level of the endocannabinoid anandamide is controlled by fatty acid amide hydrolase (FAAH). In 2011, PF-04457845, an irreversible inhibitor of FAAH, was progressed to phase II clinical trials for osteoarthritic pain. This article discusses a prospective, integrated systems pharmacology model evaluation of FAAH as a target for pain in humans, using physiologically based pharmacokinetic and systems biology approaches. The model integrated physiological compartments; endocannabinoid production, degradation, and disposition data; PF-04457845 pharmacokinetics and pharmacodynamics, and cannabinoid receptor CB1-binding kinetics. The modeling identified clear gaps in our understanding and highlighted key risks going forward, in particular relating to whether methods are in place to demonstrate target engagement and pharmacological effect. The value of this modeling exercise will be discussed in detail and in the context of the clinical phase II data, together with recommendations to enable optimal future evaluation of FAAH inhibitors.CPT: Pharmacometrics Systems Pharmacology (2014) 3, e91; doi:10.1038/psp.2013.72; published online 15 January 2014.

Systems pharmacology models can be used to understand complex pharmacokinetic-pharmacodynamic behavior: an example using 5-lipoxygenase inhibitors.

Zileuton, a 5-lipoxygenase (5LO) inhibitor, displays complex pharmaokinetic (PK)-pharmacodynamic (PD) behavior. Available clinical data indicate a lack of dose-bronchodilatory response during initial treatment, with a dose response developing after ~1-2 weeks. We developed a quantitative systems pharmacology (QSP) model to understand the mechanism behind this phenomenon. The model described the release, maturation, and trafficking of eosinophils into the airways, leukotriene synthesis by the 5LO enzyme, leukotriene signaling and bronchodilation, and the PK of zileuton. The model provided a plausible explanation for the two-phase bronchodilatory effect of zileuton-the short-term bronchodilation was due to leukotriene inhibition and the long-term bronchodilation was due to inflammatory cell infiltration blockade. The model also indicated that the theoretical maximum bronchodilation of both 5LO inhibition and leukotriene receptor blockade is likely similar. QSP modeling provided interesting insights into the effects of leukotriene modulation.CPT: Pharmacometrics & Systems Pharmacology (2013) 2, e74; doi:10.1038/psp.2013.49; advance online publication 11 September 2013.

Reducing systems biology to practice in pharmaceutical company research; selected case studies.

Reviews of the productivity of the pharmaceutical industry have concluded that the current business model is unsustainable. Various remedies for this have been proposed, however, arguably these do not directly address the fundamental issue; namely, that it is the knowledge required to enable good decisions in the process of delivering a drug that is largely absent; in turn, this leads to a disconnect between our intuition of what the right drug target is and the reality of pharmacological intervention in a system such as a human disease state. As this system is highly complex, modelling will be required to elucidate emergent properties together with the data necessary to construct such models. Currently, however, both the models and data available are limited. The ultimate solution to the problem of pharmaceutical productivity may be the virtual human, however, it is likely to be many years, if at all, before this goal is realised. The current challenge is, therefore, whether systems modelling can contribute to improving productivity in the pharmaceutical industry in the interim and help to guide the optimal route to the virtual human. In this context, this chapter discusses the emergence of systems pharmacology in drug discovery from the interface of pharmacokinetic-pharmacodynamic modelling and systems biology. Examples of applications to the identification of optimal drug targets in given pathways, selecting drug modalities and defining biomarkers are discussed, together with future directions.

EI of the Phosphotransferase System of Escherichia coli: Mathematical Modeling Approach to Analysis of Its Kinetic Properties.

The mathematical model of the operation of the first enzyme of the Escherichia coli phosphotransferase system, EI, is proposed. Parameters of the kinetic model describing the operation of EI under different conditions are identified on the basis of a large amount of known experimental data. The verified model is employed to predict modes of operation of EI under both in vivo physiological conditions and in vitro nonphysiological conditions. The model predicts that under in vivo physiological conditions, the rate of phosphotransfer from EI to the second protein of the phosphotransferase system HPr by the dimer is much higher than by the monomer. A hypothesis is proposed on the basis of calculations that the transfer by a monomer plays a role in the regulation of chemotaxis. At submicromolar pyruvate concentration, the model predicts nonmonotonic dependence of the phosphotransfer rate on the substrate (PEP) concentration.

[A kinetic model of beta-galactosidase of Escherichia coli].

On the basis of previously published experimental data, the catalytic cycle of Escherichia coli galactosidase has been reconstructed. The enzyme plays a key role in the transcription regulation of lac operon. Using the proposed scheme, we have built a kinetic model that takes into account the reactions of hydrolysis, isomerization as well as galactosylation. Using the experimental data and optimization algorithms, all parameters of the model have been estimated. On the basis of the model, the features of beta-galactosidase functioning have been predicted in a wide range of conditions.

Optimization of antimicrobial drug gramicidin S dosing regime using biosimulations.

In this paper we have developed a model of antimicrobial effect of gramicidin S. This model has allowed us to predict the dependence of antimicrobial effect of the drug applied as oral melting tablets on dosage, time of resorption and minimal inhibitory concentration (MIC) of the drug characterizing its ability to kill different bacteria. The model has been employed to optimize dosing regime of gramicidin S containing drug Grammidin. Efficacy of the drug has been studied for the diverse gram-positive and gram-negative bacteria with different MIC. The number of bacteria located in the oral cavity and killed by one-pass administration of the drug (resolution of one tablet) has been calculated under condition of various dosing regimes. Based on the simulation results it has been found that (1) twofold prolongation of prescribed resorption time (from 30 to 60min) of the tablet comprising standard dosage of 3mg of gramicidin S results in 1.5-fold increase in efficacy, (2) 1.5-fold decrease in gramicidin S dosage (from 3 to 2mg per administration) under condition of holding prescribed resorption time (30min) does not lead to any considerable decrease in the efficacy of the drug.

[A kinetic model of functioning and regulation of Escherichia coli isocitrate dehydrogenase].

A Rapid Equilibrium Random Bi Ter mechanism of formation of two dead-end complexes was proposed to describe the experimental data on the functioning of E. coli isocitrate dehydrogenase (IDH). A kinetic model for the enzyme functioning was constructed, which assumes that it is regulated through reversible phosphorylation by its kinase/phosphatase, which in turn is regulated by IDH substrates and central metabolites such as pyruvate (Pyr), 3-phosphoglycerate (3-PG), and AMP. It was shown using the model that increasing the concentration of these effectors results in an increase of the active part of IDH, thus leading to an increase in the Krebs cycle flux. We predict that the ratio of the phosphorylated and free forms of IDH (IDHP/IDH) is more sensitive to AMP, NADPH, and isocitrate concentrations than to Pyr and 3-PG. The model allows a realistic prediction of changes in the IDHP/IDH ratio, which would occur under changes of biosynthetic and energetic loading of the E. coli cell.

[A kinetic model of the cytochrome bf complex. Evaluation of kinetic parameters]. / Kineticheskaia model' tsitokhromnogo bf-kompleksa. Otsenka kineticheskikh parametrov.

A kinetic model of the cytochrome bf complex was developed on the assumption that the Q-cycle operates. The bf complex was considered as a membrane enzyme catalyzing the electron transfer from plastoquinol to plastocyanine, which is coupled with proton translocation from the chloroplast stroma to the thylakoid lumen. The dependence of the electron transfer rates on the value of the transmembrane electric potential was taken into account. The model was applied to describe the experimental data on the flash-induced turnover of cytochromes b, plastocyanine, and the kinetics of proton deposition in the thylakoid lumen. The estimation of model parameters was performed.

Signal processing at the Ras circuit: what shapes Ras activation patterns?

A systems biology approach is applied to gain a quantitative understanding of the integration of signalling by the small GTPase Ras. The Ras protein acts as a critical switch in response to signals that determine the cell's fate. In unstimulated cells, Ras switching between an inactive GDP-binding and active GTP-binding state is controlled by the intrinsic catalytic activities of Ras. The calculated high sensitivity of the basal Ras-GTP fraction to changes in the rate constant of GTP-hydrolysis by Ras can account for the carcinogenic potential of Ras mutants with decreased GTPase activities. Extracelluar stimuli initiate Ras interactions with GDP/GTP exchange factors such as SOS, and GTP-hydrolysis activating proteins such as RasGAP. Our data on freshly isolated hepatocytes stimulated with epidermal growth factor (EGF) show transient SOS activation and sustained Ras-GTP patterns. We demonstrate that these dose-response data can only be explained by transient RasGAP activitation, and not by merely switching off the SOS signal, e.g. by inhibitory phosphorylation of SOS. A transient RasGAP activity can be brought about by a number of mechanisms. A comprehensive kinetic model of the EGF receptor (EGFR) network was developed to explore feasible molecular scenarios, including the receptor-mediated recruitment of SOS and RasGAP to the plasma membrane, phosphorylation of RasGAP and p190 RhoGAP by soluble tyrosine kinases, and RasGAP interactions with phosphoinositides and p190 RhoGAP. We show that a transient RasGAP association with EGFR followed by the capture of RasGAP through the formation of complexes with p190 RhoGAP can account for data on hepatocytes. In summary, our results demonstrate that a combination of experimental monitoring and integrated dynamic analysis is capable of dissecting regulatory mechanisms that govern cellular signal transduction.

Kinetic model of imidazologlycerol-phosphate synthetase from Escherichia coli.

Based on the available experimental data, we developed a kinetic model of the catalytic cycle of imidazologlycerol-phosphate synthetase from Escherichia coli accounting for the synthetase and glutaminase activities of the enzyme. The rate equations describing synthetase and glutaminase activities of imidazologlycerol-phosphate synthetase were derived from this catalytic cycle. Using the literature data, we evaluated all kinetic parameters of the rate equations characterizing individually synthetase and glutaminase activities as well as the contribution of each activity depending on concentration of the substrates, products, and effectors. As shown, in the presence of 5 -phosphoribosylformimino-5-aminoimidazolo-4-carboxamideribonucleotide (ProFAR) and imidazologlycerol phosphate (IGP) glutaminase activity dominates over synthetase activity at sufficiently low concentrations of 5 -phosphoribulosylformimino-5-aminoimidazolo-4-carboxamideribonucleotide (PRFAR). Increased PRFAR concentrations resulted in decreased contribution of glutaminase activity and, consequently, increased the contribution of synthetase activity in the enzyme functioning.

[Kinetic model of primary processes of photosynthesis in chloroplasts. Fast phase of chlorophyll fluorescence induction under light of various intensity]. / Kineticheskaia model' pervichnykh protsessov fotosinteza v khloroplastakh. Opisanie bystroi fazy induktsii fluorestsentsii khlorofilla pri razlichnoi intensivnosti sveta.

A kinetic model was developed, which describing the system of generation and consumption of the transmembrane electrochemical proton potential delta mu H+ in primary photosynthetic processes. The model describes the catalytic cycles of photosystems I and II and the cytochrome b/f complex, as well as the ATP synthesis and passive leakage of H+, K+ [symbol: see text] Cl- ions through the thylakoid membrane. The dependence of the electron transfer rates on the value of transmembrane electric potential was taken into account. The model was applied to describe the experimental data on the registration of the fast phase of fluorescence induction. The model gives a realistic description of the fast phase of induction curves at different light intensities (from high to low).

Remediation of ammonia-rich minewater in constructed wetlands.

A three-year study of ammonia removal from minewater was carried out employing constructed wetland systems (surface flow wetland and subsurface flow wetland cells) at the former Woodey Mine in West Yorkshire, UK. The 1.4 Ha surface flow wetland (constructed in 1995) reduced the ammonia concentration from 3.5 - 45 mg l(-1) to < 2.3 mg l(-1) during the first half of the study and to essentially zero in the last year (2000 - 2001). About 25% of contained ammonia was converted to nitrate, about 10% was consumed by the plants and up to 30% was converted to nitrogen gas. This maturation effect was attributed to increased depth of sludge from sedimentation of ochre, providing increased surface area for immobilisation of ammonia oxidising bacteria. The surface flow wetland finally removed 2.3 g m(-2) day(-1) ammonia in comparison with 3.8 g m(-2) day(-1) for the subsurface flow (pea gravel) wetland cells, constructed for the present work and dosed with ammonium salts. Removal of ammonia by both systems was consistent with well-established mechanisms of nitrification and denitrification. It was also consistent with ammonia removal in wastewater wetland systems, although the greater aeration in the minewater systems obviated the need for special aeration cycles. The general role of wetland plants in such aerated conditions was attributed to maintaining hydraulic conditions (such as hydraulic efficiency and hydraulic resistance of substratum in subsurface flow systems) in the wetlands and providing a suspended solids filter for minewater.

[Kinetic modeling of energy metabolism and generation of active forms of oxygen in hepatocyte mitochondria]. / Kineticheskoe modelirovaniie énergeticheskogo metabolizma i generatsii aktivnyhkh form kisloroda v mitokhondriiakh gepatotsita.

Direct nonenzymatic oxidation of semiquinone by oxygen is one of the main sources of superoxide radicals (O2.-) in mitochondria. By using all the known data on hepatocyte mitochondria, we have revealed the correlation between the rate of superoxide generation by the bc1 complex and the transmembrane potential (delta psi). If the main electrogenic stage of the Q cycle is suggested to be the electron transfer between the cytochrome b hemes, then the rate of superoxide generation sharply increases when delta psi grows from 150 mV to 180 mV. However, this interrelation is ambiguous. Indeed, the increase of the generation rate with the growth of the potential can occur faster when succinate dehydrogenase is inhibited by malonate than when external ADP is exhausted. When the potential is changed by adding phosphate or potassium (K+), the rate of O2.- production remains constant, although the comparison of the rate values at the same delta psi reveals the effect of phosphate or potassium. It turned out that the rate of O2.- generation is a function of delta mu H rather than any of its components. Phosphate and K+ have practically no influence on delta mu H, since the change in delta psi is compensated by delta pH. The rate of superoxide generation by the bc1 complex is a multiple function of the electron-transfer activity of enzymes, the processes determining the membrane potential (e.g., loading), and of the oxygen concentration. The kinetic model proposed in this work may serve a tool to understand how the superoxide production is regulated.

Kinetics and control of oxidative phosphorylation in rat liver mitochondria after chronic ethanol feeding.

Changes in the kinetics and regulation of oxidative phosphorylation were characterized in isolated rat liver mitochondria after 2 months of ethanol consumption. Mitochondrial energy metabolism was conceptually divided into three groups of reactions, either producing protonmotive force (Deltap) (the respiratory subsystem) or consuming it (the phosphorylation subsystem and the proton leak). Manifestation of ethanol-induced mitochondrial malfunctioning of the respiratory subsystem was observed with various substrates; the respiration rate in State 3 was inhibited by 27+/-4% with succinate plus amytal, by 20+/-4% with glutamate plus malate, and by 17+/-2% with N,N,N',N'-tetramethyl-p-phenylenediamine/ascorbate. The inhibition of the respiratory activity correlated with the lower activities of cytochrome c oxidase, the bc(1) complex, and the ATP synthase in mitochondria of ethanol-fed rats. The block of reactions consuming the Deltap to produce ATP (the phosphorylating subsystem) was suppressed after 2 months of ethanol feeding, whereas the mitochondrial proton leak was not affected. The contributions of Deltap supply (the respiratory subsystem) and Deltap demand (the phosphorylation and the proton leak) to the control of the respiratory flux were quantified as the control coefficients of these subsystems. In State 3, the distribution of control exerted by different reaction blocks over respiratory flux was not significantly affected by ethanol diet, despite the marked changes in the kinetics of individual functional units of mitochondrial oxidative phosphorylation. This suggests the operation of compensatory mechanisms, when control redistributes among the different components within the same subsystem.

[Regulation levels of photosynthesis processes]. / Urovni reguliatsii protsessov fotosinteza.

The basic mechanisms of kinetic regulation of photosynthetic processes are considered, which provide a strict light regulation of electron transfer in photosynthetic reaction centers and a more flexible regulation at the level of interaction of photosystems, transmembrane ion fluxes and coupling with dark reactions of the Calvin cycle. A generalized model was developed, which integrates the modern knowledge about photosynthetic processes of higher plants. The general principles of multilevel regulation in photosynthetic systems are discussed.

Quantification of short term signaling by the epidermal growth factor receptor.

During the past decade, our knowledge of molecular mechanisms involved in growth factor signaling has proliferated almost explosively. However, the kinetics and control of information transfer through signaling networks remain poorly understood. This paper combines experimental kinetic analysis and computational modeling of the short term pattern of cellular responses to epidermal growth factor (EGF) in isolated hepatocytes. The experimental data show transient tyrosine phosphorylation of the EGF receptor (EGFR) and transient or sustained response patterns in multiple signaling proteins targeted by EGFR. Transient responses exhibit pronounced maxima, reached within 15-30 s of EGF stimulation and followed by a decline to relatively low (quasi-steady-state) levels. In contrast to earlier suggestions, we demonstrate that the experimentally observed transients can be accounted for without requiring receptor-mediated activation of specific tyrosine phosphatases, following EGF stimulation. The kinetic model predicts how the cellular response is controlled by the relative levels and activity states of signaling proteins and under what conditions activation patterns are transient or sustained. EGFR signaling patterns appear to be robust with respect to variations in many elemental rate constants within the range of experimentally measured values. On the other hand, we specify which changes in the kinetic scheme, rate constants, and total amounts of molecular factors involved are incompatible with the experimentally observed kinetics of signal transfer. Quantitation of signaling network responses to growth factors allows us to assess how cells process information controlling their growth and differentiation.

Induction of nonselective permeability of the inner membrane in deenergized mitochondria.

Induction of the nonselective cyclosporin-sensitive pore in the inner mitochondrial membrane under conditions of complete dissipation of ion gradients and transmembrane potential was studied. This approach allows the kinetics of Ca2+-dependent pore opening and the preceding processes of induction to be studied separately. The effects of mitochondrial heterogeneity were also minimized. We found that the kinetics of pore opening can be described by a minimal two-step scheme where only the rate constant at the first step depends on Ca2+ concentration. Oxidation of pyridine nucleotides in the matrix caused a slow transition in the pore complex and decreased the apparent dissociation constant of the Ca2+-binding site from >1 mM to approximately 30 microM. N-Ethylmaleimide (but not disulfide-reducing agents) prevented and slowly reverted the pore induction process. Data suggesting allosteric modulation of the pore by pyridine nucleotides are presented.

Kinetic mechanisms of biological regulation in photosynthetic organisms.

Principles of regulation on different levels of photosynthetic apparatus are discussed. Mathematical models of isolated photosynthetic reaction centers and general system of energy transduction in chloroplast are developed. A general approach to model these complex metabolic systems is suggested. Regulatory mechanisms in plant cell are correlated with the different patterns of fluorescence induction curve at different internal physiological states of the cells and external (environmental) conditions. Light regulation inside photosynthetic reaction centers, diffusion processes in thylakoid membrane, generation of transmembrane electrochemical potential, coupling with processes of CO(2) fixation in Calvin Cycle are considered as stages of control of energy transformation in chloroplasts in their connection with kinetic patterns of fluorescence induction curves and other spectrophotometric data.