Data-driven large-scale genomic analysis reveals an intricate phylogenetic and functional landscape in J-domain proteins.

The 70-kD heat shock protein (Hsp70) chaperone system is a central hub of the proteostasis network that helps maintain protein homeostasis in all organisms. The recruitment of Hsp70 to perform different and specific cellular functions is regulated by the J-domain protein (JDP) co-chaperone family carrying the small namesake J-domain, required to interact and drive the ATPase cycle of Hsp70s. Besides the J-domain, prokaryotic and eukaryotic JDPs display a staggering diversity in domain architecture, function, and cellular localization. Very little is known about the overall JDP family, despite their essential role in cellular proteostasis, development, and its link to a broad range of human diseases. In this work, we leverage the exponentially increasing number of JDP gene sequences identified across all kingdoms owing to the advancements in sequencing technology and provide a broad overview of the JDP repertoire. Using an automated classification scheme based on artificial neural networks (ANNs), we demonstrate that the sequences of J-domains carry sufficient discriminatory information to reliably recover the phylogeny, localization, and domain composition of the corresponding full-length JDP. By harnessing the interpretability of the ANNs, we find that many of the discriminatory sequence positions match residues that form the interaction interface between the J-domain and Hsp70. This reveals that key residues within the J-domains have coevolved with their obligatory Hsp70 partners to build chaperone circuits for specific functions in cells.

Light-Switchable Buffers.

A visible light-switchable buffer system based on a merocyanine photoacid is presented. Para-substitution of the indolium side with a methoxy group affords a compound suitable for making hydrolytically stable aqueous buffers whose pH can be tuned between 7 and 4 using 500 nm light.

Mathematical Modelling of Alternative Pathway of Complement System.

The complement system (CS) is an integral part of innate immunity and can be activated via three different pathways. The alternative pathway (AP) has a central role in the function of the CS. The AP of complement system is implicated in several human disease pathologies. In the absence of triggers, the AP exists in a time-invariant resting state (physiological steady state). It is capable of rapid, potent and transient activation response upon challenge with a trigger. Previous models of AP have focused on the activation response. In order to understand the molecular machinery necessary for AP activation and regulation of a physiological steady state, we built parsimonious AP models using experimentally supported kinetic parameters. The models further allowed us to test quantitative roles played by negative and positive regulators of the pathway in order to test hypotheses regarding their mechanisms of action, thus providing more insight into the complex regulation of AP.

Mechanics of Allostery: Contrasting the Induced Fit and Population Shift Scenarios.

In allosteric proteins, binding a ligand can affect function at a distant location, for example, by changing the binding affinity of a substrate at the active site. The induced fit and population shift models, which differ by the assumed number of stable configurations, explain such cooperative binding from a thermodynamic viewpoint. Yet, understanding what mechanical principles constrain these models remains a challenge. Here, we provide an empirical study on 34 proteins supporting the idea that allosteric conformational change generally occurs along a soft elastic mode presenting extended regions of high shear. We argue, based on a detailed analysis of how the energy profile along such a mode depends on binding, that in the induced fit scenario, there is an optimal stiffness ka∗ ∼ 1/N for cooperative binding, where N is the number of residues. We find that the population shift scenario is more robust to mutations affecting stiffness because binding becomes more and more cooperative with stiffness up to the same characteristic value ka∗, beyond which cooperativity saturates instead of decaying. We numerically confirm these findings in a nonlinear mechanical model. Dynamical considerations suggest that a stiffness of order ka∗ is favorable in that scenario as well, supporting that for proper function, proteins must evolve a functional elastic mode that is softer as their size increases. In consistency with this view, we find a fair anticorrelation between the stiffness of the allosteric response and protein size in our data set.

Target engagement and cellular fate of otelixizumab: a repeat dose escalation study of an anti-CD3ε mAb in new-onset type 1 diabetes mellitus patients.

AIMS: This paper describes the pharmacological findings from a study where otelixizumab, an anti-CD3ɛ mAb, was dosed in new onset Type 1 diabetes mellitus (NOT1DM) patients. This is the first time that the full dose-response of an anti-CD3ɛ mAb has been investigated in the clinic. The data have been validated using a previously developed pharmacokinetic/pharmacodynamic (PK/PD) model of otelixizumab to simulate the interplay between drug administration, CD3ɛ target engagement and downmodulation. METHODS: Patients were randomized to control or active treatment with otelixizumab (1:4), administered via infusion over 6 days, in a dose-ascending study consisted of three cohorts (n = 10 per cohort) at doses of 9, 18 or 27 mg respectively. The study allowed quantification of otelixizumab PK, CD3ɛ target engagement and its pharmacodynamic effect (CD3ε/TCR modulation on circulating T lymphocytes). RESULTS: Otelixizumab concentrations increased and averaged to 364.09 (54.3), 1625.55 (72.5) and 2781.35 (28.0) ng ml-1 (Geom.mean, %CV) at the 9, 18 and 27 mg dose respectively. CD3ɛ target engagement was found to be rapid (within the first 30 min), leading to a receptor occupancy of ~60% within 6 h of dosing in all three doses. A dose-response relationship was observed with the two highest doses achieving a ~90% target engagement and consequential CD3ɛ/TCR downmodulation by Day 6. CONCLUSIONS: Data from this study revealed maximum target engagement and CD3ɛ/TCR modulation is achieved at doses of 18, 27 mg of otelixizumab. These findings can be useful in guiding dose selection in clinical trials with anti-CD3ɛ mAbs.

Vibrational entropy estimation can improve binding affinity prediction for non-obligatory protein complexes.

Predicting the binding affinity between protein monomers is of paramount importance for the understanding of thermodynamical and structural factors that guide the formation of a complex. Several numerical techniques have been developed for the calculation of binding affinities with different levels of accuracy. Approaches such as thermodynamic integration and Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) methodologies which account for well defined physical interactions offer good accuracy but are computationally demanding. Methods based on the statistical analysis of experimental structures are much cheaper but good performances have only been obtained throughout consensus energy functions based on many different molecular descriptors. In this study we investigate the importance of the contribution to the binding free energy of the entropic term due to the fluctuations around the equilibrium structures. This term, which we estimated employing an elastic network model, is usually neglected in most statistical approaches. Our method crucially relies on a novel calibration procedure of the elastic network force constant. The residue mobility profile is fitted to the one obtained through a short all-atom molecular dynamics simulation on a subset of residues only. Our results show how the proper consideration of vibrational entropic contributions can improve the quality of the prediction on a set of non-obligatory protein complexes whose binding affinity is known.

Analysis of variability in length of sleep state bouts reveals memory-free sleep subcomponents consistent among primary insomnia patients.

The statistical distributions of bout lengths for the different (macro) sleep states (wake, N1, N2, N3, and REM sleep) are essential to understanding whether any memory-free subcomponent ("micro state") is involved in the organization of sleep. Micro state detection can be prevented by the fusion of data including various sources of variability, in particular by the differences in sleep architecture between individuals, along sleep time (or nighttime), or between different nights. In this analysis, a mathematical model of sleep was adopted to disentangle these features and advance the understanding of the dynamics and mechanisms of sleep and its states. The analysis involved 116 primary insomnia patients taking placebo before going to bed and undergoing polysomnography for one night. The individual sequences of macro sleep states had been previously modeled with a mixed-effect nonhomogeneous modified Markov chain model, from which individual conditional probability distributions for the bout durations were derived in this analysis as functions of sleep time. The probability distributions, affected by neither subject, night-time, nor multiple-night pooling, substantially changed at » and ¾ sleep time, had modified exponential shape, and were best described as the sum of one to four exponentials, depending on the sleep state. The time constants and proportions of bouts contributing to each exponential were similar in the different subjects, changing over sleep time. Variability in bout durations thus indicated the presence of multiple memory-free sleep subcomponents whose mean residence times and access probabilities could be identified and shown to be consistent among the studied subjects. NEW & NOTEWORTHY We present a new methodology for deriving, from polysomnography data, the individual conditional probability for the duration of the bouts of wake, N1, N2, N3, and REM sleep. We evaluated the variability of this probability within and between primary insomnia patients and along sleep time. The multiexponential shapes of the probability distributions within the individuals revealed memory-free mechanisms and sleep subcomponents with consistent features in the studied population.

In vivo affinity and target engagement in skin and blood in a first-time-in-human study of an anti-oncostatin M monoclonal antibody.

AIMS: The oncostatin M (OSM) pathway drives fibrosis, inflammation and vasculopathy, and is a potential therapeutic target for inflammatory and fibrotic diseases. The aim of this first-time-in-human experimental medicine study was to assess the safety, tolerability, pharmacokinetics and target engagement of single subcutaneous doses of GSK2330811, an anti-OSM monoclonal antibody, in healthy subjects. METHODS: This was a phase I, randomized, double-blind, placebo-controlled, single-dose escalation, first-time-in-human study of subcutaneously administered GSK2330811 in healthy adults (NCT02386436). Safety and tolerability, GSK2330811 pharmacokinetic profile, OSM levels in blood and skin, and the potential for antidrug antibody formation were assessed. The in vivo affinity of GSK2330811 for OSM and target engagement in serum and skin blister fluid (obtained via a skin suction blister model) were estimated using target-mediated drug disposition (TMDD) models in combination with compartmental and physiology-based pharmacokinetic (PBPK) models. RESULTS: Thirty subjects were randomized to receive GSK2330811 and 10 to placebo in this completed study. GSK2330811 demonstrated a favourable safety profile in healthy subjects; no adverse events were serious or led to withdrawal. There were no clinically relevant trends in change from baseline in laboratory values, with the exception of a reversible dose-dependent reduction in platelet count. GSK2330811 exhibited linear pharmacokinetics over the dose range 0.1-6 mg kg-1 . The estimated in vivo affinity (nM) of GSK2330811 for OSM was 0.568 [95% confidence interval (CI) 0.455, 0.710] in the compartmental with TMDD model and 0.629 (95% CI 0.494, 0.802) using the minimal PBPK with TMDD model. CONCLUSIONS: Single subcutaneous doses of GSK2330811 were well tolerated in healthy subjects. GSK2330811 demonstrated sufficient affinity to achieve target engagement in systemic circulation and target skin tissue, supporting the progression of GSK2330811 clinical development.

Toward a unified scoring function for native state discrimination and drug-binding pocket recognition.

Protein folding and receptor-ligand recognition are fundamental processes for any living organism. Although folding and ligand recognition are based on the same chemistry, the existing empirical scoring functions target just one problem: predicting the correct fold or the correct binding pose. We here introduce a statistical potential which considers moieties as fundamental units. The scoring function is able to deal with both folding and ligand pocket recognition problems with a performance comparable to the scoring functions specifically tailored for one of the two tasks. We foresee that the capability of the new scoring function to tackle both problems in a unified framework will be a key to deal with the induced fit phenomena, in which a target protein changes significantly its conformation upon binding. Moreover, the new scoring function might be useful in docking protocols towards intrinsically disordered proteins, whose flexibility cannot be handled with the available docking software.

MPBPK-TMDD models for mAbs: alternative models, comparison, and identifiability issues.

The aim of the present study was to evaluate model identifiability when minimal physiologically-based pharmacokinetic (mPBPK) models are integrated with target mediated drug disposition (TMDD) models in the tissue compartment. Three quasi-steady-state (QSS) approximations of TMDD dynamics were explored: on (a) antibody-target complex, (b) free target, and (c) free antibody concentrations in tissue. The effects of the QSS approximations were assessed via simulations, taking as reference the mPBPK-TMDD model with no simplifications. Approximation (a) did not affect model-derived concentrations, while with the inclusion of approximation (b) or (c), target concentration profiles alone, or both drug and target concentration profiles respectively deviated from the reference model profiles. A local sensitivity analysis was performed, highlighting the potential importance of sampling in the terminal pharmacokinetic phase and of collecting target concentration data. The a priori and a posteriori identifiability of the mPBPK-TMDD models were investigated under different experimental scenarios and designs. The reference model and QSS approximation (a) on antibody-target complex were both found to be a priori identifiable in all scenarios, while under the further inclusion of QSS approximation (b) target concentration data were needed for a priori identifiability to be preserved. The property could not be assessed for the model including all three QSS approximations. A posteriori identifiability issues were detected for all models, although improvement was observed when appropriate sampling and dose range were selected. In conclusion, this work provides a theoretical framework for the assessment of key properties of mathematical models before their experimental application. Attention should be paid when applying integrated mPBPK-TMDD models, as identifiability issues do exist, especially when rich study designs are not feasible.

CCL20 neutralization by a monoclonal antibody in healthy subjects selectively inhibits recruitment of CCR6+ cells in an experimental suction blister.

AIMS: GSK3050002, a humanized IgG1κ antibody with high binding affinity to human CCL20, was administered in a first-in-human study to evaluate safety, pharmacokinetics (PK) and pharmacodynamics (PD). An experimental skin suction blister model was employed to assess target engagement and the ability of the compound to inhibit recruitment of inflammatory CCR6 expressing cells. METHODS: This study was a randomized, double-blind (sponsor open), placebo-controlled, single-centre, single ascending intravenous dose escalation trial in 48 healthy male volunteers. RESULTS: GSK3050002 (0.1-20 mg kg-1 ) was well tolerated and no safety concerns were identified. The PK was linear over the dose range, with a half-life of approximately 2 weeks. Complex of GSK3050002/CCL20 increased in serum and blister fluid with increasing doses of GSK3050002. There were dose-dependent decreases in CCR6+ cell recruitment to skin blisters with maximal effects at doses of 5 mg kg-1 and higher, doses at which GSK3050002/CCL20 complex in serum and blister fluid also appeared to reach maximum levels. CONCLUSIONS: These results indicate a relationship between PK, target engagement and PD, suggesting a selective inhibition of recruitment of CCR6+ cells by GSK3050002 and support further development of GSK3050002 in autoimmune and inflammatory diseases.

Protein-protein structure prediction by scoring molecular dynamics trajectories of putative poses.

The prediction of protein-protein interactions and their structural configuration remains a largely unsolved problem. Most of the algorithms aimed at finding the native conformation of a protein complex starting from the structure of its monomers are based on searching the structure corresponding to the global minimum of a suitable scoring function. However, protein complexes are often highly flexible, with mobile side chains and transient contacts due to thermal fluctuations. Flexibility can be neglected if one aims at finding quickly the approximate structure of the native complex, but may play a role in structure refinement, and in discriminating solutions characterized by similar scores. We here benchmark the capability of some state-of-the-art scoring functions (BACH-SixthSense, PIE/PISA and Rosetta) in discriminating finite-temperature ensembles of structures corresponding to the native state and to non-native configurations. We produce the ensembles by running thousands of molecular dynamics simulations in explicit solvent starting from poses generated by rigid docking and optimized in vacuum. We find that while Rosetta outperformed the other two scoring functions in scoring the structures in vacuum, BACH-SixthSense and PIE/PISA perform better in distinguishing near-native ensembles of structures generated by molecular dynamics in explicit solvent. Proteins 2016; 84:1312-1320. © 2016 Wiley Periodicals, Inc.

Temporal pharmacokinetic/pharmacodynamic interaction between human CD3ε antigen-targeted monoclonal antibody otelixizumab and CD3ε binding and expression in human peripheral blood mononuclear cell static culture.

Otelixizumab is a monoclonal antibody (mAb) directed to human CD3ε, a protein forming part of the CD3/T-cell receptor (TCR) complex on T lymphocytes. This study investigated the temporal interaction between varying concentrations of otelixizumab, binding to human CD3 antigen, and expression of CD3/TCR complexes on lymphocytes in vitro, free from the confounding influence of changing lymphocyte frequencies observed in vivo. A static in vitro culture system was established in which primary human peripheral blood mononuclear cells (PBMCs) were incubated over an extended time course with titrated concentrations of otelixizumab. At each time point, free, bound, and total CD3/TCR expression on both CD4+ and CD8+ T cells and the amount of free otelixizumab antibody in the supernatant were measured. The pharmacokinetics of free otelixizumab in the culture supernatants was saturable, with a shorter apparent half-life at low concentration. Correspondingly, a rapid, otelixizumab concentration-, and time-dependent reduction in CD3/TCR expression was observed. These combined observations were consistent with the phenomenon known as target-mediated drug disposition (TMDD). A mechanistic, mathematical pharmacokinetic/pharmacodynamic (PK/PD) model was then used to characterize the free otelixizumab-CD3 expression-time relationship. CD3/TCR modulation induced by otelixizumab was found to be relatively fast compared with the re-expression rate of CD3/TCR complexes following otelixizumab removal from supernatants. In summary, the CD3/TCR receptor has been shown to have a major role in determining otelixizumab disposition. A mechanistic PK/PD model successfully captured the PK and PD in vitro data, confirming TMDD by otelixizumab.

Continuous-time Markov modelling of flexible-dose depression trials.

The aim of this paper is to provide a systematic methodology for modelling longitudinal data to be used in contexts of limited or even absent knowledge of the physiological mechanism underlying the disease time course. Adopting a system-theoretic paradigm, a population response model is developed where the clinical endpoint is described as a function of the patient's health state. In particular, a continuous-time stochastic approach is proposed where the clinical score and its time-derivative summarize the patient's health state affected by a random term accounting for exogenous unpredictable factors. The proposed approach is validated on experimental data from the placebo and drug arms of a Phase II depression trial. Since some subjects in the trial may undergo changes in their treatment dose due to the flexible dosing scheme, dose escalations are modelled as instantaneous perturbations on the state. In its simplest form--an integrated Wiener process--was able to correctly capture the individual responses in both treatment arms. However, a better description of inter-individual variability was obtained by means of a stable Markovian model. Parameter estimation has been carried out according to the empirical Bayes method.

Population model of longitudinal FEV1 data in asthmatics: meta-analysis and predictability of placebo response.

Asthma is an obstructive lung disease where the mechanism of disease progression is not fully understood hence motivating the use of empirical models to describe the evolution of the patient's health state. With reference to placebo response, measured in terms of FEV1 (Forced Expiratory Volume in 1 s), a range of empirical models taken from the literature were compared at a single trial level. In particular, eleven GSK trials lasting 12 weeks in mild-to-moderate asthma were used for the modelling of longitudinal placebo responses. Then, the chosen exponential model was used to carry out an individual participant data meta-analysis on eleven trials. A covariate analysis was also performed to find relevant covariates in asthma to be accounted for in the meta-analysis model. Age, gender, and height were found statistically significant (e.g. the taller the patients the higher the FEV1, the older the patients the lower the FEV1, and females have lower FEV1). By truncating each trial at week 4, the predictive properties of the meta-analysis model were also investigated, showing its ability to predict long-term FEV1 response from truncated trials. Summarizing, the study suggests that: (i) the exponential model effectively describes the placebo response; (ii) the meta-analysis approach may prove helpful to simulate new trials as well as to reduce trial duration in view of its predictive properties; (iii) the inclusion of available covariates within the meta-analysis model provides a reduction of the inter-individual variability.

A non-linear mixed effect modelling approach for metabolite correction of the arterial input function in PET studies.

Quantitative PET studies with arterial blood sampling usually require the correction of the measured total plasma activity for the presence of metabolites. In particular, if labelled metabolites are found in the plasma in significant amounts their presence has to be accounted for, because it is the concentration of the parent tracer which is required for data quantification. This is achieved by fitting a Parent Plasma fraction (PPf) model to discrete metabolite measurements. The commonly used method is based on an individual approach, i.e. for each subject the PPf model parameters are estimated from its own metabolite samples, which are, in general, sparse and noisy. This fact can compromise the quality of the reconstructed arterial input functions, and, consequently, affect the quantification of tissue kinetic parameters. In this study, we proposed a Non-Linear Mixed Effect Modelling (NLMEM) approach to describe metabolite kinetics. Since NLMEM has been developed to provide robust parameter estimates in the case of sparse and/or noisy data, it has the potential to be a reliable method for plasma metabolite correction. Three different PET datasets were considered: [11C]-(+)-PHNO (54 scans), [11C]-PIB (22 scans) and [11C]-DASB (30 scans). For each tracer both simulated and measured data were considered and NLMEM performance was compared with that provided by individual analysis. Results showed that NLMEM provided improved estimates of the plasma parent input function over the individual approach when the metabolite data were sparse or contained outliers.

Non linear mixed effects analysis in PET PK-receptor occupancy studies.

The characterisation of a pharmacokinetic-receptor occupancy (PK-RO) relationship derived from a PET study is typically modelled in a conventional non-linear least squares (NLLS) framework. In the present work, we explore the application of a non-linear mixed effects approach (NLME) and compare this with NLLS estimation (using both naive pooled data and two-stage approaches) in the context of a direct PK-RO relationship described by an Emax model, using simulated data sets. Target and reference tissue time-activity curves were simulated using a two-tissue compartmental model and an arterial plasma input function for a typical PET study (12 subjects in 3 dose groups with 3 scans each). A range of different PET scenarios was considered to evaluate the impact of between-subject variability and reference region availability. The PET outcome measures derived from the simulations were then used to estimate the parameters of the PK-RO model. The performance of the two approaches was compared in terms of parameters estimates (square mean error SME, root mean square error RMSE) and prediction of the exposure-occupancy relationship. In general, both NLME and NLLS estimation methods provided unbiassed and precise population estimates for the Emax model parameters, although a slight bias was observed for the individual-NLLS method due to a few outliers. The increased value of NLME over NLLS was most notable in the estimation of the between-subject variability (BSV), especially in the case of a more complex PK-RO model when no reference region was available (maximum SME and RMSE values related to BSV of EC50 of 27.6% and 86.5% from NLME versus 264.6% and 689.5% from NLLS). Overall, the NLME approach provided a more robust estimation and produced less-biassed estimates of the population means and variances than either the NLLS approach for the simulations considered.

A PCA approach to population analysis: with application to a Phase II depression trial.

For psychiatric diseases, established mechanistic models are lacking and alternative empirical mathematical structures are usually explored by a trial-and-error procedure. To address this problem, one of the most promising approaches is an automated model-free technique that extracts the model structure directly from the statistical properties of the data. In this paper, a linear-in-parameter modelling approach is developed based on principal component analysis (PCA). The model complexity, i.e. the number of components entering the PCA-based model, is selected by either cross-validation or Mallows' Cp criterion. This new approach has been validated on both simulated and clinical data taken from a Phase II depression trial. Simulated datasets are generated through three parametric models: Weibull, Inverse Bateman and Weibull-and-Linear. In particular, concerning simulated datasets, it is found that the PCA approach compares very favourably with some of the popular parametric models used for analyzing data collected during psychiatric trials. Furthermore, the proposed method performs well on the experimental data. This approach can be useful whenever a mechanistic modelling procedure cannot be pursued. Moreover, it could support subsequent semi-mechanistic model building.

ABC transporters are billion-year-old Maxwell Demons.

ATP-Binding Cassette (ABC) transporters are a broad family of biological machines, found in most prokaryotic and eukaryotic cells, performing the crucial import or export of substrates through both plasma and organellar membranes, and maintaining a steady concentration gradient driven by ATP hydrolysis. Building upon the present biophysical and biochemical characterization of ABC transporters, we propose here a model whose solution reveals that these machines are an exact molecular realization of the autonomous Maxwell Demon, a century-old abstract device that uses an energy source to drive systems away from thermodynamic equilibrium. In particular, the Maxwell Demon does not perform any direct mechanical work on the system, but simply selects which spontaneous processes to allow and which ones to forbid based on information that it collects and processes. In its autonomous version, the measurement device is embedded in the system itself. In the molecular model introduced here, the different operations that characterize Maxwell Demons (measurement, feedback, resetting) are features that emerge from the biochemical and structural properties of ABC transporters, revealing the crucial role of allostery to process information. Our framework allows us to develop an explicit bridge between the molecular-level description and the higher-level language of information theory for ABC transporters.