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Table S2 shows a selectivity screen of PF-06840003 in in vitro pharmacological assays.

Supplementary Methods

Table S1 shows the plasma protein binding and blood to plasma ratio in mouse, rat, dog and human. Table S3 shows the plasma concentrations following a single oral dose of PF-06840003. Figure S1 shows that PF-06840003 does not impact cell viability. Figure S2 shows that PF-06840003 rescues T-cell proliferation in a co-culture assay. Figure S3 shows tumor growth inhibition of CT26 tumors at different dose levels. Figure S4 shows that IDO1 inhibitor mediated tumor growth inhibition depends on CD8+ T cells. Figure S5 shows a combination benefit with anti-PD-L1 treatment in CT26 tumors. Figure S6 shows IDO1i mediated tumor growth inhibition of MDA-MB-231 breast tumors in humanized mice. Figure S7 shows that PF-06840003 improves the TGI of avelumab in a humanized mouse breast tumor model. Figure S8 shows the fractions of CT26 tumor immune infiltrating cells.

Tumors use indoleamine 2,3-dioxygenase-1 (IDO1) as a major mechanism to induce an immunosuppressive microenvironment. IDO1 expression is upregulated in many cancers and considered to be a resistance mechanism to immune checkpoint therapies. IDO1 is induced in response to inflammatory stimuli such as IFNγ and promotes immune tolerance by depleting tryptophan and producing tryptophan catabolites, including kynurenine, in the tumor microenvironment. This leads to effector T-cell anergy and enhanced Treg function through upregulation of FoxP3. As a nexus for the induction of key immunosuppressive mechanisms, IDO1 represents an important immunotherapeutic target in oncology. Here, we report the identification and characterization of the novel selective, orally bioavailable IDO1 inhibitor EOS200271/PF-06840003. It reversed IDO1-induced T-cell anergy in vitro. In mice carrying syngeneic tumor grafts, PF-06840003 reduced intratumoral kynurenine levels by over 80% and inhibited tumor growth both in monotherapy and, with an increased efficacy, in combination with antibodies blocking the immune checkpoint ligand PD-L1. We demonstrate that anti–PD-L1 therapy results in increased IDO1 metabolic activity thereby providing additional mechanistic rationale for combining PD-(L)1 blockade with IDO1 inhibition in cancer immunotherapies. Supported by these preclinical data and favorable predicted human pharmacokinetic properties of PF-06840003, a phase I open-label, multicenter clinical study (NCT02764151) has been initiated.

Purpose: Develop a quantitative LC–MS/MS method for FDG, FDG-monophosphate, glucose and glucose-monophosphate in mouse tumor models to assist in validating the use of [18F]FDG-positron emission tomography (PET) imaging for anticancer therapies in a clinical setting. Methodology/results: Analytes were isolated from tumors by protein precipitation and detected on a Sciex API-5500 mass spectrometer. Improved assay robustness and selectivity were achieved through chromatographic separation of FDG-monophosphate from glucose-monophosphate, selection of a unique ion transition and incorporation of stable isotope labeled internal standards. In a mouse JIMT-1 tumor model, FDG-monophosphate levels measured by LC–MS/MS correlated with [18F]FDG-PET imaging results. Conclusion: LC–MS/MS analysis of FDG-monophosphate accumulation in tumors is a cost-effective tool to gauge the translational potential of [18F]FDG-PET imaging as a noninvasive biomarker in clinical studies.

B cell maturation antigen (BCMA) is a membrane-bound receptor that is overexpressed on multiple myeloma cells and can be targeted with biotherapeutics. Soluble shed forms of membrane-associated receptors in circulation can act as a drug sink, especially when it is present in high molar ratio compared to drug concentration, potentially derailing the intended pharmacological mechanism and impacting pharmacokinetic (PK) measurements and efficacious dose predictions. In this study, we present a bioanalytical strategy for assessing dynamic levels of total soluble BCMA before and during treatment with a bispecific antibody targeting BCMA and CD3. Implementation of a ligand binding assay was not successful due to extensive bispecific antibody interference. Instead, we explored two types of immunoaffinity (IA) liquid chromatography-tandem mass spectrometry (LC-MS/MS) assays, one at the protein level and one at the surrogate peptide level. Ultimately, the protein-level IA-LC-MS/MS method was optimized for use in a cynomolgus monkey PK/pharmacodynamic study. In addition, we demonstrated that the method was easily adapted for use with human samples in preparation for translation to the clinic. This work demonstrates the benefit of flexibility and agility in bioanalytical method development in early drug development. Multiplatform suitability assessments enable rapid, resource-sparing identification and qualification of clinically translatable assays. We recommend early adoption of this strategy to provide enough time for critical reagent development and assay validation for analysis of shed targets.

Tumors use indoleamine 2,3-dioxygenase-1 (IDO1) as a major mechanism to induce an immunosuppressive microenvironment. IDO1 expression is upregulated in many cancers and considered to be a resistance mechanism to immune checkpoint therapies. IDO1 is induced in response to inflammatory stimuli such as IFNγ and promotes immune tolerance by depleting tryptophan and producing tryptophan catabolites, including kynurenine, in the tumor microenvironment. This leads to effector T-cell anergy and enhanced Treg function through upregulation of FoxP3. As a nexus for the induction of key immunosuppressive mechanisms, IDO1 represents an important immunotherapeutic target in oncology. Here, we report the identification and characterization of the novel selective, orally bioavailable IDO1 inhibitor EOS200271/PF-06840003. It reversed IDO1-induced T-cell anergy in vitro. In mice carrying syngeneic tumor grafts, PF-06840003 reduced intratumoral kynurenine levels by over 80% and inhibited tumor growth both in monotherapy and, with an increased efficacy, in combination with antibodies blocking the immune checkpoint ligand PD-L1. We demonstrate that anti–PD-L1 therapy results in increased IDO1 metabolic activity thereby providing additional mechanistic rationale for combining PD-(L)1 blockade with IDO1 inhibition in cancer immunotherapies. Supported by these preclinical data and favorable predicted human pharmacokinetic properties of PF-06840003, a phase I open-label, multicenter clinical study (NCT02764151) has been initiated.

Blood-based soluble protein biomarkers provide invaluable clinical information about patients and are used as diagnostic, prognostic, and pharmacodynamic markers. The most commonly used blood sample matrices are serum and different types of plasma. In drug development research, the impact of sample matrix selection on successful protein biomarker quantification is sometimes overlooked. The sample matrix for a specific analyte is often chosen based on prior experience or literature searches, without good understanding of the possible effects on analyte quantification. Using a data set of 32 different soluble protein markers measured in matched serum and plasma samples, we examined the differences between serum and plasma and discussed how platelet or immune cell activation can change the quantified concentration of the analyte. We have also reviewed the effect of anticoagulant on analyte quantification. Finally, we provide specific recommendations for biomarker sample matrix selection and propose a systematic and data-driven approach for sample matrix selection. This review is intended to raise awareness of the impact and considerations of sample matrix selection on biomarker quantification.

BACKGROUND Cardiovascular disease (CVD) disparities are a particularly devastating manifestation of health inequity. Despite advancements in prevention and treatment, CVD is still the leading cause of death in the United States. Additionally, research indicates that African American (AA) and other ethnic-minority populations are affected by CVD at earlier ages than white Americans. Given that AAs are the fastest-growing population of smartphone owners and users, mobile health (mHealth) technologies offer the unparalleled potential to prevent or improve self-management of chronic disease among this population. OBJECTIVE To address the unmet need for culturally tailored primordial prevention CVD–focused mHealth interventions, the MOYO app was cocreated with the involvement of young people from this priority community. The overall project aims to develop and evaluate the effectiveness of a novel smartphone app designed to reduce CVD risk factors among urban-AAs, 18-29 years of age. METHODS The theoretical underpinning will combine the principles of community-based participatory research and the agile software development framework. The primary outcome goals of the study will be to determine the usability, acceptability, and functionality of the MOYO app, and to build a cloud-based data collection infrastructure suitable for digital epidemiology in a disparity population. Changes in health-related parameters over a 24-week period as determined by both passive (eg, physical activity levels, sleep duration, social networking) and active (eg, use of mood measures, surveys, uploading pictures of meals and blood pressure readings) measures will be the secondary outcome. Participants will be recruited from a majority AA “large city” school district, 2 historically black colleges or universities, and 1 urban undergraduate college. Following baseline screening for inclusion (administered in person), participants will receive the beta version of the MOYO app. Participants will be monitored during a 24-week pilot period. Analyses of varying data including social network dynamics, standard metrics of activity, percentage of time away from a given radius of home, circadian rhythm metrics, and proxies for sleep will be performed. Together with external variables (eg, weather, pollution, and socioeconomic indicators such as food access), these metrics will be used to train machine-learning frameworks to regress them on the self-reported quality of life indicators. RESULTS This 5-year study (2015-2020) is currently in the implementation phase. We believe that MOYO can build upon findings of classical epidemiology and longitudinal studies like the Jackson Heart Study by adding greater granularity to our knowledge of the exposures and behaviors that affect health and disease, and creating a channel for outreach capable of launching interventions, clinical trials, and enhancements of health literacy. CONCLUSIONS The results of this pilot will provide valuable information about community cocreation of mHealth programs, efficacious design features, and essential infrastructure for digital epidemiology among young AA adults. INTERNATIONAL REGISTERED REPORT DERR1-10.2196/16699

With the growing focus on translational research and the use of biomarkers to drive drug development and approvals, biomarkers have become a significant area of research within the pharmaceutical industry. However, until the US Food and Drug Administration’s (FDA) 2013 draft guidance on bioanalytical method validation included consideration of biomarker assays using LC-MS and LBA, those assays were created, validated, and used without standards of performance. This lack of expectations resulted in the FDA receiving data from assays of varying quality in support of efficacy and safety claims. The AAPS Crystal City VI (CC VI) Workshop in 2015 was held as the first forum for industry-FDA discussion around the general issues of biomarker measurements (e.g., endogenous levels) and specific technology strengths and weaknesses. The 2-day workshop served to develop a common understanding among the industrial scientific community of the issues around biomarkers, informed the FDA of the current state of the science, and will serve as a basis for further dialogue as experience with biomarkers expands with both groups.

O1 IL-15 primes an mTOR-regulated gene-expression program to prolong anti-tumor capacity of human natural killer cells #### Andreas Lundqvist1, Vincent van Hoef1, Xiaonan Zhang1, Erik Wennerberg2, Julie Lorent1, Kristina Witt1, Laia Masvidal Sanz1, Shuo Liang1, Shannon Murray3, Ola Larsson1

The 2013 7th Workshop on Recent Issues in Bioanalysis was held in Long Beach, California, USA, where close to 500 professionals from pharmaceutical and biopharmaceutical companies, CROs and regulatory agencies convened to discuss current topics of interest in bioanalysis. These ‘hot’ topics, which covered both small and large molecules, were the starting point for fruitful exchanges of knowledge, and sharing of ideas among speakers, panelists and attendees. The discussions led to specific recommendations pertinent to bioanalytical science. Such as the previous editions, this 2013 White Paper addresses important bioanalytical issues and provides practical answers to the topics presented, discussed and agreed upon by the global bioanalytical community attending the 7th Workshop on Recent Issues in Bioanalysis.

There are many sources of analytical variability in ligand binding assays (LBA). One strategy to reduce variability has been duplicate analyses. With recent advances in LBA technologies, it is conceivable that singlet analysis is possible. We retrospectively evaluated singlet analysis using Gyrolab data. Relative precision of duplicates compared to singlets was evaluated using 60 datasets from toxicokinetic (TK) or pharmacokinetic (PK) studies which contained over 23,000 replicate pairs composed of standards, quality control (QC), and animal samples measured with 23 different bioanalytical assays. The comparison was first done with standard curve and QCs followed by PK parameters (i.e., Cmax and AUC). Statistical analyses were performed on combined duplicate versus singlets using a concordance correlation coefficient (CCC), a measurement used to assess agreement. Variance component analyses were conducted on PK estimates to assess the relative analytical and biological variability. Overall, 97.5% of replicate pairs had a %CV of11% and 50% of the results had a %CV of ≤1.38%. There was no observable bias in concentration comparing the first replicate with the second (CCC of 0.99746 and accuracy value of 1). The comparison of AUC and Cmax showed no observable difference between singlet and duplicate (CCC for AUC and Cmax0.99999). Analysis of variance indicated an AUC inter-subject variability 35.3-fold greater than replicate variability and 8.5-fold greater for Cmax. Running replicates from the same sample will not significantly reduce variation or change PK parameters. These analyses indicated the majority of variance was inter-subject and supported the use of a singlet strategy.

This chapter serves as an introduction to the terms and definitions of biomarkers as well as the validation assay process which includes: a standard curve, validation samples, accuracy and precision (reproducibility), limits of quantification, parallelism, dilution linearity, specificity and interference, stability, and normal range. Different biomarkers exist for the various stages of the drug discovery and development process. The main objective of this chapter is to introduce concepts that will facilitate the successful use of biomarkers in drug development—from selection, to validation, and then implementation.

Single molecule force spectroscopy is often used to study the dissociation of single molecules by applying mechanical force to the intermolecular bond. These measurements provide the kinetic parameters of dissociation. We present what to our knowledge is a new atomic force microscopy-based approach to obtain the activation energy of the association reaction and approximate grafting density of reactive receptors using the dependence of the probability to form molecular bonds on probe velocity when one of the interacting molecules is tethered by a flexible polymeric linker to the atomic force microscopy probe. Possible errors in the activation energy measured with this approach are considered and resulting corrections are included in the data analysis. This new approach uses the same experimental setup as traditional force spectroscopy measurements that quantify dissociation kinetics. We apply the developed methodology to measure the activation energy of biotin-streptavidin association (including a contribution from the steric factor) and obtain a value of 8 ± 1 kT. This value is consistent with the association rate measured previously in solution. Comparison with the solution-derived activation energy indicates that kinetics of biotin-streptavidin binding is mainly controlled by the reaction step.

The pulling coordinate dependence of hexadecane dimer dissociation in water was studied using AFM-based single molecule force spectroscopy. Hexadecanes were covalently bound to both the AFM cantilever and to the glass substrates through hydrophilic poly-(ethylene glycol) tethers. The polymer tether was attached either to the end of hexadecane or in the middle of the molecule. Experimentally studied configurations of hexadecanes tethered to the AFM probe and to the glass substrate include a symmetric end-attached configuration (EE), an asymmetric end-attached vs middle-attached configuration (ME), and a symmetric middle-attached configuration (MM). Kinetic parameters of the distance to the transition state barrier (barrier width) and activation energy of dissociation were extracted from the statistical analysis of double tether rupture events. The rupture force analysis employs a recently introduced two-bond model that corrects for errors induced by potential multiple simultaneous rupture events and accounts for the tether stiffening effects. Effects of the shape of intermolecular potential were considered by using the Bell−Evans and Hummer−Szabo force spectroscopy models. The activation energies to dissociation were similar for all configurations while the barrier width was significantly shorter for the MM and ME configurations than for EE configurations. Primitive models that include touching or merging spherical or cylindrical shapes were considered. These models were inconsistent with the extracted kinetic parameters. It is suggested that the observed anisotropy may be a result of conformational transition of hexadecane from extended to collapsed state during dimerization. A flexible four-bead model of hexadecane was introduced to account for conformational flexibility. Using the length and solvent accessible surface area of hexadecane, the four-bead model gave molecular dissociation parameters consistent with the experimental data. This suggests that conformational flexibility is an important factor in hydrophobic interactions between alkane chains.

Force spectroscopy measurements of the rupture of the molecular bond between biotin and streptavidin often results in a wide distribution of rupture forces. We attribute the long tail of high rupture forces to the nearly simultaneous rupture of more than one molecular bond. To decrease the number of possible bonds, we employed hydrophilic polymeric tethers to attach biotin molecules to the atomic force microscope probe. It is shown that the measured distributions of rupture forces still contain high forces that cannot be described by the forced dissociation from a deep potential well. We employed a recently developed analytical model of simultaneous rupture of two bonds connected by polymer tethers with uneven length to fit the measured distributions. The resulting kinetic parameters agree with the energy landscape predicted by molecular dynamics simulations. It is demonstrated that when more than one molecular bond might rupture during the pulling measurements there is a noise-limited range of probe velocities where the kinetic parameters measured by force spectroscopy correspond to the true energy landscape. Outside this range of velocities, the kinetic parameters extracted by using the standard most probable force approach might be interpreted as artificial energy barriers that are not present in the actual energy landscape. Factors that affect the range of useful velocities are discussed.

Interactions between fullerene C_(60) molecules in water were measured by force spectroscopy. Fullerene molecules were covalently connected to bifunctional water-soluble poly(ethylene glycol) (PEG) linkers and subsequently tethered to the substrate and to the tip of the atomic force microscope to facilitate single molecule detection and avoid spurious surface effects. The distributions of rupture forces for substrates prepared with different incubation times of C_(60)-PEG-NH_2 exhibit high rupture forces that cannot be explained by the theoretical distribution of single molecule binding. Moreover, the relative amplitude of the high force peak in the histogram increases with incubation time. These observations are explained by attributing the measured high forces to the rupture of multiple bonds between fullerene molecules. Force spectroscopy data analysis based on the most probable forces gives significantly different dissociation rates for samples that exhibit different amplitudes of the high force peak. An approximate analytical model that considers ruptures of two bonds that are simultaneously loaded by tethers with different lengths is proposed. This model successfully fits the distributions of the rupture forces using the same set of kinetic parameters for samples prepared with different grafting densities. It is proposed that this model can be used as a common tool to analyze the probability distributions of rupture forces that contain peaks or shoulders on the high force side of the distribution.

We measured transforming growth factor (TGF)-beta-dependent biomarkers in plasma and in peripheral blood mononuclear cells (PBMCs) to identify suitable pharmacodynamic markers for future clinical trials with TGF-beta inhibitors. Forty-nine patients with bone metastasis were enrolled in the study, including patients with breast (n=23) and prostate cancer (n=15). Plasma TGF-beta1 levels were elevated in more than half of the cancer patients (geometric mean 2.63 ng ml(-1)) and positively correlated with increased platelet factor 4 (PF4) levels, parathyroid-related protein (PTHrP), von Willebrand Factor (vWF) and interleukin (IL)-10. PBMC were stimulated ex vivo to determine the individual biological variability of an ex vivo assay measuring pSMAD expression. This assay performed sufficiently well to allow its future use in a clinical trial of a TGF-beta inhibitor.

The hydrophobic effect is important for many biological and technological processes. Despite progress in theory, experimental data clarifying the structure of water and the interactions between hydrophobic solutes at the nanometer scale are scarce because of the very low solubility of hydrophobic species. This article describes single-molecule force spectroscopy measurements of interactions between single fullerene C60 molecules in water. The C60 molecules were tethered by flexible poly(ethylene glycol) linkers to AFM probes and substrates, removing the uncertainty of the aggregation state of solution-based approaches and spurious surface effects. Our analysis of the dependence of the measured most-probable rupture force on the most-probable loading rate considered the deviations from the conventional Bell−Evans model caused by the effects of the anharmonic tether, as well as by the finite depth and shape of the potential well. The kinetic parameters of the activation barrier width, the dissociation rate ...

Force spectroscopy is a new and valuable tool in physical chemistry and biophysics. However, data analysis has yet to be standardized, hindering the advancement of the technique. In this article, treatment of the rupture forces is described in the framework of the Bell-Evans model, and the systematic errors associated with the tether effect for approaches that utilize the most probable, the median, and the mean rupture forces are compared. It is shown that significant systematic errors in the dissociation rate can result from nonlinear loading with polymeric tethers even if the apparent loading rate is used in the analysis. Analytical expressions for the systematic errors are provided for the most probable and median forces. The use of these expressions to correct the associated systematic errors is illustrated by the analysis of the measured rupture forces between single hexadecane molecules in water. It is noted that the measured distributions of rupture forces often contain high forces that are unaccounted for by theoretical models. Experimental data indicate that the most significant effect of the high forces "tail" is on the dissociation rate obtained from the median force analysis whereas the barrier width appears to be unaffected.

Single-molecule force spectroscopy has become a valuable tool for the investigation of intermolecular energy landscapes for a wide range of molecular associations. Atomic force microscopy (AFM) is often used as an experimental technique in these measurements, and the Bell-Evans model is commonly used in the statistical analysis of rupture forces. Most applications of the Bell-Evans model consider a constant loading rate of force applied to the intermolecular bond. The data analysis is often inconsistent because either the probe velocity or the apparent loading rate is being used as an independent parameter. These approaches provide different results when used in AFM-based experiments. Significant variations in results arise from the relative stiffness of the AFM force sensor in comparison with the stiffness of polymeric tethers that link the molecules under study to the solid surfaces. An analytical model presented here accounts for the systematic errors in force-spectroscopy parameters arising from the nonlinear loading induced by polymer tethers. The presented analytical model is based on the Bell-Evans model of the kinetics of forced dissociation and on the asymptotic models of tether stretching. The two most common data reduction procedures are analyzed, and analytical expressions for the systematic errors are provided. The model shows that the barrier width is underestimated and that the dissociation rate is significantly overestimated when force-spectroscopy data are analyzed without taking into account the elasticity of the polymeric tether. Systematic error estimates for asymptotic freely jointed chain and wormlike chain polymer models are given for comparison. The analytical model based on the asymptotic freely jointed chain stretching is employed to analyze and correct the results of the double-tether force-spectroscopy experiments of disjoining "hydrophobic bonds" between individual hexadecane molecules that are covalently tethered via poly(ethylene glycol) linkers of different lengths to the substrates and to the AFM probes. Application of the correction algorithm decreases the spread of the data from the mean value, which is particularly important for measurements of the dissociation rate, and increases the barrier width to 0.43 nm, which might be indicative of the theoretically predicted hydrophobic dewetting.

Purpose Measurements of cytokine release in whole blood after ex vivo stimulation are useful in drug development. The components contributing to variation within such assays have not been clearly defined. Therefore, we characterized the sources of variability within an ex vivo stimulation assay for TNF-α release. Method Fresh whole blood or mononuclear cells from a cell preparation tube were added to silanized, screw-top tubes with a final concentration of 1 μg/mL lipopolysaccharide (LPS). Each tube was purged with 95% air/5%CO 2 and incubated 4 or 6 h at 37 °C in a metabolic water bath. Plasma TNF-α was next measured in supernatants by immunoassay. Total method variability was assessed in 10 normal donors each drawn in the morning and afternoon over 3 days. Four additional samples were pre-treated with dexamethasone to investigate inhibition of TNF-α release. Results Our analysis indicated precise temperature control, the timing and duration of stimulation, and the surface properties of the stimulation vessel most significantly influenced assay performance. A comparison of multiple anticoagulants indicated that careful consideration should be taken in selecting the optimal anticoagulant. The estimated total assay CV for all anticoagulants tested was less than 33.81%. The analytical variability (stimulation and measurement) was less than 25.88% CV. The one exception was mononuclear cells collected in sodium heparin. The total variability estimate incorporated day-to-day, diurnal, inter-donor, tube-to-tube and immunoassay variability. Using our optimized conditions, TNF-α release was inhibited by dexamethasone with a mean IC 50 of 33.3 ± 4.6 nM. Conclusions We have described an optimal set of conditions for collection, storage and processing of an ex vivo cytokine stimulation assay. These conditions were selected for operational feasibility, minimal imprecision and elimination of potential confounding factors. The end result is a more robust method that can be applied to clinical drug development.

In the upcoming case of Teva Pharmaceuticals v. Sandoz, the U.S. Supreme Court will address how much deference the appellate court should afford to a trial court’s claim construction ruling. The effect of this decision will be far-reaching, as how claims are construed can determine whether a patent is infringed or not infringed, valid or invalid.

Quantification of biomarkers can provide important information about the safety and efficacy of candidate drugs. Unfortunately, limited sample volume and excess costs often limit analysis of multiple biomarkers. We developed, optimized, validated, and implemented a multiplex immunoassay for simultaneous measurement of multiple circulating cytokines: IL-1beta, TNFalpha, IL-6, IL-8, and IL-10. Multiplex immuoassays were performed using the Luminex LabMAP instrument. Capture antibodies for each cytokine were covalently bound to distinct microsphere subsets distinguished by differing dye ratios. The concentration of each individual cytokine determined by measuring orange fluorescence produced by a complex of a biotinylated cytokine-specific antibody and streptavidin-phycoerythrin. The lower limit of quantification for all assays was 20 pg/mL with the exception of IL-8 which was 100 pg/mL. The inter-assay precision was less than 25%CV for all analytes at all control levels both pre-study and in-study. The percent recovery ranged from 83 to 108% pre-study and 90 to 125% in-study. In a linearity assessment, a 15,000 pg/mL multi-analyte control could be diluted 1:50 and maintain expected accuracy. We measured the cytokine concentrations in more than 2000 serum samples from patients with sepsis. Multiplex results for IL-6 were compared to a conventional commercially available ELISA kit. The degree of agreement between the two methods as measured by the concordance correlation coefficient was 84.5%. Multiplex results were 2.36-fold higher than ELISA values on the average. After adjusting for this mean difference, the 95% empirical limits of agreement for the ratio of individual sample values were 0.33, 2.65. This multiplex immunoassay provided simultaneous measurement of circulating cytokines using 80% less patient specimen compared to traditional approaches and at a significantly decreased cost. Efficient use of this platform requires process improvements to fully maximize the positive impact of multiplex assays in clinical drug development.

Contemporary drug discovery leverages quantitative modeling and simulation with increasing emphasis, both to gain deeper knowledge of drug targets and mechanisms as well as improve predictions between preclinical models and clinical applications, such as first-in-human dose projections. Proliferation of novel biotherapeutic modalities increases the need for applied PK/PD modeling as a quantitative tool to advance new therapies. Of particular relevance is the understanding of exposure, target binding and associated pharmacology at the target site of interest. Bioanalytical methods are key to informing PK/PD models and require assessment of both PK and PD end points. Where targets are sequestered in tissues (noncirculating), the ability to quantitatively measure drug or biomarker in tissue compartments becomes particularly important. This perspective provides an overview of contemporary applications of quantitative bioanalysis in tissue compartments as applied to PK and PD assessments associated with novel biotherapeutics. Case studies and key references are provided.

The 21st Century Bioanalytical Laboratory Platforms initiative in the BIOTEC section of the American Association of Pharmaceutical Scientists (AAPS) began with a pre-conference workshop held in Seattle, WA in June of 2009. This workshop brought together members of the pharmaceutical and biotechnology industries, with instrument and reagent manufacturers to discuss the current and potential future state of the bioanalytical laboratories supporting biologics development. At the conclusion of the workshop, four sub-teams were formed to further develop the ideas and concepts raised during the 2-day workshop. The sub-teams are reagents, automation, e-solutions, and platforms. This paper discusses the critical attributes of a research and development ligand binding assay (LBA) platform and the desired characteristics new platforms should strive to offer in the future. This paper is not intended to be a review and comparison of the current platforms on the market, as this has been done and published elsewhere (1–9). The platforms team consists of a balanced cross-section of the industry with representatives from pharmaceutical, biotechnology, contract research organizations, and instrument manufacturers. The Platforms team have collaborated to discuss and arrive at a consensus regarding the most useful characteristics of a bioanalytical platform for biologics. We present here the results of these discussions. A platform is the technology employed in an analytical method to transduce a biochemical event into a measureable output or signal. This signal allows the bioanalytical scientist to accurately and reproducibly make measurements to analyze different aspects of a specific biologic target (therapeutic, biomarker, and anti-drug antibody) such as its pharmacokinetics, immunogenicity, potency, or effect of biomarkers. An instrument is the tool utilized minimally to measure a platform’s output and convert the resultant signal into interpretable information the analytical scientist can use but can incorporate other aspects such as liquid handling. Many platforms employ optical signals including the absorbance of light through a medium (10) or the emission of fluorescence (10) or luminescence (11). A variety of light detectors are used to measure these optical signals including photo diodes, charge-coupled device cameras, and photo-multiplier tubes (Table I). Sections in this paper provide details on the desirable analytical characteristics, multiplexing, platform flexibility and throughput, desirable instrument characteristics, and finally, life cycle management of the ideal LBA platform. Table I Commonly Used Platforms The analytical characteristics of today’s ligand binding assays are primarily influenced by three major factors—the quality of the reagents, assay format, and the choice of the analytical platform. This paper describes only those aspects derived from the analytical platform.

In June 2009, a group of ligand binding assay experts met in Seattle, WA to discuss the need for greater efficiency in bioanalytical laboratories. The central premise was increased utilization of technological innovation will lead to increased quality, throughput, and efficiency. Currently, there are very few laboratories that have reached the ideal or utopian level desired. The biggest challenge currently facing the ligand binding community is a reliance on manual processes and paper-based systems, ineffective integration, and a lack of standardization in many areas. In order to address these gaps, we identified speakers who had developed solutions to parts of the overall problem. The event spanned 2 days with participation from three distinct groups: biopharmaceutical companies, contract research organizations, and research equipment providers. The goal was to share best practices, identify gaps, and define next steps. The outcome of themeeting was the development of four sub-teams that included: reagents, instrument platforms, automation, and electronic solutions. Each sub-team was given the task of identifying the most achievable and high-impact facets to change or improve.

Circulating alpha fetoprotein (AFP) is a diagnostic and prognostic biomarker for hepatocellular carcinoma (HCC) with potential utility as a pharmacodynamic endpoint in rodent tumor models. This application is limited, however, by low sample volumes, highlighting the need for sensitive, sample-sparing biomarker assay methods. In order to improve the utility of AFP as an oncology biomarker, we developed a method for AFP using the Gyrolab™, an automated microimmunoassay platform. Commercially available antibodies were screened to identify optimal combinations that were then used in a multi-factorial design of experiments (DOE) to optimize reaction conditions. Analytical validation included assessments of accuracy and precision (A&P), and dilutional linearity/hook effect, as well as reagent and sample stability. The method is reliable, with total error, a measure of accuracy and precision, less than 30% for all concentrations tested. AFP concentrations were measurable in diseased mice and undetectable in normal mice. Therefore, this novel, low volume AFP immunoassay is suitable for pre-clinical drug development, where its miniaturized format facilitates serial sampling in rodent models of cancer.

Substantial experimental evidence indicates that the mechanical force applied to pull apart non-covalent molecular bonds (such as receptor-ligand pairs) can significantly decrease the bond lifetime. This evidence is often generated in single-molecule experiments that are designed to specifically test effects of pulling forces. However, the effect of compressive forces on the lifetime of receptor-ligand bonds remains largely unexplored. Here we extend the common usage of the atomic force microscopy technique to study whether compressive forces applied to bound streptavidin-biotin species can significantly accelerate the rate of dissociation. Presented experimental data indicate that compressive forces can substantially decrease the lifetime of the molecular bond. Surprisingly, the efficiency of accelerating dissociation by compressive forces sometimes exceeds the enhancement of the dissociation rate measured in pulling experiments, indicating that compressive forces applied to the bound species might be efficiently used to control the lifetime of adhesion bonds.

The detection probability of rupture events in AFM force spectroscopy measurements presents a viable alternative to standard methods for extracting kinetic parameters of dissociation. The detection probability has a maximum as a function of the probe velocity where (1) the probability to form a molecular bond is independent of the probe velocity and (2) the detection of rupture events is limited by noise and performed with a constant density of data points per distance of the probe displacement. This newly developed model indicates that the optimal detection velocity is independent of dissociation rate and depends on the distance to the barrier kinetic parameter. Therefore, the kinetic parameters of bond dissociation can be extracted from the dependence of detection probability on probe velocity and the detection threshold. This approach is sensitive to low rupture forces and therefore is complementary to the common most probable force data analysis approach. The developed approach is tested using rupture forces measured with specific bonds between biotin and streptavidin and with nonspecific bonds between linear alkanes in water. Results for the analysis of specific bonds rupture are consistent with the previous measurements, suggesting that rupture forces spanning a wide range of values originate from the same binding potential. Kinetic parameters obtained for linear alkanes are significantly different from previous measurements suggesting possible heterogeneity of the bound state.

Assessing the pharmacodynamics (PD) of a potential therapeutic through the use of a downstream biomarker is essential. This is traditionally performed in the target tissue but limited volume and invasiveness of sampling pose challenges with solid tumours. Currently, there are several small molecule receptor kinase inhibitors and large molecule therapeutic antibodies in clinical trials that interfere with TGFbeta signalling to treat various forms of cancer. With the advent of these new therapies, there is a need for a surrogate tissue that is easily accessible and indicative of tumour response. We propose the use of an ex vivo TGFbeta1 stimulation of peripheral blood mononuclear cells (PBMCs) coupled with the measurement of phosphorylated SMAD2 (Sma/Mothers Against dpp, a downstream transcriptional activator) using a sandwich ELISA. TGFbeta is involved in many different cellular responses, such as proliferation, angiogenesis, migration, invasion and immunomodulation. SMAD2 and SMAD3 are phosphorylated as a result of the canonical cascade through ligand binding and receptor kinase activation. These phosphorylated SMADs (pSMAD) associate with SMAD4, a co-SMAD, and transcriptionally activate TGFbeta-mediated genes. This paper describes the novel method for measuring the downstream effects of inhibiting canonical TGFbeta signalling using ex vivo stimulation of surrogate tissue to predict tumour response. In addition, we present the assay validation rationale and data. This novel, validated assay can be used to gain insight into clinical trials regarding TGFbeta signal modulation by multiple inhibitor platforms for both large and small molecules.

Activating mutations in EGFR confer constitutive activity providing the oncogenic drive in EGFR-mutant NSCLC. First and 2nd generation EGFR tyrosine kinase inhibitors (TKIs) are effective drugs in this setting, but are constrained by dose-limiting toxicities attributed to inhibition of wild type (WT) EGFR and by drug resistance caused, in the majority of cases, via a T790M secondary mutation in EGFR. We report the pharmacology of a novel irreversible 3rd generation EGFR TKI active against EGFR with activating and T790M mutations, but sparing WT EGFR. Our novel 3rd generation EGFR TKI was studied in a variety of in vitro and in vivo models to determine its inhibitory potencies on different EGFR variants, pharmacokinetics (PK), antitumor efficacy, exposure-response relationships, mechanism of action, and predicted human efficacious dose. In enzyme and cell assays, our compound is a highly potent inhibitor of EGFR double mutants (L858R/T790M and Del/T790M) and EGFR activating mutants (L858R and Del), but a weak inhibitor of WT EGFR (26-fold margin over mutant target potencies). Effects on downstream signaling and function indicate the underlying mechanism of the compound is direct inhibition of EGFR, with subsequent inhibition of downstream signaling that results in apoptosis and viable cell decline. In xenograft mouse models, the compound demonstrates tumor growth inhibition and regression at well-tolerated doses in models driven by EGFR double mutants and EGFR activating mutants. The antitumor efficacy is dose-dependent and strongly correlates with inhibition of EGFR phosphorylation and EGFR-mediated downstream signaling, and induction of apoptosis. Plasma concentrations assumed to be sufficient for efficacy (Ceff) were defined using a mathematical model incorporating the plasma levels of the compound, the associated inhibitory effects on EGFR phosphorylation, and the antitumor efficacy in the double and activating mutant xenograft models. Ceff was in agreement across several models and was used with in vitro human PK properties to calculate required human dose. While our compound possesses a similar profile as other recently disclosed 3rd generation EGFR TKIs, this molecule is distinguished by better potency on the activating mutants and by the widest potency margin on WT EGFR. Given that the target potencies and WT margins of 3rd generation EGFR TKIs have been sufficient for tolerated clinical efficacy in preliminary results, it can be inferred that our compound will have similar promise in the clinic. These results support our compound as a novel EGFR TKI with an inhibitory profile and favorable drug-like properties that suggest utility for treating patients with NSCLC with EGFR activating and resistance mutations. Citation Format: Mike Zientek, Sangita Baxi, Henry Cheng, Valeria Fantin, Jun Li Feng, Allison Given, Zelanna Goldberg, Jie Guo, Michelle Hemkens, John Kath, Jennifer Lafontaine, Gary Li, Pramod Mehta, Brion Murray, Sajiv Nair, Simon Planken, Chad Ray, Yuli Wang, Manli Shi, Anand Sistla, Tod Smeal, Greg Stevens, Wei Tan, Paolo Vicini, Marlena Walls, Liu Yang, Min-Jean Yin, Scott L. Weinrich. Characterization of a novel irreversible third generation EGFR TKI that targets T790M-mediated resistant EGFR-mutant NSCLC while sparing wild type EGFR. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2594. doi:10.1158/1538-7445.AM2015-2594

The hydrophobic effect is important for many biological and technological processes. Despite progress in theory, experimental data clarifying water structure and the interaction between hydrophobic solutes at the nanometer scale are scarce due to the very low solubility of hydrophobic species. This article describes an AFM single molecule force spectroscopy method to probe the interaction between molecules with low solubility and reports measurements of the strength and the length scale of the "hydrophobic bond" between hexadecane molecules. Hexadecane molecules are tethered by flexible poly(ethylene glycol) linkers to AFM probes and substrates, removing the aggregation state uncertainty of solution-based approaches as well as spurious surface effects. A shorter hydrophilic polymer layer is added to increase the accessibility of hydrophobic molecules for the force spectroscopy measurements. Statistical analysis of the rupture forces yields a barrier width of 0.24 nm, and a dissociation rate of 1.1 s(-1). The results of single molecule measurements are related to the theoretical predictions of the free energy of cavitation in water and to the empirical model of micellization of nonionic surfactants. It is estimated that approximately one-quarter of each molecule's surface is hydrated during forced dissociation, consistent with an extended (nonglobular) conformation of the hexadecane molecules in the dimer.

Purpose: To evaluate the effects of the novel protein kinase C (PKC) inhibitor enzastaurin on intracellular phosphoprotein signaling using flow cytometry and to use this approach to measure enzastaurin effects on surrogate target cells taken from cancer patients that were orally dosed with this agent. Experimental Design: The activity of PKC was assayed in intact cells using a modification of published techniques. The U937 cell line and peripheral blood mononuclear cells were stimulated with phorbol ester, fixed, permeabilized, and reacted with an antibody specific for the phosphorylated forms of PKC substrates. The processed samples were quantitatively analyzed using flow cytometry. The assay was validated for selectivity, sensitivity, and reproducibility. Finally, blood was obtained from volunteer cancer patients before and after receiving once daily oral doses of enzastaurin. These samples were stimulated ex vivo with phorbol ester and were assayed for PKC activity using this approach. Results: Assay of U937 cells confirmed the selectivity of the antibody reagent and enzastaurin for PKC. Multiparametric analysis of peripheral blood mononuclear cells showed monocytes to be the preferred surrogate target cell. Day-to-day PKC activity in normal donors was reproducible. Initial results showed that five of six cancer patients had decreased PKC activity following enzastaurin administration. In a following study, a group of nine patients displayed a significant decrease in PKC activity after receiving once daily oral doses of enzastaurin. Conclusion: An inhibition of surrogate target cell PKC activity was observed both in vitro and ex vivo after exposure to the novel kinase inhibitor, enzastaurin.

A force-spectroscopy-based approach is used to characterize separation between amyloidogenic peptide fragments of alpha-synuclein. Interactions between individual molecules are studied using a scanning-force-microscopy-based technique. Alpha-synuclein fragments are attached to the solid surfaces via flexible long poly-(ethylene glycol) linkers removing aggregation state uncertainty of solution-based approaches and spurious surface effects. Tethering one fragment to the scanning probe tip and another fragment to the second surface ensures that interactions between tethered molecules are studied. Control experiments with only one tethered peptide indicate peptide-peptide interactions as the source of observed interaction forces in the double-tether experiment. The temperature dependence of rupture forces from 17.5 degrees C to 40 degrees C reveals similar molecular parameters indicating that no significant conformational changes occur in the associated molecules over this temperature range. Rate-dependent measurements indicate conformational heterogeneity of joined peptide molecules.

Despite major advances in modern drug discovery and development, the number of new drug approvals has not kept pace with the increased cost of their development. Increasingly, innovative uses of biomarkers are employed in an attempt to speed new drugs to market. Still, widespread adoption of biomarkers is impeded by limited experience interpreting biomarker data and an unclear regulatory climate. Key differences preclude the direct application of existing validation paradigms for drug analysis to biomarker research. Following the AAPS 2003 Biomarker Workshop (J. W. Lee, R. S. Weiner, J. M. Sailstad, et al. Method validation and measurement of biomarkers in nonclinical and clinical samples in drug development. A conference report. Pharm Res 22:499-511, 2005), these and other critical issues were addressed. A practical, iterative, "fit-for-purpose" approach to biomarker method development and validation is proposed, keeping in mind the intended use of the data and the attendant regulatory requirements associated with that use. Sample analysis within this context of fit-for-purpose method development and validation are well suited for successful biomarker implementation, allowing increased use of biomarkers in drug development.

In vitro (or ex vivo) quantification of cellular parameters is often employed to inform systems models that define the relationship between drug exposure and response. We developed two flow cytometry based assays to evaluate the interaction between the IL-7 receptor (IL-7R) and an anti-IL-7R monoclonal antibody (Ab1). IL-7R occupancy and rate of internalization in the presence of Ab1 was determined using flow cytometry in monkeys and human whole blood. Two commercially available antibodies were used to detect IL-7R. One detected “free” and the other determined “total” receptor. Receptor internalization was measured ex vivo at various time points at 37 °C. The receptor occupancy assay was used in vivo following administration of Ab1 into cynomolgus monkeys at 0.3, 3, and 30 mg/kg. The amount of Ab1 bound to receptor and the total amount of receptor was quantified. The ex vivo receptor occupancy mean IC50 values in monkey and human whole blood were 5.64 ± 2.38 and 9.39 ± 1.54 ng/ml, respectively. The ex vivo rate of internalization of Ab1-IL-7R complex was characterized by a slope of 384 ± 24 and 2482 ± 319, for monkey and human, respectively. In the in vivo monkey study, no free IL-7R was detectable on the CD3 T cell surface at 0.25 h post-dose in all treatment groups. Free receptor levels returned to 78% on day 8 at 0.3 mg/kg, 55% on day 15 at 3 mg/kg, and 12% on day 15 at 30 mg/kg, compared to pre-dose levels. By Day 22, free IL-7R levels in all dose groups returned to their baseline. Ab1 treatment resulted in a significant reduction in total IL-7R. Effective biomeasures provide a link between species and the ex vivo and in vivo systems. Integration of these values into systems models reduces the number of model assumptions and increases the likelihood of success.

The bent d(0) titanium metallocene (Cp)(2)Ti(NCS)(2) exhibits an intense phosphorescence from a ligand-to-metal charge transfer triplet excited state at 77 K in an organic glass substrate and a poly(methyl methacrylate) plastic substrate. Quantum chemical calculations and spectroscopic studies show that the orbital parentage of this triplet state arises from the promotion of an electron from an essentially nonbonding symmetry adapted pi molecular orbital located on the NCS(-) ligands to a d(z)2-(y)2 orbital located on the Ti metal. Standard infrared spectroscopy of (Cp)(2)Ti(NCS)(2) in its ground electronic state at 77 K reveals a pair of closely spaced absorptions at (2072 cm(-1), 2038 cm(-1))(glass) and (2055 cm(-1), 2015 cm(-1))(plastic) that are assigned, respectively, to the symmetric and antisymmetric CN stretching modes of the two coordinated NCS(-) ligands. Low-temperature (77 K) time-resolved infrared spectroscopy that accesses the phosphorescing triplet excited state on the ns time scale shows an IR bleach that is coincident with the two ground state CN stretching bands and an associated grow-in of a pair of new IR bands at slightly lower energies (2059 cm(-1), 2013 cm(-1))(glass) and (2049 cm(-1), 1996 cm(-1))(plastic) that are assigned, respectively, to the symmetric and antisymmetric CN stretches in the emitting triplet state. These transient IR bands decay with virtually identical lifetimes to those observed for the phosphorescence decays when measured under identical experimental conditions. Singular value decomposition analysis of the time-resolved infrared data shows that the observed transient IR features arise from the same electronic manifold as measured through luminescence studies. The close similarity between the ground state and excited-state CN stretching bands in (Cp)(2)Ti(NCS)(2) indicates that symmetry breaking does not occur in forming the charge-transfer triplet excited-state manifold; i.e., electron density is withdrawn from a delocalized pi MO spread across both NCS(-) ligands. Calculations at several levels of theory reveal a delocalized ligand-to-metal charge transfer excited triplet manifold. These calculations closely reproduce the relative intensity ratios and frequencies of the symmetric and antisymmetric transient infrared vibrations in the CN region. This study is the first time-resolved infrared investigation of a ligand-to-metal charge-transfer excited state and the first to be performed at cryogenic temperatures in thin-film organic glass and plastic substrates.