Membrane Permeability in a Large Macrocyclic Peptide Driven by a Saddle-Shaped Conformation

The effort to modulate challenging protein targets has stimulated interest in ligands that are larger and more complex than typical small-molecule drugs. While combinatorial techniques such as mRNA display routinely produce high-affinity macrocyclic peptides against classically undruggable targets, poor membrane permeability has limited their use toward primarily extracellular targets. Understanding the passive membrane permeability of macrocyclic peptides would, in principle, improve our ability to design libraries whose leads can be more readily optimized against intracellular targets. Here, we investigate the permeabilities of over 200 macrocyclic 10-mers using the thioether cyclization motif commonly found in mRNA display macrocycle libraries. We identified the optimal lipophilicity range for achieving permeability in thioether-cyclized 10-mer cyclic peptide-peptoid hybrid scaffolds and showed that permeability could be maintained upon extensive permutation in the backbone. In one case, changing a single amino acid from d-Pro to d-NMe-Ala, representing the loss of a single methylene group in the side chain, resulted in a highly permeable scaffold in which the low-dielectric conformation shifted from the canonical cross-beta geometry of the parent compounds into a novel saddle-shaped fold in which all four backbone NH groups were sequestered from the solvent. This work provides an example by which pre-existing physicochemical knowledge of a scaffold can benefit the design of macrocyclic peptide mRNA display libraries, pointing toward an approach for biasing libraries toward permeability by design. Moreover, the compounds described herein are a further demonstration that geometrically diverse, highly permeable scaffolds exist well beyond conventional drug-like chemical space.

Current status and future directions of high-throughput ADME screening in drug discovery

During the last decade high-throughput in vitro absorption, distribution, metabolism and excretion (HT-ADME) screening has become an essential part of any drug discovery effort of synthetic molecules. The conduct of HT-ADME screening has been "industrialized" due to the extensive development of software and automation tools in cell culture, assay incubation, sample analysis and data analysis. The HT-ADME assay portfolio continues to expand in emerging areas such as drug-transporter interactions, early soft spot identification, and ADME screening of peptide drug candidates. Additionally, thanks to the very large and high-quality HT-ADME data sets available in many biopharma companies, in silico prediction of ADME properties using machine learning has also gained much momentum in recent years. In this review, we discuss the current state-of-the-art practices in HT-ADME screening including assay portfolio, assay automation, sample analysis, data processing, and prediction model building. In addition, we also offer perspectives in future development of this exciting field.

Development of Cassette PAMPA for Permeability Screening

The parallel artificial membrane permeability assay (PAMPA) is widely used in early-stage drug discovery to discriminate compounds by intestinal permeability. The purpose of the current study was to establish a cassette (n-in-1) PAMPA to enable permeability screening of lipophilic compounds. A double-sink PAMPA consisting of a pH gradient (i.e., pH 6.5 and 7.4 for the donor and receiver compartments, respectively) and a lipophilic sink (i.e., a surfactant in the receiver solution) was utilized with cassette incubation of 10 reference compounds. Sample analysis was conducted using selected reaction monitoring (SRM) with a triple quadrupole LC-MS/MS system. Correlation between PAMPA permeability and human intestinal absorption (HIA) of the reference compounds yielded two false negatives, namely propranolol (PPN) and verapamil (VER); these two compounds showed a substantially lower recovery (ca. 10%) than other reference compounds (>69%). This cassette PAMPA was repeated subsequently with polysorbate 80 added to the donor compartments, which resulted in a significant increase in both the recovery and the permeability of the false negatives. Accordingly, the permeability class of all reference compounds could be unambiguously differentiated using this cassette PAMPA. Also, a strong linear correlation (r=0.9845) was observed between the cassette and discrete permeability of all reference compounds.

Database of Optimized Proteomic Quantitative Methods for Human Drug Disposition-Related Proteins for Applications in Physiologically Based Pharmacokinetic Modeling

The purpose of this study was to create an open access repository of validated liquid chromatography tandem mass spectrometry (LC‐MS/MS) multiple reaction monitoring (MRM) methods for quantifying 284 important proteins associated with drug absorption, distribution, metabolism, and excretion (ADME). Various in silico and experimental approaches were used to select surrogate peptides and optimize instrument parameters for LC‐MS/MS quantification of the selected proteins. The final methods were uploaded to an online public database (QPrOmics; www.qpromics.uw.edu/qpromics/assay/), which provides essential information for facile method development in triple quadrupole mass spectrometry (MS) instruments. To validate the utility of the methods, the differential tissue expression of 107 key ADME proteins was characterized in the tryptic digests of the pooled subcellular fractions of human liver, kidneys, intestines, and lungs. These methods and the data are critical for development of physiologically based pharmacokinetic (PBPK) models to predict xenobiotic disposition.

HRMS using a Q-Exactive series mass spectrometer for regulated quantitative bioanalysis: how, when, and why to implement

High-resolution MS (HRMS) has seen an uptake in use for discovery qual/quan workflows, however, its utilization in late discovery/development has been slow. Past reports comparing HRMS to triple quadrupole (QQQ) instrumentation to date have indicated that HRMS instruments are capable of producing data acceptable for regulated bioanalysis, however lack the sensitivity required for sub ng/ml LLOQ assays. Recent advances in HRMS instrumentation have closed the sensitivity gap with QQQ and have even provided improved selectivity and sensitivity over QQQ SRM assays. Herein, the authors will describe how, when, and why HRMS (specifically Q-Exactive series mass spectrometers) should be considered for implementation in regulated quantitative bioanalysis assays.

Recent developments in software tools for high-throughput in vitro ADME support with high-resolution MS

The last several years have seen the rapid adoption of the high-resolution MS (HRMS) for bioanalytical support of high throughput in vitro ADME profiling. Many capable software tools have been developed and refined to process quantitative HRMS bioanalysis data for ADME samples with excellent performance. Additionally, new software applications specifically designed for quan/qual soft spot identification workflows using HRMS have greatly enhanced the quality and efficiency of the structure elucidation process for high throughput metabolite ID in early in vitro ADME profiling. Finally, novel approaches in data acquisition and compression, as well as tools for transferring, archiving and retrieving HRMS data, are being continuously refined to tackle the issue of large data file size typical for HRMS analyses.

Application of Cassette Ultracentrifugation Using Non-labeled Compounds and Liquid Chromatography-Tandem Mass Spectrometry Analysis for High-Throughput Protein Binding Determination

Membrane-based devices typically used for serum protein binding determination are not fully applicable to highly lipophilic compounds because of nonspecific binding to the device membrane. Ultracentrifugation, however, completely eliminates the issue by using a membrane-free approach, although its wide application has been limited. This lack of utilization is mainly attributed to 2 factors: the high cost in acquiring and handling of radiolabeled compounds and low assay throughput owing to the difficulties in process automation. To overcome these challenges, we report a high-throughput workflow by cassette ultracentrifugation of nonradiolabeled compounds followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. Twenty compounds with diverse physicochemical and protein binding properties were selected for the evaluation of the workflow. To streamline the working process, approaches of matrix balancing for all the samples for LC-MS/MS analysis and determining free fraction without analytical calibration curves were adopted. Both the discrete ultracentrifugation of individual compounds and cassette ultracentrifugation of all the test compounds followed by simultaneous LC-MS/MS analysis exhibited a linear correlation with literature values, demonstrating respectively the validity of the ultracentrifugation process and the cassette approach. The cassette ultracentrifugation using nonradiolabeled compounds followed by LC-MS/MS analysis has greatly facilitated its application for high-throughput protein binding screening in drug discovery.

Evolution of Orbitrap Mass Spectrometry Instrumentation

We discuss the evolution of Orbitrap mass spectrometry (MS) from its birth in the late 1990s to its current role as one of the most prominent techniques for MS. The Orbitrap mass analyzer is the first high-performance mass analyzer that employs trapping of ions in electrostatic fields. Tight integration with the ion injection process enables the high-resolution, mass accuracy, and sensitivity that have become essential for addressing analytical needs in numerous areas of research, as well as in routine analysis. We examine three major families of instruments (related to the LTQ Orbitrap, Q Exactive, and Orbitrap Fusion mass spectrometers) in the context of their historical development over the past ten eventful years. We discuss as well future trends and perspectives of Orbitrap MS. We illustrate the compelling potential of Orbitrap-based mass spectrometers as (ultra) high-resolution platforms, not only for high-end proteomic applications, but also for routine targeted analysis.

Sample reduction strategies in discovery bioanalysis

It is a constant challenge to provide timely bioanalytical support for the evaluation of drug-like properties and PK/PD profiles for the ever-increasing numbers of new chemical entities in a cost-effective manner. While technological advancement in various aspects of LC–MS/MS analysis has significantly improved bioanalytical efficiency, a number of simple sample reduction strategies can be employed to reduce the number of samples requiring analysis, and as a result increase the bioanalytical productivity without deploying additional instruments. In this review, advantages and precautions of common sample reduction strategies, such as sample pooling and cassette dosing, are discussed. In addition, other approaches such as reducing calibration standards and eliminating over-the-curve sample reanalysis will also be discussed. Taken together, these approaches can significantly increase the capacity and throughput of discovery bioanalysis without adding instruments, and are viable means to enhance the overall productivity of the bioanalytical laboratory.

Applications of high-resolution MS in bioanalysis

High-resolution MS (HRMS) in conjunction with LC (LC–HRMS) has become available to many laboratories in the pharmaceutical industry. Due to its enhanced, though sometime perceived, specificity using the high-resolution power and its capability of simultaneous quantitation and structural elucidation using the post-acquisition data mining feature, utilization of LC–HRMS for bioanalysis could lead to potential rapid and reliable method development as well as sample analysis, thus generating both cost and resource savings. Here, we would like to share our perspectives about several current and future applications of LC–HRMS in bioanalysis. We will also discuss the factors influencing the quality of method establishment and potential pitfalls that need to be considered for the utilization of LC–HRMS in the field of regulated bioanalysis. We believe when utilized appropriately, LC–HRMS will play a significant role in the future landscape of quantitative bioanalysis.

High-resolution MS in regulated bioanalysis: where are we now and where do we go from here?

While triple quadrupole MS remains the workhorse of bionanalytical laboratories, LC coupled with high-resolution MS (LC–HRMS) is making headway in drug discovery. LC–HRMS is well suited for quantitative bioanalysis with the inherent advantage of post-acquisition data mining, which is not possible with triple quadrupole systems operated in SRM mode. LC–HRMS can, thus, accomplish the core task of a bioanalytical laboratory – accurate determination of a targeted analyte – with the added bonus of being able to monitor other compounds of interest either at the time of sample analysis, or as an afterthought, after sample analysis, with no additional effort in sample preparation, chromatographic optimization or sample reinjection. Despite these advantages, LC–HRMS has not been broadly adopted in regulated bioanalytical laboratories. The slow progress in embracing the technology may be due, in part, to difficulties in replacing an entire fleet of triple quadrupole MS. Additional reasons are that data mining is of less benefit in development, especially late-stage, than in discovery and that the technical and regulatory challenges associated with the change of platform are perceived to be significant. In addition, the current platform of LC–HRMS introduced by instrument companies has not been tailored to the core responsibility of the bioanalytical community. In marketing current LC–HRMS systems, there is a tendency to combine the needs of the bioanalytical community with those of the drug metabolism community, despite their inherent differences. As a result, the current HRMS systems available lack some basic features desired for bioanalysis, but include features that are not important for bioanalysis making the systems unnecessarily complex and expensive. A simple, cost effective, ideal HRMS system for a bioanalytical laboratory would provide HRMS with high resolving power (the higher the better), no MS/MS capability, and with software suitable for quantitative analysis and appropriate for use in regulated laboratories. Under this scenario, one can foresee a future where part of the regulated bioanalytical work will be accomplished using LC–HRMS, reserving triple quadrupole-based LC–MS/MS for assays that require exquisite sensitivity.

Applicability of a blood-brain barrier specific artificial membrane permeability assay at the early stage of natural product-based CNS drug discovery

While numerous natural products (NPs) possess activity on central nervous system (CNS) targets, there has been no analytical approach to effectively identify compounds with high brain penetration potential in complex mixtures at the early stage of drug discovery. To overcome this issue, the performance of an in vitro parallel artificial membrane permeability assay for the blood-brain barrier (PAMPA-BBB) for natural products and for plant extracts has been validated and characterized. It was found that the PAMPA-BBB assay preserves its predictive power in the case of natural products and provides high phytochemical selectivity, which enables its use as a unique filtering tool in terms of selecting brain-penetrable compounds from plant extracts. Moreover, the present study has demonstrated that simple modifications in the assay design allow the direct use of PAMPA-BBB filtered samples in a dereplication process, as performed by NMR and LC-MS. The applicability of this procedure was demonstrated using extracts prepared from Tanacetum parthenium, Vinca major, Salvia officinalis, and Corydalis cava, representing different types of chemical diversity and complexity. Thus, the proposed protocol represents a potentially valuable strategy in the NP-based CNS drug discovery environment with a high-throughput screening platform.

Utility of high-resolution accurate MS to eliminate interferences in the bioanalysis of ribavirin and its phosphate metabolites

BACKGROUND

The polar nucleoside drug ribavirin (RBV) combined with IFN-α is a front-line treatment for chronic hepatitis C virus infection. RBV acts as a prodrug and exerts its broad antiviral activity primarily through its active phosphorylated metabolite ribavirin 5´-triphosphate (RTP), and also possibly through ribavirin 5´-monophosphate (RMP). To study RBV transport, diffusion, metabolic clearance and its impact on drug-metabolizing enzymes, a LC-MS method is needed to simultaneously quantify RBV and its phosphorylated metabolites (RTP, ribavirin 5´-diphosphate and RMP). In a recombinant human UGT1A1 assay, the assay buffer components uridine and its phosphorylated derivatives are isobaric with RBV and its phosphorylated metabolites, leading to significant interference when analyzed by LC-MS with the nominal mass resolution mode.

RESULTS

Presented here is a LC-MS method employing LC coupled with full-scan high-resolution accurate MS analysis for the simultaneous quantitative determination of RBV, RMP, ribavirin 5´-diphosphate and RTP by differentiating RBV and its phosphorylated metabolites from uridine and its phosphorylated derivatives by accurate mass, thus avoiding interference.

CONCLUSION

The developed LC-high-resolution accurate MS method allows for quantitation of RBV and its phosphorylated metabolites, eliminating the interferences from uridine and its phosphorylated derivatives in recombinant human UGT1A1 assays.

Recent development in software and automation tools for high-throughput discovery bioanalysis

Bioanalysis with LC–MS/MS has been established as the method of choice for quantitative determination of drug candidates in biological matrices in drug discovery and development. The LC–MS/MS bioanalytical support for drug discovery, especially for early discovery, often requires high-throughput (HT) analysis of large numbers of samples (hundreds to thousands per day) generated from many structurally diverse compounds (tens to hundreds per day) with a very quick turnaround time, in order to provide important activity and liability data to move discovery projects forward. Another important consideration for discovery bioanalysis is its fit-for-purpose quality requirement depending on the particular experiments being conducted at this stage, and it is usually not as stringent as those required in bioanalysis supporting drug development. These aforementioned attributes of HT discovery bioanalysis made it an ideal candidate for using software and automation tools to eliminate manual steps, remove bottlenecks, improve efficiency and reduce turnaround time while maintaining adequate quality. In this article we will review various recent developments that facilitate automation of individual bioanalytical procedures, such as sample preparation, MS/MS method development, sample analysis and data review, as well as fully integrated software tools that manage the entire bioanalytical workflow in HT discovery bioanalysis. In addition, software tools supporting the emerging high-resolution accurate MS bioanalytical approach are also discussed.