High-Throughput Bioassays using "Dip-and-Go" Multiplexed Electrospray Mass Spectrometry

Mobility capillary electrophoresis-native mass spectrometry reveals the dynamic conformational equilibrium of calmodulin and its complexes

Benefitting from the rapid evolution of artificial intelligence and structural biology, an expanding collection of high-resolution protein structures has greatly improved our understanding of protein functions. Yet, proteins are inherently flexible, and these static structures can only offer limited snapshots of their true dynamic nature. The conformational and functional changes of calmodulin (CaM) induced by Ca2+ binding have always been a focus of research. In this study, the conformational dynamics of CaM and its complexes were investigated using a mobility capillary electrophoresis (MCE) and native mass spectrometry (native MS) based method. By analyzing the ellipsoidal geometries of CaM in the solution phase at different Ca2+ concentrations, it is interesting to discover that CaM molecules, whether bound to Ca2+ or not, possess both closed and open conformations. Moreover, each individual CaM molecule actively "jumps" (equilibrium exchange) between these two distinct conformations on a timescale ranging from milli- to micro-seconds. The binding of Ca2+ ions did not affect the structural dynamics of CaM, while the binding of a peptide ligand would stabilize CaM, leading to the observation of a single, compact conformation of the resulting protein complex. A target recognition mechanism was also proposed based on these new findings, suggesting that CaM's interaction with targets may favor a conformational selection model. This enriches our understanding of the binding principles between CaM and its numerous targets.

Data processing for high-throughput mass spectrometry in drug discovery

INTRODUCTION

High-throughput mass spectrometry that could deliver > 10 times faster sample readout speed than traditional LC-based platforms has emerged as a powerful analytical technique, enabling the rapid analysis of complex biological samples. This increased speed of MS data acquisition has brought a critical demand for automatic data processing capabilities that should match or surpass the speed of data acquisition. Those data processing capabilities should serve the different requirements of drug discovery workflows.

AREAS COVERED

This paper introduced the key steps of the automatic data processing workflows for high-throughput MS technologies. Specific examples and requirements are detailed for different drug discovery applications.

EXPERT OPINION

The demand for automatic data processing in high-throughput mass spectrometry is driven by the need to keep pace with the accelerated speed of data acquisition. The seamless integration of processing capabilities with LIMS, efficient data review mechanisms, and the exploration of future features such as real-time feedback, automatic method optimization, and AI model training is crucial for advancing the drug discovery field. As technology continues to evolve, the synergy between high-throughput mass spectrometry and intelligent data processing will undoubtedly play a pivotal role in shaping the future of high-throughput drug discovery applications.

Surface charge-induced electrospray for high-throughput analysis of complex samples and electrochemical reaction intermediates using mass spectrometry

Electrospray-related ion sources are promising for direct mass spectrometric analysis of complex samples, but current protocols suffer from complicated components and low analytical sensitivity. Here, we propose a surface charge-induced electrospray ionization (SCIESI) inspired by flashover on an insulator surface under high voltage. This protocol not only effectively avoids contact between the sample solution and metal electrode, but also allows completion of the entire analytical process in less than 40 seconds and limits of detection in the pictogram per milliliter range. SCIESI coupled to mass spectrometry can also be used to monitor electro-chemical processes, and a number of oxidation and reduction reactions have been studied, demonstrating that it is a powerful tool for understanding electrochemical reaction mechanisms.

A Direct Infusion Probe for Rapid Metabolomics of Low-Volume Samples

Targeted and nontargeted metabolomics has the potential to evaluate and detect global metabolite changes in biological systems. Direct infusion mass spectrometric analysis enables detection of all ionizable small molecules, thus simultaneously providing information on both metabolites and lipids in chemically complex samples. However, to unravel the heterogeneity of the metabolic status of cells in culture and tissue a low number of cells per sample should be analyzed with high sensitivity, which requires low sample volumes. Here, we present the design and characterization of the direct infusion probe, DIP. The DIP is simple to build and position directly in front of a mass spectrometer for rapid metabolomics of chemically complex biological samples using pneumatically assisted electrospray ionization at 1 μL/min flow rate. The resulting data is acquired in a square wave profile with minimal carryover between samples that enhances throughput and enables several minutes of uniform MS signal from 5 μL sample volumes. The DIP was applied to study the intracellular metabolism of insulin secreting INS-1 cells and the results show that exposure to 20 mM glucose for 15 min significantly alters the abundance of several small metabolites, amino acids, and lipids.

High-Throughput Screening Using a Synchronized Pulsed Self-aspiration Vacuum Electrospray Ionization Miniature Mass Spectrometer

With the advantages of rapid analysis, high sensitivity, and multicomponent identification, mass spectrometry (MS) is recognized as an appealing choice for high-throughput screening (HTS) analysis. Aiming at the small size, simple operation, and adequate performance, the development of miniature mass spectrometers has made great progress over the last 2 decades. Besides the essential analytical performance, simple operation and HTS capability are two other crucial features desired in miniature MS instruments. In this paper, an induced self-aspiration vacuum electrospray ionization source (ISA-VESI) was developed and coupled to a miniature ion trap mass spectrometer. A special timing sequence was designed to synchronize all the operation steps in each measurement, including dual-pulse sample injection, multipulse gas injection, MS analysis, and the movement of the homemade HTS platform used as the sampler. Then, the automatic high-throughput analysis of multiple samples can be accomplished with close coordination among the sample delivery, the sample introduction and ionization, and the ion trap operation. The measurement time of each ISA-VESI-MS analysis was about 7 s, with a sample consumption of less than 100 nL.

High-throughput glycolytic inhibitor discovery targeting glioblastoma by graphite dots-assisted LDI mass spectrometry

Malignant tumors will become vulnerable if their uncontrolled biosynthesis and energy consumption engaged in metabolic reprogramming can be cut off. Here, we report finding a glycolytic inhibitor targeting glioblastoma with graphite dots-assisted laser desorption/ionization mass spectrometry as an integrated drug screening and pharmacokinetic platform (GLMSD). We have performed high-throughput virtual screening to narrow an initial library of 240,000 compounds down to the docking of 40 compounds and identified five previously unknown chemical scaffolds as promising hexokinase-2 inhibitors. The best inhibitor (Compd 27) can regulate the reprogrammed metabolic pathway in U87 glioma cells (median inhibitory concentration ~ 11.3 μM) for tumor suppression. Highly effective therapy against glioblastoma has been demonstrated in both subcutaneous and orthotopic brain tumors by synergizing Compd 27 and temozolomide. Our glycolytic inhibitor discovery can inspire personalized medicine targeting reprogrammed metabolisms of malignant tumors. GLMSD enables large, high-quality data for next-generation artificial intelligence-aided drug development.

Introducing Nafion for In Situ Desalting and Biofluid Profiling in Spray Mass Spectrometry

We introduce Nafion into the ambient ionization technique of spray mass spectrometry to serve for in situ desalting and direct analysis of biological fluids. Nafion was coated onto the surface of the triangular spray tip as the cation exchange material. Because the sulfonic group from the Nafion membrane effectively exchanges their carried protons with inorganic salt ions (e.g., Na+ and K+), the analyte's ionization efficiency can be significantly enhanced by reducing ion suppression. The desalting efficiency can reach 90% and the maximum tolerance of the absolute salt amount reaches 100 μmol. The mass spectral profile can also be simplified by removing the multiple adducted ion types from small-molecule drugs and metabolites ([M + Na]+ and [M + K]+), or multiply charged ions formed by proteins ([M + nNa]n+ and [M + nK]n+). Thus, the Nafion coating makes less ambiguous data interpretation collected from spray mass spectrometry for qualitative profiling or quantitative measurement of a target analyte.

A Deep-Learning Proteomic-Scale Approach for Drug Design

Computational approaches have accelerated novel therapeutic discovery in recent decades. The Computational Analysis of Novel Drug Opportunities (CANDO) platform for shotgun multitarget therapeutic discovery, repurposing, and design aims to improve their efficacy and safety by employing a holistic approach that computes interaction signatures between every drug/compound and a large library of non-redundant protein structures corresponding to the human proteome fold space. These signatures are compared and analyzed to determine if a given drug/compound is efficacious and safe for a given indication/disease. In this study, we used a deep learning-based autoencoder to first reduce the dimensionality of CANDO-computed drug-proteome interaction signatures. We then employed a reduced conditional variational autoencoder to generate novel drug-like compounds when given a target encoded "objective" signature. Using this approach, we designed compounds to recreate the interaction signatures for twenty approved and experimental drugs and showed that 16/20 designed compounds were predicted to be significantly (p-value ≤ 0.05) more behaviorally similar relative to all corresponding controls, and 20/20 were predicted to be more behaviorally similar relative to a random control. We further observed that redesigns of objectives developed via rational drug design performed significantly better than those derived from natural sources (p-value ≤ 0.05), suggesting that the model learned an abstraction of rational drug design. We also show that the designed compounds are structurally diverse and synthetically feasible when compared to their respective objective drugs despite consistently high predicted behavioral similarity. Finally, we generated new designs that enhanced thirteen drugs/compounds associated with non-small cell lung cancer and anti-aging properties using their predicted proteomic interaction signatures. his study represents a significant step forward in automating holistic therapeutic design with machine learning, enabling the rapid generation of novel, effective, and safe drug leads for any indication.

Hypochlorous acid initiated lipid chlorination at air-water interface

There has been a surge of interest in interfacial hypochlorous acid (HOCl) chemistry for indoor air quality and public health. Here we combined nanoelectrospray mass spectrometry (nESI-MS) and acoustic levitation (AL) techniques to study the chlorination chemistry of three model lipids (DPPE, POPG, DOPG) mediated by HOCl at the air-water interface of levitated water droplet. For DPPE with no CC double bonds, HOCl was insensitive to the alkane chains, and showed considerable delay directing to head amino groups compared to that in aqueous environment. Chlorination chemistry, for POPG and DOPG with CC double bonds, preferentially reacted with double bonds of one chain. The mechanism was discussed in light of these observations, and it is concluded that the increased hydrophilicity of the chlorinated chain disturbed the lipid packing and attracted it toward the water phase. In addition, the reaction rate constant and reactive uptake coefficient suggested that the chlorination of lipids exposed to HOCl at the air-water interface is likely to occur rapidly. These results gain the knowledge of HOCl mediated lipid interface reaction at the molecule level, and would better understand the adverse health effects associated with elevated indoor pollutants.

Biocatalysis in the Chemistry of Lupane Triterpenoids

Pentacyclic triterpenes are important representatives of natural products that exhibit a wide variety of biological activities. These activities suggest that these compounds may represent potential medicines for the treatment of cancer and viral, bacterial, or protozoal infections. Naturally occurring triterpenes usually have several drawbacks, such as limited activity and insufficient solubility and bioavailability; therefore, they need to be modified to obtain compounds suitable for drug development. Modifications can be achieved either by methods of standard organic synthesis or with the use of biocatalysts, such as enzymes or enzyme systems within living organisms. In most cases, these modifications result in the preparation of esters, amides, saponins, or sugar conjugates. Notably, while standard organic synthesis has been heavily used and developed, the use of the latter methodology has been rather limited, but it appears that biocatalysis has recently sparked considerably wider interest within the scientific community. Among triterpenes, derivatives of lupane play important roles. This review therefore summarizes the natural occurrence and sources of lupane triterpenoids, their biosynthesis, and semisynthetic methods that may be used for the production of betulinic acid from abundant and inexpensive betulin. Most importantly, this article compares chemical transformations of lupane triterpenoids with analogous reactions performed by biocatalysts and highlights a large space for the future development of biocatalysis in this field. The results of this study may serve as a summary of the current state of research and demonstrate the potential of the method in future applications.

Electric field-assisted multiphase extraction to increase selectivity and sensitivity in liquid chromatography-mass spectrometry and paper spray mass spectrometry

In this work, for the first time, chromatographic paper was used for a multiphase extraction assisted by an electric field (MPEF) and directly coupled to paper spray mass spectrometry (PS-MS). Using this approach, five tricyclic antidepressants (TCAs) were determined in oral fluid. Firstly, the MPEF conditions were optimized using liquid chromatography-mass spectrometry (LC-MS/MS). The effects of the chromatographic paper and the types of electrolyte used in the acceptor phase, the organic solvent type and the amount used in the donor phase, the extraction time, and the applied electric potential were all investigated. After optimization, the analytes were extracted from the donor solution (sample and acetonitrile 1:1 (v/v)) over a period of 10 min at 300 V, crossing the free liquid membrane (1-octanol) and reaching the acceptor phase (chromatographic paper wetted with 400 mmol L^-1 acetic acid). The method using LC-MS/MS was validated, demonstrating a linear range from 2 to 12 ng mL^-1, with detection and quantification limits of 0.13-0.25 and 0.44-0.84 ng mL^-1, respectively, an intraday precision of less than 20%, and no matrix effect observed. The optimized MPEF conditions were then applied to determine TCAs by PS-MS and for this analysis cyclobenzaprine was used as an internal standard. The easy, fast and direct approach of coupling MPEF with PS-MS analysis, as well as the pre-concentration and the low standard deviation of replicates (less than 20%), demonstrates that this method can be useful for screening in clinical and toxicological analysis.

High-Throughput Mass Spectrometry for Hit Identification: Current Landscape and Future Perspectives

For nearly two decades mass spectrometry has been used as a label-free, direct-detection method for both functional and affinity-based screening of a wide range of therapeutically relevant target classes. Here, we present an overview of several established and emerging mass spectrometry platforms and summarize the unique strengths and performance characteristics of each as they apply to high-throughput screening. Multiple examples from the recent literature are highlighted in order to illustrate the power of each individual technique, with special emphasis given to cases where the use of mass spectrometry was found to be differentiating when compared with other detection formats. Indeed, as many of these examples will demonstrate, the inherent strengths of mass spectrometry-sensitivity, specificity, wide dynamic range, and amenability to complex matrices-can be leveraged to enhance the discriminating power and physiological relevance of assays included in screening cascades. It is our hope that this review will serve as a useful guide to readers of all backgrounds and experience levels on the applicability and benefits of mass spectrometry in the search for hits, leads, and, ultimately, drugs.

Emerging Chromatography-Free High-Throughput Mass Spectrometry Technologies for Generating Hits and Leads

Mass spectrometry (MS) detection can offer unmatched selectivity and sensitivity. The use of MS without chromatography greatly increases the throughput, making it suitable for high throughput screening. However, the trade-offs of direct MS detection need to be carefully evaluated along with the development of novel strategies to ensure successful implementation. In this review, we will discuss the pros and cons of chromatography-free MS and discuss some of the currently used and future technologies being investigated to enable high-throughput MS.

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.

Induced Self-aspiration Electrospray Ionization Mass Spectrometry for Flexible Sampling and Analysis

Electrospray ionization (ESI) operating in pulse mode can enhance the utilization efficiency of the electrospray ions by a mass spectrometer. Herein, a novel ionization technique called induced self-aspiration-electrospray ionization (ISA-ESI) was developed based on self-aspiration sampling and capacitive induction. The sample solution polarized in a strong electric field was pulsed drawn into a capillary that was connected to a subambient chamber. The sample solution with polarized ions forms a charged liquid column, which can initiate an electrospray when reaching the capillary outlet. In addition to the self-aspiration ability, the use of a constant high voltage supply and no electrical contact with the solution can also simplify the sampling and ionization operation, enabling a convenient ESI mass spectrometry analysis. The developed ISA-ESI source has been used for multidimensional monitoring of chemical reactions as well as liquid extraction surface analysis of plant tissues. It was expected that this special ionization method could be extended to automated high-throughput ESI-MS analysis.