1
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Liu C, Zhang H. Data processing for high-throughput mass spectrometry in drug discovery. Expert Opin Drug Discov 2024; 19:815-825. [PMID: 38785418 DOI: 10.1080/17460441.2024.2354871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024]
Abstract
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.
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Affiliation(s)
| | - Hui Zhang
- Iambic Therapeutics, San Diego, CA, USA
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2
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Henderson A, Heaney LM, Rankin-Turner S. Ambient ionisation mass spectrometry for drug and toxin analysis: A review of the recent literature. Drug Test Anal 2024. [PMID: 38326879 DOI: 10.1002/dta.3644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/17/2023] [Accepted: 12/28/2023] [Indexed: 02/09/2024]
Abstract
Ambient ionisation mass spectrometry (AIMS) is a form of mass spectrometry whereby analyte ionisation occurs outside of a vacuum source under ambient conditions. This enables the direct analysis of samples in their native state, with little or no sample preparation and without chromatographic separation. The removal of these steps facilitates a much faster analytical process, enabling the direct analysis of samples within minutes if not seconds. Consequently, AIMS has gained rapid popularity across a diverse range of applications, in particular the analysis of drugs and toxins. Numerous fields rely upon mass spectrometry for the detection and identification of drugs, including clinical diagnostics, forensic chemistry, and food safety. However, all of these fields are hindered by the time-consuming and laboratory-confined nature of traditional techniques. As such, the potential for AIMS to resolve these challenges has resulted in a growing interest in ambient ionisation for drug and toxin analysis. Since the early 2000s, forensic science, diagnostic testing, anti-doping, pharmaceuticals, environmental analysis and food safety have all seen a marked increase in AIMS applications, foreshadowing a new future for drug testing. In this review, some of the most promising AIMS techniques for drug analysis will be discussed, alongside different applications of AIMS published over a 5-year period, to provide a summary of the recent research activity for ambient ionisation for drug and toxin analysis.
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Affiliation(s)
- Alisha Henderson
- School of Sport, Exercise and Health Sciences, Loughborough University, Loughborough, UK
| | - Liam M Heaney
- School of Sport, Exercise and Health Sciences, Loughborough University, Loughborough, UK
| | - Stephanie Rankin-Turner
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
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3
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Hu H, Singh AN, Lehnherr D, Mdluli V, Chun SW, Makarewicz AM, Gouker JR, Ukaegbu O, Li S, Wen X, McLaren DG, Velasquez JE, Moore JC, Galanie S, Appiah-Amponsah E, Regalado EL. Accelerating Pharmaceutical Process Development with an Acoustic Droplet Ejection-Multiple Reaction Monitoring-Mass Spectrometry Workflow. Anal Chem 2024; 96:1138-1146. [PMID: 38165811 DOI: 10.1021/acs.analchem.3c04211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
Fast-paced pharmaceutical process developments (e.g., high-throughput experimentation, directed evolution, and machine learning) involve the introduction of fast, sensitive, and accurate analytical assays using limited sample volumes. In recent years, acoustic droplet ejection (ADE) coupled with an open port interface has been invented as a sampling technology for mass spectrometry, providing high-throughput nanoliter analytical measurements directly from the standard microplates. Herein, we introduce an ADE-multiple reaction monitoring-mass spectrometry (ADE-MRM-MS) workflow to accelerate pharmaceutical process research and development (PR&D). This systematic workflow outlines the selection of MRM transitions and optimization of assay parameters in a data-driven manner using rapid measurements (1 sample/s). The synergy between ADE sampling and MRM analysis enables analytical assays with excellent sensitivity, selectivity, and speed for PR&D reaction screenings. This workflow was utilized to develop new ADE-MRM-MS assays guiding a variety of industrial processes, including (1) screening of Ni-based catalysts for C-N cross-coupling reaction at 1 Hz and (2) high-throughput regioisomer analysis-enabled enzyme library screening for peptide ligation reaction. ADE-MRM-MS assays were demonstrated to deliver accurate results that are comparable to conventional liquid chromatography (LC) experiments while providing >100-fold throughput enhancement.
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Affiliation(s)
- Hang Hu
- Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Andrew N Singh
- Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Dan Lehnherr
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Velabo Mdluli
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Stephanie W Chun
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Amanda M Makarewicz
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Joseph R Gouker
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Ophelia Ukaegbu
- Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Shasha Li
- Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Xiujuan Wen
- Quantitative Biosciences, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - David G McLaren
- Quantitative Biosciences, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Juan E Velasquez
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Jeffrey C Moore
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Stephanie Galanie
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | | | - Erik L Regalado
- Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
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4
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Huang KH, Morato NM, Feng Y, Cooks RG. High-Throughput Diversification of Complex Bioactive Molecules by Accelerated Synthesis in Microdroplets. Angew Chem Int Ed Engl 2023; 62:e202300956. [PMID: 36941213 PMCID: PMC10182919 DOI: 10.1002/anie.202300956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/17/2023] [Accepted: 03/20/2023] [Indexed: 03/23/2023]
Abstract
Late-stage diversification of drug molecules is an important strategy in drug discovery that can be facilitated by reaction screening using high-throughput experimentation. Here we present a rapid method for functionalizing bioactive molecules based on accelerated reactions in microdroplets. Reaction mixtures are nebulized at throughputs better than 1 reaction/second and the accelerated reactions occurring in the microdroplets are followed by desorption electrospray ionization mass spectrometry (DESI-MS). Because the accelerated reactions occur on the millisecond timescale, they allow an overall screening throughput of 1 Hz working at the low nanogram scale. Using this approach, an opioid agonist (PZM21) and an antagonist (naloxone) were diversified using three reactions important in medicinal chemistry: sulfur fluoride exchange (SuFEx) click reactions, imine formation reactions, and ene-type click reactions. Some 269 functionalized analogs of naloxone and PZM21 were generated and characterized by tandem mass spectrometry (MS/MS) after screening over 500 reactions.
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Affiliation(s)
- Kai-Hung Huang
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Nicolás M Morato
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Yunfei Feng
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - R Graham Cooks
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
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5
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Taylor CJ, Pomberger A, Felton KC, Grainger R, Barecka M, Chamberlain TW, Bourne RA, Johnson CN, Lapkin AA. A Brief Introduction to Chemical Reaction Optimization. Chem Rev 2023; 123:3089-3126. [PMID: 36820880 PMCID: PMC10037254 DOI: 10.1021/acs.chemrev.2c00798] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
From the start of a synthetic chemist's training, experiments are conducted based on recipes from textbooks and manuscripts that achieve clean reaction outcomes, allowing the scientist to develop practical skills and some chemical intuition. This procedure is often kept long into a researcher's career, as new recipes are developed based on similar reaction protocols, and intuition-guided deviations are conducted through learning from failed experiments. However, when attempting to understand chemical systems of interest, it has been shown that model-based, algorithm-based, and miniaturized high-throughput techniques outperform human chemical intuition and achieve reaction optimization in a much more time- and material-efficient manner; this is covered in detail in this paper. As many synthetic chemists are not exposed to these techniques in undergraduate teaching, this leads to a disproportionate number of scientists that wish to optimize their reactions but are unable to use these methodologies or are simply unaware of their existence. This review highlights the basics, and the cutting-edge, of modern chemical reaction optimization as well as its relation to process scale-up and can thereby serve as a reference for inspired scientists for each of these techniques, detailing several of their respective applications.
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Affiliation(s)
- Connor J Taylor
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
- Innovation Centre in Digital Molecular Technologies, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Alexander Pomberger
- Innovation Centre in Digital Molecular Technologies, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Kobi C Felton
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K
| | - Rachel Grainger
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Magda Barecka
- Chemical Engineering Department, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
- Chemistry and Chemical Biology Department, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
- Cambridge Centre for Advanced Research and Education in Singapore, 1 Create Way, 138602 Singapore
| | - Thomas W Chamberlain
- Institute of Process Research and Development, School of Chemistry and School of Chemical and Process Engineering, University of Leeds, Leeds LS2 9JT, U.K
| | - Richard A Bourne
- Institute of Process Research and Development, School of Chemistry and School of Chemical and Process Engineering, University of Leeds, Leeds LS2 9JT, U.K
| | - Christopher N Johnson
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Alexei A Lapkin
- Innovation Centre in Digital Molecular Technologies, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
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6
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Arciniega C, Garrard KP, Guymon JP, Manni JG, Apffel A, Fjeldsted JC, Muddiman DC. Quasi-continuous infrared matrix-assisted laser desorption electrospray ionization source coupled to a quadrupole time-of-flight mass spectrometer for direct analysis from well plates. JOURNAL OF MASS SPECTROMETRY : JMS 2023; 58:e4902. [PMID: 36694312 PMCID: PMC9944147 DOI: 10.1002/jms.4902] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 12/03/2022] [Accepted: 01/07/2023] [Indexed: 06/17/2023]
Abstract
High-throughput screening (HTS) is a technique mostly used by pharmaceutical companies to rapidly screen multiple libraries of compounds to find drug hits with biological or pharmaceutical activity. Mass spectrometry (MS) has become a popular option for HTS given that it can simultaneously resolve hundreds to thousands of compounds without additional chemical derivatization. For this application, it is convenient to do direct analysis from well plates. Herein, we present the development of an infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) source coupled directly to an Agilent 6545 for direct analysis from well plates. The source is coupled to a quadrupole time-of-flight (Q-TOF) mass spectrometer to take advantage of the high acquisition rates without sacrificing resolving power as required with Orbitrap or Fourier-transform ion cyclotron resonance (FTICR) instruments. The laser used for this source operates at 100 Hz, firing 1 pulse-per-burst, and delivers around 0.7 mJ per pulse. Continuously firing this laser for an extended duration makes it a quasi-continuous ionization source. Additionally, a metal capillary was constructed to extend the inlet of the mass spectrometer, increase desolvation of electrospray charged droplets, improve ion transmission, and increase sensitivity. Its efficiency was compared with the conventional dielectric glass capillary by measured signal and demonstrated that the metal capillary increased ionization efficiency due to its more uniformly distributed temperature gradient. Finally, we present the functionality of the source by analyzing tune mix directly from well plates. This source is a proof of concept for HTS applications using IR-MALDESI coupled to a different MS platform.
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Affiliation(s)
- Cristina Arciniega
- FTMS Laboratory for Human Health Research, Department of ChemistryNorth Carolina State UniversityRaleighNC27695USA
| | - Kenneth P. Garrard
- FTMS Laboratory for Human Health Research, Department of ChemistryNorth Carolina State UniversityRaleighNC27695USA
- Precision Engineering ConsortiumNorth Carolina State UniversityRaleighNC27695USA
- Molecular Education, Technology and Research Innovation Center (METRIC)North Carolina State UniversityRaleighNC27695USA
| | - Jacob P. Guymon
- Precision Engineering ConsortiumNorth Carolina State UniversityRaleighNC27695USA
| | | | | | | | - David C. Muddiman
- FTMS Laboratory for Human Health Research, Department of ChemistryNorth Carolina State UniversityRaleighNC27695USA
- Molecular Education, Technology and Research Innovation Center (METRIC)North Carolina State UniversityRaleighNC27695USA
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7
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Morato NM, Brown HM, Garcia D, Middlebrooks EH, Jentoft M, Chaichana K, Quiñones-Hinojosa A, Cooks RG. High-throughput analysis of tissue microarrays using automated desorption electrospray ionization mass spectrometry. Sci Rep 2022; 12:18851. [PMID: 36344609 PMCID: PMC9640715 DOI: 10.1038/s41598-022-22924-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 10/20/2022] [Indexed: 11/09/2022] Open
Abstract
Tissue microarrays (TMAs) are commonly used for the rapid analysis of large numbers of tissue samples, often in morphological assessments but increasingly in spectroscopic analysis, where specific molecular markers are targeted via immunostaining. Here we report the use of an automated high-throughput system based on desorption electrospray ionization (DESI) mass spectrometry (MS) for the rapid generation and online analysis of high-density (6144 samples/array) TMAs, at rates better than 1 sample/second. Direct open-air analysis of tissue samples (hundreds of nanograms) not subjected to prior preparation, plus the ability to provide molecular characterization by tandem mass spectrometry (MS/MS), make this experiment versatile and applicable to both targeted and untargeted analysis in a label-free manner. These capabilities are demonstrated in a proof-of-concept study of frozen brain tissue biopsies where we showcase (i) a targeted MS/MS application aimed at identification of isocitrate dehydrogenase mutation in glioma samples and (ii) an untargeted MS tissue type classification using lipid profiles and correlation with tumor cell percentage estimates from histopathology. The small sample sizes and large sample numbers accessible with this methodology make for a powerful analytical system that facilitates the identification of molecular markers for later use in intraoperative applications to guide precision surgeries and ultimately improve patient outcomes.
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Affiliation(s)
- Nicolás M. Morato
- grid.169077.e0000 0004 1937 2197Department of Chemistry, Purdue Center for Cancer Research, and Bindley Bioscience Center, Purdue University, 560 Oval Drive, West Lafayette, IN 47907 USA
| | - Hannah Marie Brown
- grid.169077.e0000 0004 1937 2197Department of Chemistry, Purdue Center for Cancer Research, and Bindley Bioscience Center, Purdue University, 560 Oval Drive, West Lafayette, IN 47907 USA ,grid.4367.60000 0001 2355 7002Present Address: Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO USA
| | - Diogo Garcia
- grid.417467.70000 0004 0443 9942Department of Neurosurgery, Mayo Clinic, Jacksonville, FL USA
| | - Erik H. Middlebrooks
- grid.417467.70000 0004 0443 9942Department of Neurosurgery, Mayo Clinic, Jacksonville, FL USA ,grid.417467.70000 0004 0443 9942Department of Radiology, Mayo Clinic, Jacksonville, FL USA
| | - Mark Jentoft
- grid.417467.70000 0004 0443 9942Department of Laboratory Medicine and Pathology, Mayo Clinic, Jacksonville, FL USA
| | - Kaisorn Chaichana
- grid.417467.70000 0004 0443 9942Department of Neurosurgery, Mayo Clinic, Jacksonville, FL USA
| | | | - R. Graham Cooks
- grid.169077.e0000 0004 1937 2197Department of Chemistry, Purdue Center for Cancer Research, and Bindley Bioscience Center, Purdue University, 560 Oval Drive, West Lafayette, IN 47907 USA
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8
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High-throughput synthesis of silver nanoplates and optimization of optical properties by machine learning. Chem Eng Sci 2022. [DOI: 10.1016/j.ces.2022.118009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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9
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Shi L, Habib A, Bi L, Hong H, Begum R, Wen L. Ambient Ionization Mass Spectrometry: Application and Prospective. Crit Rev Anal Chem 2022:1-50. [PMID: 36206159 DOI: 10.1080/10408347.2022.2124840] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2022]
Abstract
Mass spectrometry (MS) is a formidable analytical tool for the analysis of non-polar to polar compounds individually and/or from mixtures, providing information on the molecular weights and chemical structures of the analytes. During the last more than one-decade, ambient ionization mass spectrometry (AIMS) has developed quickly, producing a wide range of platforms and proving scientific improvements in a variety of domains, from biological imaging to quick quality control. These methods have made it possible to detect target analytes in real time without sample preparation in an open environment, and they can be connected to any MS system with an atmospheric pressure interface. They also have the ability to analyze explosives, illicit drugs, disease diagnostics, drugs in biological samples, adulterants in food and agricultural products, reaction progress, and environmental monitoring. The development of novel ambient ionization techniques, such as probe electrospray ionization, paper spray ionization, and fiber spray ionization, employed even at picolitre to femtolitre solution levels to provide femtogram to attogram levels of the target analytes. The special characteristic of this ambient ion source, which has been extensively used, is the noninvasive property of PESI of examination of biological real samples. The results in the current review supports the idea that AIMS has emerged as a pioneer in MS-based approaches and that methods will continue to be developed along with improvements to existing ones in the near future.
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Affiliation(s)
- Lulu Shi
- Shanghai Institute of Technical Physics, Chinese Academy of Sciences, Shanghai, China
- China Innovation Instrument Co., Ltd, Ningbo, Zhejiang, China
| | - Ahsan Habib
- China Innovation Instrument Co., Ltd, Ningbo, Zhejiang, China
- The Research Institute of Advanced Technologies, Ningbo University, Ningbo, Zhejiang, China
- Department of Chemistry, University of Dhaka, Dhaka, Bangladesh
| | - Lei Bi
- China Innovation Instrument Co., Ltd, Ningbo, Zhejiang, China
- The Research Institute of Advanced Technologies, Ningbo University, Ningbo, Zhejiang, China
| | - Huanhuan Hong
- China Innovation Instrument Co., Ltd, Ningbo, Zhejiang, China
- The Research Institute of Advanced Technologies, Ningbo University, Ningbo, Zhejiang, China
| | - Rockshana Begum
- Department of Chemistry, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Luhong Wen
- China Innovation Instrument Co., Ltd, Ningbo, Zhejiang, China
- The Research Institute of Advanced Technologies, Ningbo University, Ningbo, Zhejiang, China
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10
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Peterson TL, Nagy G. Rapid cyclic ion mobility separations of monosaccharide building blocks as a first step toward a high-throughput reaction screening platform for carbohydrate syntheses. RSC Adv 2021; 11:39742-39747. [PMID: 35494126 PMCID: PMC9044565 DOI: 10.1039/d1ra08746k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 12/07/2021] [Indexed: 12/12/2022] Open
Abstract
Herein we present a new high-throughput screening method for carbohydrate syntheses based on cyclic ion mobility spectrometry-mass spectrometry (cIMS-MS)-based separations. We rapidly resolved the α/β anomers for carbohydrates with varying protecting groups after only 5 m of cIMS-MS separation and also detected their respective unwanted anomeric impurities at levels lower than 2%. All experiments were performed in 1 minute of total acquisition time demonstrating our method's high-throughput nature. Our methodology was also extended to the separation of an isomeric mixtures of two protected disaccharides illustrating its utility beyond only monosaccharides. We envision our presented workflow as a first step toward the development of a high-throughput screening platform for the rapid and sensitive detection of α/β anomeric selectivities and for trace isomeric/isobaric impurities.
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Affiliation(s)
- Tyler L Peterson
- Department of Chemistry, University of Utah 315 South 1400 East, Room 2020 Salt Lake City Utah 84112 USA
| | - Gabe Nagy
- Department of Chemistry, University of Utah 315 South 1400 East, Room 2020 Salt Lake City Utah 84112 USA
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11
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Overhoff B, Falls Z, Mangione W, Samudrala R. A Deep-Learning Proteomic-Scale Approach for Drug Design. Pharmaceuticals (Basel) 2021; 14:1277. [PMID: 34959678 PMCID: PMC8709297 DOI: 10.3390/ph14121277] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/27/2021] [Accepted: 11/29/2021] [Indexed: 12/26/2022] Open
Abstract
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.
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Affiliation(s)
| | | | | | - Ram Samudrala
- Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14203, USA; (B.O.); (Z.F.); (W.M.)
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12
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Inter-platform assessment of performance of high-throughput desorption electrospray ionization mass spectrometry. TALANTA OPEN 2021. [DOI: 10.1016/j.talo.2021.100046] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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13
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Morato NM, Le MT, Holden DT, Graham Cooks R. Automated High-Throughput System Combining Small-Scale Synthesis with Bioassays and Reaction Screening. SLAS Technol 2021; 26:555-571. [PMID: 34697962 DOI: 10.1177/24726303211047839] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The Purdue Make It system is a unique automated platform capable of small-scale in situ synthesis, screening small-molecule reactions, and performing direct label-free bioassays. The platform is based on desorption electrospray ionization (DESI), an ambient ionization method that allows for minimal sample workup and is capable of accelerating reactions in secondary droplets, thus conferring unique advantages compared with other high-throughput screening technologies. By combining DESI with liquid handling robotics, the system achieves throughputs of more than 1 sample/s, handling up to 6144 samples in a single run. As little as 100 fmol/spot of analyte is required to perform both initial analysis by mass spectrometry (MS) and further MSn structural characterization. The data obtained are processed using custom software so that results are easily visualized as interactive heatmaps of reaction plates based on the peak intensities of m/z values of interest. In this paper, we review the system's capabilities as described in previous publications and demonstrate its utilization in two new high-throughput campaigns: (1) the screening of 188 unique combinatorial reactions (24 reaction types, 188 unique reaction mixtures) to determine reactivity trends and (2) label-free studies of the nicotinamide N-methyltransferase enzyme directly from the bioassay buffer. The system's versatility holds promise for several future directions, including the collection of secondary droplets containing the products from successful reaction screening measurements, the development of machine learning algorithms using data collected from compound library screening, and the adaption of a variety of relevant bioassays to high-throughput MS.
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Affiliation(s)
- Nicolás M Morato
- Department of Chemistry and Center for Analytical Instrumentation Development, Purdue University, West Lafayette, IN, USA
| | - MyPhuong T Le
- Department of Chemistry and Center for Analytical Instrumentation Development, Purdue University, West Lafayette, IN, USA
| | - Dylan T Holden
- Department of Chemistry and Center for Analytical Instrumentation Development, Purdue University, West Lafayette, IN, USA
| | - R Graham Cooks
- Department of Chemistry and Center for Analytical Instrumentation Development, Purdue University, West Lafayette, IN, USA
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14
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Kafeenah H, Jen HH, Chen SH. Microdroplet mass spectrometry: Accelerating reaction and application. Electrophoresis 2021; 43:74-81. [PMID: 34591317 DOI: 10.1002/elps.202100208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/29/2021] [Accepted: 09/25/2021] [Indexed: 12/17/2022]
Abstract
Electrospray ionization (ESI) and desorption electrospray ionization (DESI) are common soft ionization method of mass spectrometry (MS). However, recent studies revealed that some chemical reactions can be induced or greatly accelerated in the sprayed microdroplets compared to the same reaction in the bulk. These open a new area in using microdroplet MS to explore new chemistry and develop new applications. This minireview will introduce microdroplet chemistries and explore various microdroplet techniques most of which are ESI- or DESI-based extensions by incorporating transfer tube, supersonic nebulizing gas, droplet fusion, spray extraction, laser irradiation, or laser ablation for online/offline MS analysis. Potential applications associated with new techniques, including real-time reaction monitoring, high-throughput reaction screening, protein identification, and protein characterization, are also described. Future outlook, such as coupling microdroplet MS with separation techniques, is proposed and discussed.
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Affiliation(s)
- Husam Kafeenah
- Department of Chemistry, National Cheng Kung University, Tainan, Taiwan
| | - Hung-Hsiang Jen
- Department of Chemistry, National Cheng Kung University, Tainan, Taiwan
| | - Shu-Hui Chen
- Department of Chemistry, National Cheng Kung University, Tainan, Taiwan
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15
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Le MT, Morato NM, Kaerner A, Welch CJ, Cooks RG. Fragmentation of Polyfunctional Compounds Recorded Using Automated High-Throughput Desorption Electrospray Ionization. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2261-2273. [PMID: 34280312 DOI: 10.1021/jasms.1c00176] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Using desorption electrospray ionization (DESI) as part of an automated high-throughput system, tandem mass spectra of the compounds in a pharmaceutical library were recorded in the positive mode under standardized conditions. Quality control filtering yielded an MS/MS library of 16 662 spectra. Fragmentation of subsets of the compounds in the library chosen to contain a single instance of a particular functional group (amide, piperazine, sulfonamide) was predicted by experts, and the results were compared with the experimental data. Expert performance was good to excellent for all the cases evaluated. Substituents on the functional groups were found to exert important secondary control over the fragmentation, with the main effect observed being product ion stabilization by aromatic substitution, which was consistent across the different groups evaluated. These substituent effects are generally explicable in terms of standard physical organic chemistry considerations of product ion stability as controlling fragmentation. A somewhat unexpected feature was the incidence of homolytic cleavages, driven by the stability of substituted amine radical cations. The findings of this study are intended to lay the groundwork for machine learning approaches to performing MS/MS spectrum → structure and structure → MS/MS spectrum operations on the same experimental data set. The effort involved and the success achieved in computer-aided interpretation, now underway, will be compared with the expert performance as described here.
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Affiliation(s)
- MyPhuong T Le
- Department of Chemistry and Bindley Bioscience Center, Purdue University, West Lafayette, Indiana 47907, United States
| | - Nicolás M Morato
- Department of Chemistry and Bindley Bioscience Center, Purdue University, West Lafayette, Indiana 47907, United States
| | - Andreas Kaerner
- Discovery Chemistry Research and Technologies, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Christopher J Welch
- Indiana Consortium for Analytical Science and Engineering (ICASE), Indianapolis, Indiana 46202, United States
| | - R Graham Cooks
- Department of Chemistry and Bindley Bioscience Center, Purdue University, West Lafayette, Indiana 47907, United States
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16
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Li Y, Huang KH, Morato NM, Cooks RG. Glass surface as strong base, 'green' heterogeneous catalyst and degradation reagent. Chem Sci 2021; 12:9816-9822. [PMID: 34349955 PMCID: PMC8294000 DOI: 10.1039/d1sc02708e] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 06/23/2021] [Indexed: 12/18/2022] Open
Abstract
Systematic screening of accelerated chemical reactions at solid/solution interfaces has been carried out in high-throughput fashion using desorption electrospray ionization mass spectrometry and it provides evidence that glass surfaces accelerate various base-catalyzed chemical reactions. The reaction types include elimination, solvolysis, condensation and oxidation, whether or not the substrates are pre-charged. In a detailed mechanistic study, we provide evidence using nanoESI showing that glass surfaces can act as strong bases and convert protic solvents into their conjugate bases which then act as bases/nucleophiles when participating in chemical reactions. In aprotic solvents such as acetonitrile, glass surfaces act as 'green' heterogeneous catalysts that can be recovered and reused after simple rinsing. Besides their use in organic reaction catalysis, glass surfaces are also found to act as degradation reagents for phospholipids with increasing extents of degradation occurring at low concentrations. This finding suggests that the storage of base/nucleophile-labile compounds or lipids in glass containers should be avoided.
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Affiliation(s)
- Yangjie Li
- Department of Chemistry, Purdue University West Lafayette IN 47907 USA
| | - Kai-Hung Huang
- Department of Chemistry, Purdue University West Lafayette IN 47907 USA
| | - Nicolás M Morato
- Department of Chemistry, Purdue University West Lafayette IN 47907 USA
| | - R Graham Cooks
- Department of Chemistry, Purdue University West Lafayette IN 47907 USA
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17
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Rankin‐Turner S, Heaney LM. Applications of ambient ionization mass spectrometry in 2020: An annual review. ANALYTICAL SCIENCE ADVANCES 2021; 2:193-212. [PMID: 38716454 PMCID: PMC10989608 DOI: 10.1002/ansa.202000135] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 01/22/2021] [Accepted: 01/25/2021] [Indexed: 06/26/2024]
Abstract
Recent developments in mass spectrometry (MS) analyses have seen a concerted effort to reduce the complexity of analytical workflows through the simplification (or removal) of sample preparation and the shortening of run-to-run analysis times. Ambient ionization mass spectrometry (AIMS) is an exemplar MS-based technology that has swiftly developed into a popular and powerful tool in analytical science. This increase in interest and demonstrable applications is down to its capacity to enable the rapid analysis of a diverse range of samples, typically in their native state or following a minimalistic sample preparation approach. The field of AIMS is constantly improving and expanding, with developments of powerful and novel techniques, improvements to existing instrumentation, and exciting new applications added with each year that passes. This annual review provides an overview of applications of AIMS techniques over the past year (2020), with a particular focus on the application of AIMS in a number of key fields of research including biomedical sciences, forensics and security, food sciences, the environment, and chemical synthesis. Novel ambient ionization techniques are introduced, including picolitre pressure-probe electrospray ionization and fiber spray ionization, in addition to modifications and improvements to existing techniques such as hand-held devices for ease of use, and USB-powered ion sources for on-site analysis. In all, the information provided in this review supports the view that AIMS has become a leading approach in MS-based analyses and that improvements to existing methods, alongside the development of novel approaches, will continue across the foreseeable future.
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Affiliation(s)
- Stephanie Rankin‐Turner
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public HealthJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Liam M. Heaney
- School of Sport, Exercise and Health SciencesLoughborough UniversityLoughboroughLeicestershireUK
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18
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Grainger R, Whibley S. A Perspective on the Analytical Challenges Encountered in High-Throughput Experimentation. Org Process Res Dev 2021. [DOI: 10.1021/acs.oprd.0c00463] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Rachel Grainger
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Stuart Whibley
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
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