1
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Li J, Morato NM, Westover LS, Abeywickrema P, Geng J, Piassek M, Harden D, Strambeanu I, Shi Z, Cooks RG, Meng J. High-Throughput Assessment of Bile Salt Export Pump Inhibition Using RapidFire-MS and DESI-MS. ACS Med Chem Lett 2024; 15:1584-1590. [PMID: 39291028 PMCID: PMC11403724 DOI: 10.1021/acsmedchemlett.4c00302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 08/01/2024] [Accepted: 08/08/2024] [Indexed: 09/19/2024] Open
Abstract
The bile salt export pump (BSEP) assay is widely used to evaluate the potential for drug-induced liver injury (DILI) early in the drug discovery process. While traditional liquid chromatography-mass spectrometry (LC-MS)-based approaches have been utilized for BSEP activity testing, they have intrinsic limitations in either throughput or the requirement for sample preparation and are difficult to scale up in order to screen drug candidates. Here we demonstrate the use of two different high-throughput MS methods based on solid-phase extraction (SPE) and desorption electrospray ionization (DESI) for high-throughput BSEP activity assessment in a label-free manner, with minimal needs for sample workup, at sampling rates of ∼11 and ∼5.5 s/sample, respectively. Both approaches were validated, compared, and successfully applied to the evaluation of 96 drug candidates for the inhibition of taurocholic acid (TCA) transport using BSEP vesicles.
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Affiliation(s)
- Jie Li
- Global Discovery Chemistry, Janssen Research and Development, Spring House, Pennsylvania 19477, United States
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Nicolás M Morato
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Lori S Westover
- Discovery Technology and Molecular Pharmacology, Janssen Research and Development, Spring House, Pennsylvania 19477, United States
| | - Pravien Abeywickrema
- Discovery Technology and Molecular Pharmacology, Janssen Research and Development, Spring House, Pennsylvania 19477, United States
| | - Jieping Geng
- Discovery Technology and Molecular Pharmacology, Janssen Research and Development, Spring House, Pennsylvania 19477, United States
| | - Madison Piassek
- Discovery Technology and Molecular Pharmacology, Janssen Research and Development, Spring House, Pennsylvania 19477, United States
| | - David Harden
- Discovery Technology and Molecular Pharmacology, Janssen Research and Development, Spring House, Pennsylvania 19477, United States
| | - Iulia Strambeanu
- Global Discovery Chemistry, Janssen Research and Development, Spring House, Pennsylvania 19477, United States
| | - Zhicai Shi
- Global Discovery Chemistry, Janssen Research and Development, Spring House, Pennsylvania 19477, United States
| | - R Graham Cooks
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Juncai Meng
- Discovery Technology and Molecular Pharmacology, Janssen Research and Development, Spring House, Pennsylvania 19477, United States
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2
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Feng Y, Morato NM, Huang KH, Lin M, Cooks RG. High-throughput label-free opioid receptor binding assays using an automated desorption electrospray ionization mass spectrometry platform. Chem Commun (Camb) 2024; 60:8224-8227. [PMID: 39007214 PMCID: PMC11293027 DOI: 10.1039/d4cc02346c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 07/09/2024] [Indexed: 07/16/2024]
Abstract
The current opioid epidemic has incentivized the discovery of new non-addictive analgesics, a process that requires the screening of opioid receptor binding, traditionally performed using radiometric assays. Here we describe a label-free alternative based on high-throughput (1 Hz) ambient mass spectrometry for screening the receptor binding of new opioid analogues.
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Affiliation(s)
- Yunfei Feng
- Department of Chemistry, Bindley Bioscience Center, and Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA.
| | - Nicolás M Morato
- Department of Chemistry, Bindley Bioscience Center, and Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA.
| | - Kai-Hung Huang
- Department of Chemistry, Bindley Bioscience Center, and Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA.
| | - Mina Lin
- Department of Chemistry, Bindley Bioscience Center, and Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA.
| | - R Graham Cooks
- Department of Chemistry, Bindley Bioscience Center, and Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA.
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3
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Chitre A, Querimit RCM, Rihm SD, Karan D, Zhu B, Wang K, Wang L, Hippalgaonkar K, Lapkin AA. Accelerating Formulation Design via Machine Learning: Generating a High-throughput Shampoo Formulations Dataset. Sci Data 2024; 11:728. [PMID: 38961122 PMCID: PMC11222379 DOI: 10.1038/s41597-024-03573-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 06/25/2024] [Indexed: 07/05/2024] Open
Abstract
Liquid formulations are ubiquitous yet have lengthy product development cycles owing to the complex physical interactions between ingredients making it difficult to tune formulations to customer-defined property targets. Interpolative ML models can accelerate liquid formulations design but are typically trained on limited sets of ingredients and without any structural information, which limits their out-of-training predictive capacity. To address this challenge, we selected eighteen formulation ingredients covering a diverse chemical space to prepare an open experimental dataset for training ML models for rinse-off formulations development. The resulting design space has an over 50-fold increase in dimensionality compared to our previous work. Here, we present a dataset of 812 formulations, including 294 stable samples, which cover the entire design space, with phase stability, turbidity, and high-fidelity rheology measurements generated on our semi-automated, ML-driven liquid formulations workflow. Our dataset has the unique attribute of sample-specific uncertainty measurements to train predictive surrogate models.
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Affiliation(s)
- Aniket Chitre
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
- Cambridge Centre for Advanced Research and Education in Singapore, CARES Ltd. 1 CREATE Way, CREATE Tower #05-05, Singapore, 138602, Singapore
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research (A*STAR), Singapore, 138634, Singapore
| | - Robert C M Querimit
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research (A*STAR), Singapore, 138634, Singapore
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, 637459, Singapore
| | - Simon D Rihm
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
- Cambridge Centre for Advanced Research and Education in Singapore, CARES Ltd. 1 CREATE Way, CREATE Tower #05-05, Singapore, 138602, Singapore
| | - Dogancan Karan
- Cambridge Centre for Advanced Research and Education in Singapore, CARES Ltd. 1 CREATE Way, CREATE Tower #05-05, Singapore, 138602, Singapore
| | - Benchuan Zhu
- BASF Advanced Chemicals Co. Ltd., No. 300, Jiang Xin Sha Road, Pudong, Shanghai, 200137, China
| | - Ke Wang
- BASF Advanced Chemicals Co. Ltd., No. 300, Jiang Xin Sha Road, Pudong, Shanghai, 200137, China
| | - Long Wang
- BASF Advanced Chemicals Co. Ltd., No. 300, Jiang Xin Sha Road, Pudong, Shanghai, 200137, China
| | - Kedar Hippalgaonkar
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research (A*STAR), Singapore, 138634, Singapore.
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, 639798, Singapore.
| | - Alexei A Lapkin
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK.
- Cambridge Centre for Advanced Research and Education in Singapore, CARES Ltd. 1 CREATE Way, CREATE Tower #05-05, Singapore, 138602, Singapore.
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4
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Williams JD, Pu F, Sawicki JW, Elsen NL. Ultra-high-throughput mass spectrometry in drug discovery: fundamentals and recent advances. Expert Opin Drug Discov 2024; 19:291-301. [PMID: 38111363 DOI: 10.1080/17460441.2023.2293153] [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: 10/06/2023] [Accepted: 12/06/2023] [Indexed: 12/20/2023]
Abstract
INTRODUCTION Ultra-high-throughput mass spectrometry, uHT-MS, is a technology that utilizes ionization and sample delivery technologies optimized to enable sampling from well plates at > 1 sample per second. These technologies do not need a chromatographic separation step and can be utilized in a wide variety of assays to detect a broad range of analytes including small molecules, lipids, and proteins. AREAS COVERED This manuscript provides a brief historical review of high-throughput mass spectrometry and the recently developed technologies that have enabled uHT-MS. The report also provides examples and references on how uHT-MS has been used in biochemical and chemical assays, nuisance compound profiling, protein analysis and high throughput experimentation for chemical synthesis. EXPERT OPINION The fast analysis time provided by uHT-MS is transforming how biochemical and chemical assays are performed in drug discovery. The potential to associate phenotypic responses produced by 1000's of compound treatments with changes in endogenous metabolite and lipid signals is becoming feasible. With the augmentation of simple, fast, high-throughput sample preparation, the scope of uHT-MS usage will increase. However, it likely will not supplant LC-MS for analyses that require low detection limits from complex matrices or characterization of complex biotherapeutics such as antibody-drug conjugates.
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Affiliation(s)
| | - Fan Pu
- Abbvie Discovery Research, North Chicago, IL, USA
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5
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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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6
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Affiliation(s)
- Nicolás M Morato
- Department of Chemistry and Bindley Bioscience Center, Purdue University, West Lafayette, Indiana 47907, United States
| | - R Graham Cooks
- Department of Chemistry and Bindley Bioscience Center, Purdue University, West Lafayette, Indiana 47907, United States
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7
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Basuri P, Volmer DA. Detecting Early-Stage Intermediates of Free-Radical Oxidative Degradation in Charged Aqueous Microdroplets. J Phys Chem A 2023; 127:7612-7617. [PMID: 37648376 DOI: 10.1021/acs.jpca.3c04143] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
We report the detection of early-stage intermediates of spontaneous free-radical oxidation of organic pollutants such as aliphatic amino alcohols and diamines in charged aqueous microdroplets in the ambient atmosphere. We propose that the intrinsic formation of reactive oxygen species at the air-water interface is responsible for the radical oxidation of the sp3 carbon. We suggest that our work will aid the understanding of the degradation mechanisms of organic molecules in the environment.
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Affiliation(s)
- Pallab Basuri
- Institute of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany
| | - Dietrich A Volmer
- Institute of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany
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8
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Javanshad R, Taylor CJ, Delavari N, Barkman TJ, Stull F, Venter AR. Analysis of histidine-tagged recombinant proteins from nickel and copper coated surfaces by direct electrospray ionization and desorption electrospray ionization mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2023; 37 Suppl 1:e9516. [PMID: 37013403 DOI: 10.1002/rcm.9516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/28/2023] [Accepted: 03/31/2023] [Indexed: 06/19/2023]
Abstract
RATIONALE Purification of recombinant proteins is a necessary step for functional or structural studies and other applications. Immobilized metal affinity chromatography is a common recombinant protein purification method. Mass spectrometry (MS) allows for confirmation of identity of expressed proteins and unambiguous detection of enzymatic substrates and reaction products. We demonstrate the detection of enzymes purified on immobilized metal affinity surfaces by direct or ambient ionization MS, and follow their enzymatic reactions by direct electrospray ionization (ESI) or desorption electrospray ionization (DESI). METHODS A protein standard, His-Ubq, and two recombinant proteins, His-SHAN and His-CS, expressed in Escherichia coli were immobilized on two immobilized metal affinity systems, Cu-nitriloacetic acid (Cu-NTA) and Ni-NTA. The proteins were purified on surface, and released in the ESI spray solvent for direct infusion, when using the 96-well plate form factor, or analyzed directly from immobilized metal affinity-coated microscope slides by DESI-MS. Enzyme activity was followed by incubating the substrates in wells or by depositing substrate on immobilized protein on coated slides for analysis. RESULTS Small proteins (His-Ubq) and medium proteins (His-SAHN) could readily be detected from 96-well plates by direct infusion ESI, or from microscope slides by DESI-MS after purification on surface from clarified E. coli cell lysate. Protein oxidation was observed for immobilized proteins on both Cu-NTA and Ni-NTA; however, this did not hamper the enzymatic reactions of these proteins. Both the nucleosidase reaction products for His-SAHN and the methylation product of His-CS (theobromine to caffeine) were detected. CONCLUSIONS The immobilization, purification, release and detection of His-tagged recombinant proteins using immobilized metal affinity surfaces for direct infusion ESI-MS or ambient DESI-MS analyses were successfully demonstrated. Recombinant proteins were purified to allow identification directly out of clarified cell lysate. Biological activities of the recombinant proteins were preserved allowing the investigation of enzymatic activity via MS.
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Affiliation(s)
- Roshan Javanshad
- Department of Chemistry, Western Michigan University, Kalamazoo, MI, USA
| | | | - Niusha Delavari
- Department of Chemistry, Western Michigan University, Kalamazoo, MI, USA
| | - Todd J Barkman
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI, USA
| | - Frederick Stull
- Department of Chemistry, Western Michigan University, Kalamazoo, MI, USA
| | - Andre R Venter
- Department of Chemistry, Western Michigan University, Kalamazoo, MI, USA
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9
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Cooks RG, Feng Y, Huang KH, Morato NM, Qiu L. Re-Imagining Drug Discovery using Mass Spectrometry. Isr J Chem 2023; 63:e202300034. [PMID: 37829547 PMCID: PMC10569432 DOI: 10.1002/ijch.202300034] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Indexed: 03/22/2023]
Abstract
It is argued that each of the three key steps in drug discovery, (i) reaction screening to find successful routes to desired drug candidates, (ii) scale up of the synthesis to produce amounts adequate for testing, and (iii) bioactivity assessment of the candidate compounds, can all be performed using mass spectrometry (MS) in a sequential fashion. The particular ionization method of choice, desorption electrospray ionization (DESI), is both an analytical technique and a procedure for small-scale synthesis. It is also highly compatible with automation, providing for high throughput in both synthesis and analysis. Moreover, because accelerated reactions take place in the secondary DESI microdroplets generated from individual reaction mixtures, this allows either online analysis by MS or collection of the synthetic products by droplet deposition. DESI also has the unique advantage, amongst spray-based MS ionization methods, that complex buffered biological solutions can be analyzed directly, without concern for capillary blockage. Here, all these capabilities are illustrated, the unique chemistry at droplet interfaces is presented, and the possible future implementation of DESI-MS based drug discovery is discussed.
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Affiliation(s)
- R Graham Cooks
- Department of Chemistry and Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907 USA
| | - Yunfei Feng
- Department of Chemistry and Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907 USA
| | - Kai-Hung Huang
- Department of Chemistry and Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907 USA
| | - Nicolás M Morato
- Department of Chemistry and Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907 USA
| | - Lingqi Qiu
- Department of Chemistry and Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907 USA
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10
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Kates PA, Cook JN, Ghan R, Nguyen HJ, Sitasuwan P, Lee LA. Incorporation of automated buffer exchange empowers high-throughput protein and plasmid purification for downstream uses. SLAS Technol 2023; 28:243-250. [PMID: 36736961 DOI: 10.1016/j.slast.2023.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 01/12/2023] [Accepted: 01/24/2023] [Indexed: 02/04/2023]
Abstract
The continued acceleration of time-to-market product development and rising demand for biotherapeutics have hastened the need for higher throughput within the biopharmaceutical industry. Automated liquid handlers (ALH) are increasingly popular due to flexible programming that enables processing of multiple samples with an array of functions. This flexibility is useful in streamlining research that requires chromatographic procedures to achieve product purity for downstream analysis. However, purification of biologics often requires additional off-deck buffer exchange steps due to undesirable elution conditions such as high acid or high salt content. Expanding the capability of ALHs to perform purification in sequence with buffer exchange would, therefore, increase workflow efficiency by eliminating the need for manual intervention, thus expediting sample preparation. Here we demonstrate two different automated purifications using pipet-based dispersive solid-phase extraction (dSPE). The first is an affinity purification of His-tagged proteins from bacterial lysate. The second is an anion-exchange purification of plasmid DNA. Both methods are followed by buffer exchange performed by an ALH. Percent recoveries for the three purified recombinant proteins ranged from 51 ± 1.2 to 86 ± 10%. The yields were inversely correlated to starting sample load and protein molecular weight. Yields for plasmid purification ranged between 11.4 ± 0.8 and 13.7 ± 0.9 µg, with the largest plasmid providing the highest yield. Both programs were rapid, with protein purification taking <80 min and plasmid purification <60 min. Our results demonstrate that high-quality, ready-to-use biologics can be obtained rapidly from a crude sample after two separate chromatographic processes without manual intervention.
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Affiliation(s)
- Patrick A Kates
- Integrated Micro-Chromatography Systems, Inc., 110 Centrum Drive, Irmo, SC 29063, United States
| | - Jordan N Cook
- Integrated Micro-Chromatography Systems, Inc., 110 Centrum Drive, Irmo, SC 29063, United States
| | - Ryan Ghan
- Hamilton Company, Inc., Reno, NV, United States
| | - Huey J Nguyen
- Integrated Micro-Chromatography Systems, Inc., 110 Centrum Drive, Irmo, SC 29063, United States
| | - Pongkwan Sitasuwan
- Integrated Micro-Chromatography Systems, Inc., 110 Centrum Drive, Irmo, SC 29063, United States
| | - L Andrew Lee
- Integrated Micro-Chromatography Systems, Inc., 110 Centrum Drive, Irmo, SC 29063, United States.
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11
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Talaty NN, Johnson RW, Sawicki J, Nacham O, Djuric SW. Recent Developments in Mass Spectrometry to Support Next-Generation Synthesis and Screening. ACS Med Chem Lett 2023; 14:711-718. [PMID: 37312853 PMCID: PMC10258828 DOI: 10.1021/acsmedchemlett.3c00040] [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: 02/02/2023] [Accepted: 05/10/2023] [Indexed: 06/15/2023] Open
Abstract
The complexity of new therapeutics continues to increase and the timeline for the discovery of these therapeutics continues to shrink. This creates demand for new analytical techniques to facilitate quicker discovery and development of novel drugs. Mass spectrometry is one of the most prolific analytical techniques that has been applied across the entire drug discovery pipeline. New mass spectrometers and the associated methods for sampling have been introduced at a rate that keeps pace with new chemistries, therapeutic types, and screening practices used by modern drug hunters. This microperspective covers application and implementation of new mass spectrometry workflows that enable current and future efforts in screening and synthesis for drug discovery.
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Affiliation(s)
- Nari N. Talaty
- Discovery
Platform Technologies, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Robert W. Johnson
- Discovery
Platform Technologies, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - James Sawicki
- Discovery
Platform Technologies, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Omprakash Nacham
- Discovery
Platform Technologies, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Stevan W. Djuric
- Discovery
Chemistry and Technology Consulting LLC, New Bern, North Carolina 28562, United States
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12
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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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13
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Vasina M, Kovar D, Damborsky J, Ding Y, Yang T, deMello A, Mazurenko S, Stavrakis S, Prokop Z. In-depth analysis of biocatalysts by microfluidics: An emerging source of data for machine learning. Biotechnol Adv 2023; 66:108171. [PMID: 37150331 DOI: 10.1016/j.biotechadv.2023.108171] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 05/04/2023] [Accepted: 05/04/2023] [Indexed: 05/09/2023]
Abstract
Nowadays, the vastly increasing demand for novel biotechnological products is supported by the continuous development of biocatalytic applications which provide sustainable green alternatives to chemical processes. The success of a biocatalytic application is critically dependent on how quickly we can identify and characterize enzyme variants fitting the conditions of industrial processes. While miniaturization and parallelization have dramatically increased the throughput of next-generation sequencing systems, the subsequent characterization of the obtained candidates is still a limiting process in identifying the desired biocatalysts. Only a few commercial microfluidic systems for enzyme analysis are currently available, and the transformation of numerous published prototypes into commercial platforms is still to be streamlined. This review presents the state-of-the-art, recent trends, and perspectives in applying microfluidic tools in the functional and structural analysis of biocatalysts. We discuss the advantages and disadvantages of available technologies, their reproducibility and robustness, and readiness for routine laboratory use. We also highlight the unexplored potential of microfluidics to leverage the power of machine learning for biocatalyst development.
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Affiliation(s)
- Michal Vasina
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 602 00 Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, 656 91 Brno, Czech Republic
| | - David Kovar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 602 00 Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, 656 91 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 602 00 Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, 656 91 Brno, Czech Republic
| | - Yun Ding
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland
| | - Tianjin Yang
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland; Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Andrew deMello
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland
| | - Stanislav Mazurenko
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 602 00 Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, 656 91 Brno, Czech Republic.
| | - Stavros Stavrakis
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland.
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 602 00 Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, 656 91 Brno, Czech Republic.
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14
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Ghosh J, Mendoza J, Cooks RG. Accelerated and Concerted Aza-Michael Addition and SuFEx Reaction in Microdroplets in Unitary and High-Throughput Formats. Angew Chem Int Ed Engl 2022; 61:e202214090. [PMID: 36253886 PMCID: PMC10099520 DOI: 10.1002/anie.202214090] [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: 09/25/2022] [Indexed: 11/12/2022]
Abstract
The sulfur fluoride exchange (SuFEx) reaction is significant in drug discovery, materials science, and chemical biology. Conventionally, it involves installation of SO2 F followed by fluoride exchange by a catalyst. We report catalyst-free Aza-Michael addition to install SO2 F and then SuFEx reaction with amines, both occurring in concert, in microdroplets under ambient conditions. The microdroplet reaction is accelerated by a factor of ∼104 relative to the corresponding bulk reaction. We suggest that the superacidic microdroplet surface assists SuFEx reaction by protonating fluorine to create a good leaving group. The reaction scope was established by performing individual reactions in microdroplets of 18 amines in four solvents and confirmed using high-throughput desorption electrospray ionization experiments. The study demonstrates the value of microdroplet-assisted accelerated reactions in combination with high-throughput experimentation for characterization of reaction scope.
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Affiliation(s)
- Jyotirmoy Ghosh
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, USA
| | - Joshua Mendoza
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, USA
| | - R Graham Cooks
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, USA
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15
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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: 12] [Impact Index Per Article: 6.0] [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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16
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Qiu L, Cooks RG. Simultaneous and Spontaneous Oxidation and Reduction in Microdroplets by the Water Radical Cation/Anion Pair. Angew Chem Int Ed Engl 2022; 61:e202210765. [PMID: 35994573 PMCID: PMC9825976 DOI: 10.1002/anie.202210765] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Indexed: 01/11/2023]
Abstract
Microdroplets show unique chemistry, especially in their intrinsic redox properties, and to this we here add a case of simultaneous and spontaneous oxidation and reduction. We report the concurrent conversions of several phosphonates to phosphonic acids by reduction (R-P → H-P) and to pentavalent phosphoric acids by oxidation. The experimental results suggest that the active reagent is the water radical cation/anion pair. The water radical cation is observed directly as the ionized water dimer while the water radical anion is only seen indirectly though the spontaneous reduction of carbon dioxide to formate. The coexistence of oxidative and reductive species in turn supports the proposal of a double-layer structure at the microdroplet surface, where the water radical cation and radical anion are separated and accumulated.
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Affiliation(s)
- Lingqi Qiu
- Department of ChemistryPurdue University560 Oval. Dr.West LafayetteIN 47907USA
| | - R. Graham Cooks
- Department of ChemistryPurdue University560 Oval. Dr.West LafayetteIN 47907USA
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17
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Qiu L, Cooks RG. Simultaneous and Spontaneous Oxidation and Reduction in Microdroplets by the Water Radical Cation/Anion Pair. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202210765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Lingqi Qiu
- Purdue University Chemistry UNITED STATES
| | - R Graham Cooks
- Purdue University Chemistry 560 Oval Drive 47907 West Lafayette UNITED STATES
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18
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Qiu L, Morato NM, Huang KH, Cooks RG. Spontaneous Water Radical Cation Oxidation at Double Bonds in Microdroplets. Front Chem 2022; 10:903774. [PMID: 35559217 PMCID: PMC9086510 DOI: 10.3389/fchem.2022.903774] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 04/11/2022] [Indexed: 12/20/2022] Open
Abstract
Spontaneous oxidation of compounds containing diverse X=Y moieties (e.g., sulfonamides, ketones, esters, sulfones) occurs readily in organic-solvent microdroplets. This surprising phenomenon is proposed to be driven by the generation of an intermediate species [M+H2O]+·: a covalent adduct of water radical cation (H2O+·) with the reactant molecule (M). The adduct is observed in the positive ion mass spectrum while its formation in the interfacial region of the microdroplet (i.e., at the air-droplet interface) is indicated by the strong dependence of the oxidation product formation on the spray distance (which reflects the droplet size and consequently the surface-to-volume ratio) and the solvent composition. Importantly, based on the screening of a ca. 21,000-compound library and the detailed consideration of six functional groups, the formation of a molecular adduct with the water radical cation is a significant route to ionization in positive ion mode electrospray, where it is favored in those compounds with X=Y moieties which lack basic groups. A set of model monofunctional systems was studied and in one case, benzyl benzoate, evidence was found for oxidation driven by hydroxyl radical adduct formation followed by protonation in addition to the dominant water radical cation addition process. Significant implications of molecular ionization by water radical cations for oxidation processes in atmospheric aerosols, analytical mass spectrometry and small-scale synthesis are noted.
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19
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Meng W, Ma C, Xu P, Gao C. Biotechnological production of chiral acetoin. Trends Biotechnol 2022; 40:958-973. [DOI: 10.1016/j.tibtech.2022.01.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 01/13/2022] [Accepted: 01/13/2022] [Indexed: 11/28/2022]
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20
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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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21
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Markossian S, Coussens NP, Dahlin JL, Sittampalam GS. Assay Guidance Manual for Drug Discovery: Technologies That Matter. SLAS Technol 2021; 26:553-554. [PMID: 34813399 PMCID: PMC9590672 DOI: 10.1177/24726303211056338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Sarine Markossian
- National Center for Advancing Translational Sciences (NCATS), Rockville, MD, USA
| | - Nathan P. Coussens
- Molecular Pharmacology Laboratories, Applied and Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Jayme L. Dahlin
- National Center for Advancing Translational Sciences (NCATS), Rockville, MD, USA
| | - G. Sitta Sittampalam
- National Center for Advancing Translational Sciences (NCATS), Rockville, MD, USA
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