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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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Bingham M, Pesnot T, Scott AD. Biophysical screening and characterisation in medicinal chemistry. PROGRESS IN MEDICINAL CHEMISTRY 2023; 62:61-104. [PMID: 37981351 DOI: 10.1016/bs.pmch.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2023]
Abstract
In the last two decades the use of biophysical assays and methods in medicinal chemistry has increased significantly, to meet the demands of the novel targets and modalities that drug discoverers are looking to tackle. The desire to obtain accurate affinities, kinetics, thermodynamics and structural data as early as possible in the drug discovery process has fuelled this innovation. This review introduces the principles underlying the techniques in common use and provides a perspective on the weaknesses and strengths of different methods. Case studies are used to further illustrate some of the applications in medicinal chemistry and a discussion of the emerging biophysical methods on the horizon is presented.
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Campuzano IDG. A Research Journey: Over a Decade of Denaturing and Native-MS Analyses of Hydrophobic and Membrane Proteins in Amgen Therapeutic Discovery. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2413-2431. [PMID: 37643331 DOI: 10.1021/jasms.3c00175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Membrane proteins and associated complexes currently comprise the majority of therapeutic targets and remain among the most challenging classes of proteins for analytical characterization. Through long-term strategic collaborations forged between industrial and academic research groups, there has been tremendous progress in advancing membrane protein mass spectrometry (MS) analytical methods and their concomitant application to Amgen therapeutic project progression. Herein, I will describe a detailed and personal account of how electrospray ionization (ESI) native mass spectrometry (nMS), ion mobility-MS (IM-MS), reversed phase liquid chromatographic mass spectrometry (RPLC-MS), high-throughput solid phase extraction mass spectrometry, and matrix-assisted laser desorption ionization mass spectrometry methods were developed, optimized, and validated within Amgen Research, and importantly, how these analytical methods were applied for membrane and hydrophobic protein analyses and ultimately therapeutic project support and progression. Additionally, I will discuss all the highly important and productive collaborative efforts, both internal Amgen and external academic, which were key in generating the samples, methods, and associated data described herein. I will also describe some early and previously unpublished nano-ESI (nESI) native-MS data from Amgen Research and the highly productive University of California Los Angeles (UCLA) collaboration. I will also present previously unpublished examples of real-life Amgen biotherapeutic membrane protein projects that were supported by all the MS (and IM) analytical techniques described herein. I will start by describing the initial nESI nMS experiments performed at Amgen in 2011 on empty nanodisc molecules, using a quadrupole time-of-flight MS, and how these experiments progressed on to the 15 Tesla Fourier transform ion cyclotron resonance MS at UCLA. Then described are monomeric and multimeric membrane protein data acquired in both nESI nMS and tandem-MS modes, using multiple methods of ion activation, resulting in dramatic spectral simplification. Also described is how we investigated the far less established and less published subject, that is denaturing RPLC-MS analysis of membrane proteins, and how we developed a highly robust and reproducible RPLC-MS method capable of effective separation of membrane proteins differing in only the presence or absence of an N-terminal post translational modification. Also described is the evolution of the aforementioned RPLC-MS method into a high-throughput solid phase extraction MS method. Finally, I will give my opinion on key developments and how the area of nMS of membrane proteins needs to evolve to a state where it can be applied within the biopharmaceutical research environment for routine therapeutic project support.
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Affiliation(s)
- Iain D G Campuzano
- Amgen Research, Center for Research Acceleration by Digital Innovation, Molecular Analytics, Thousand Oaks, California 91320, United States
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4
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Liu C. High-throughput MS for intact protein analysis. Bioanalysis 2023; 15:1017-1019. [PMID: 37584366 DOI: 10.4155/bio-2023-0139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2023] Open
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5
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Radford HM, Toft CJ, Sorenson AE, Schaeffer PM. Inhibition of Replication Fork Formation and Progression: Targeting the Replication Initiation and Primosomal Proteins. Int J Mol Sci 2023; 24:ijms24108802. [PMID: 37240152 DOI: 10.3390/ijms24108802] [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: 03/31/2023] [Revised: 05/02/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Over 1.2 million deaths are attributed to multi-drug-resistant (MDR) bacteria each year. Persistence of MDR bacteria is primarily due to the molecular mechanisms that permit fast replication and rapid evolution. As many pathogens continue to build resistance genes, current antibiotic treatments are being rendered useless and the pool of reliable treatments for many MDR-associated diseases is thus shrinking at an alarming rate. In the development of novel antibiotics, DNA replication is still a largely underexplored target. This review summarises critical literature and synthesises our current understanding of DNA replication initiation in bacteria with a particular focus on the utility and applicability of essential initiation proteins as emerging drug targets. A critical evaluation of the specific methods available to examine and screen the most promising replication initiation proteins is provided.
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Affiliation(s)
- Holly M Radford
- Molecular and Cell Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Douglas, QLD 4811, Australia
| | - Casey J Toft
- Molecular and Cell Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Douglas, QLD 4811, Australia
| | - Alanna E Sorenson
- Molecular and Cell Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Douglas, QLD 4811, Australia
| | - Patrick M Schaeffer
- Molecular and Cell Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Douglas, QLD 4811, Australia
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6
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Gao J, Zhou C, Zhong Y, Shi L, Luo X, Su H, Li M, Xu Y, Zhang N, Zhou H. Dipyridamole interacts with the N-terminal domain of HSP90 and antagonizes the function of the chaperone in multiple cancer cell lines. Biochem Pharmacol 2023; 207:115376. [PMID: 36513142 DOI: 10.1016/j.bcp.2022.115376] [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: 10/14/2022] [Revised: 12/06/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022]
Abstract
Molecular chaperone HSP90 has been considered as a promising target for anti-cancer drug development for years. However, due to the heat shock response induced by the ATP competitive inhibitors against HSP90, the therapeutic efficacies of the compounds are compromised, which consequently restricts the clinical use of HSP90-targeted inhibitors. Therefore, there is a need to discover novel HSP90-targeted modulators which exhibit acceptable inhibition activity against the chaperone and do not induce significant heat shock response in the meantime. Here in this study, we firstly developed a tip-based affinity selection-mass spectrometry platform with optimized experimental conditions/parameters for HSP90-targeted active compound screening, and then applied it to fish out inhibitors against HSP90 from a collection of 2,395 compounds composed of FDA-approved drugs and drug candidates. Dipyridamole, which acts as an anti-thrombotic agent by modulating multiple targets and has a long history of safe use, was identified to interact with HSP90's N-terminal domain. The following conducted biophysical and biochemical experiments demonstrated that Dipyridamole could bind to HSP90's ATP binding pocket and function as an ATP competitive inhibitor of the chaperone. Finally, cellular-based assays including CESTA, cell viability assessment and proteomic analysis etc. were performed to evaluate whether the interaction between HSP90 and Dipyridamole contributes to the anti-tumor effects of the compound. We then found that Dipyridamole inhibits the growth and proliferation of human cancer cells by downregulating cell cycle regulators and upregulating apoptotic cell signaling, which are potentially mediated by the binding of Dipyridamole to HSP90 and to PDEs (phosphodiesterases), respectively.
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Affiliation(s)
- Jing Gao
- Analytical Research Center for Organic and Biological Molecules, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
| | - Chen Zhou
- Analytical Research Center for Organic and Biological Molecules, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
| | - Yan Zhong
- Analytical Research Center for Organic and Biological Molecules, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China; University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Li Shi
- Analytical Research Center for Organic and Biological Molecules, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
| | - Xuanyang Luo
- Analytical Research Center for Organic and Biological Molecules, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China; University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Haixia Su
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China; University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Minjun Li
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Yechun Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China; University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Naixia Zhang
- Analytical Research Center for Organic and Biological Molecules, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China; University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China.
| | - Hu Zhou
- Analytical Research Center for Organic and Biological Molecules, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China; University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China.
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7
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Ginsburg-Moraff C, Grob J, Chin K, Eastman G, Wildhaber S, Bayliss M, Mues HM, Palmieri M, Poirier J, Reck M, Luneau A, Rodde S, Reilly J, Wagner T, Brocklehurst CE, Wyler R, Dunstan D, Marziale AN. Integrated and automated high-throughput purification of libraries on microscale. SLAS Technol 2022; 27:350-360. [PMID: 36028206 DOI: 10.1016/j.slast.2022.08.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 08/04/2022] [Accepted: 08/21/2022] [Indexed: 12/14/2022]
Abstract
We herein report the development of an automation platform for rapid purification and quantification of chemical libraries including reformatting of chemical matter to 10 mM DMSO stock solutions. This fully integrated workflow features tailored conditions for preparative reversed-phase (RP) HPLC-MS on microscale based on analytical data, online fraction QC and CAD-based quantification as well as automated reformatting to enable rapid purification of chemical libraries. This automated workflow is entirely solution-based, eliminating the need to weigh or handle solids. This increases process efficiency and creates a link between high-throughput synthesis and profiling of novel chemical matter with respect to biological and physicochemical properties in relevant assays.
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Affiliation(s)
- Carol Ginsburg-Moraff
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Novartis Pharma AG., Cambridge, MA 02139, USA.
| | - Jonathan Grob
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Novartis Pharma AG., Cambridge, MA 02139, USA
| | - Karl Chin
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Novartis Pharma AG., Cambridge, MA 02139, USA
| | - Grant Eastman
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Novartis Pharma AG., Cambridge, MA 02139, USA
| | - Sandra Wildhaber
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Novartis Pharma AG., Fabrikstrasse 1, Basel 4056, Switzerland
| | | | - Heinrich M Mues
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Novartis Pharma AG., Fabrikstrasse 1, Basel 4056, Switzerland
| | - Marco Palmieri
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Novartis Pharma AG., Fabrikstrasse 1, Basel 4056, Switzerland
| | - Jennifer Poirier
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Novartis Pharma AG., Cambridge, MA 02139, USA
| | - Marcel Reck
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Novartis Pharma AG., Fabrikstrasse 1, Basel 4056, Switzerland
| | - Alexandre Luneau
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Novartis Pharma AG., Fabrikstrasse 1, Basel 4056, Switzerland
| | - Stephane Rodde
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Novartis Pharma AG., Fabrikstrasse 1, Basel 4056, Switzerland
| | - John Reilly
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Novartis Pharma AG., Fabrikstrasse 1, Basel 4056, Switzerland
| | - Trixie Wagner
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Novartis Pharma AG., Fabrikstrasse 1, Basel 4056, Switzerland
| | - Cara E Brocklehurst
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Novartis Pharma AG., Fabrikstrasse 1, Basel 4056, Switzerland
| | - René Wyler
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Novartis Pharma AG., Fabrikstrasse 1, Basel 4056, Switzerland
| | - David Dunstan
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Novartis Pharma AG., Cambridge, MA 02139, USA.
| | - Alexander N Marziale
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Novartis Pharma AG., Fabrikstrasse 1, Basel 4056, Switzerland.
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8
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Mak T, Rossjohn J, Littler DR, Liu M, Quinn RJ. Collision-Induced Affinity Selection Mass Spectrometry for Identification of Ligands. ACS BIO & MED CHEM AU 2022; 2:450-455. [PMID: 37101899 PMCID: PMC10125361 DOI: 10.1021/acsbiomedchemau.2c00021] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Hyphenated mass spectrometry has been used to identify ligands binding to proteins. It involves mixing protein and compounds, separation of protein-ligand complexes from unbound compounds, dissociation of the protein-ligand complex, separation to remove protein, and injection of the supernatant into a mass spectrometer to observe the ligand. Here we report collision-induced affinity selection mass spectrometry (CIAS-MS), which allows separation and dissociation inside the instrument. The quadrupole was used to select the ligand-protein complex and allow unbound molecules to be exhausted to vacuum. Collision-induced dissociation (CID) dissociated the protein-ligand complex, and the ion guide and resonance frequency were used to selectively detect the ligand. A known SARS-CoV-2 Nsp9 ligand, oridonin, was successfully detected when it was mixed with Nsp9. We provide proof-of-concept data that the CIAS-MS method can be used to identify binding ligands for any purified protein.
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Affiliation(s)
- Tin Mak
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland 4111, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3168, Australia
| | - Dene R. Littler
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3168, Australia
| | - Miaomiao Liu
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland 4111, Australia
| | - Ronald J. Quinn
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland 4111, Australia
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9
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Muchiri RN, Kibitel J, Redick MA, van Breemen RB. Advances in Magnetic Microbead Affinity Selection Screening: Discovery of Natural Ligands to the SARS-CoV-2 Spike Protein. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:181-188. [PMID: 34939787 PMCID: PMC9429804 DOI: 10.1021/jasms.1c00318] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Affinity selection-mass spectrometry, which includes magnetic microbead affinity selection-screening (MagMASS), is ideal for the discovery of ligands in complex mixtures that bind to pharmacological targets. Therapeutic agents are needed to prevent or treat COVID-19, which is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Infection of human cells by SARS-CoV-2 involves binding of the virus spike protein subunit 1 (S1) to the human cell receptor angiotensin converting enzyme-2 (ACE2). Like antibodies, small molecules have the potential to block the interaction of the viral S1 protein with human ACE2 and prevent SARS-CoV-2 infection. Therefore, a MagMASS assay was developed for the discovery of ligands to the S1 protein. Unlike previous MagMASS approaches, this new assay used robotics for 5-fold enhancement of throughput and sensitivity. The assay was validated using the SBP-1 peptide, which is identical to the ACE2 amino acid sequence recognized by the S1 protein, and then applied to the discovery of natural ligands from botanical extracts. Small molecule ligands to the S1 protein were discovered in extracts of the licorice species, Glycyrrhiza inflata. In particular, the licorice ligand licochalcone A was identified through dereplication and comparison with standards using HPLC with high-resolution tandem mass spectrometry.
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Affiliation(s)
- Ruth N. Muchiri
- Linus Pauling Institute and College of Pharmacy, Oregon State University, Corvallis, OR 97331 USA
| | | | - Margaret A. Redick
- Linus Pauling Institute and College of Pharmacy, Oregon State University, Corvallis, OR 97331 USA
| | - Richard B. van Breemen
- Linus Pauling Institute and College of Pharmacy, Oregon State University, Corvallis, OR 97331 USA
- Corresponding author: 373 Linus Pauling Science Center, Corvallis, OR 97331 USA, TEL: 541-737-5080,
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10
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Scholle MD, McLaughlin D, Gurard-Levin ZA. High-Throughput Affinity Selection Mass Spectrometry Using SAMDI-MS to Identify Small-Molecule Binders of the Human Rhinovirus 3C Protease. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2021; 26:974-983. [PMID: 34151629 DOI: 10.1177/24725552211023211] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Affinity selection mass spectrometry (ASMS) has emerged as a powerful high-throughput screening tool used in drug discovery to identify novel ligands against therapeutic targets. This report describes the first high-throughput screen using a novel self-assembled monolayer desorption ionization (SAMDI)-ASMS methodology to reveal ligands for the human rhinovirus 3C (HRV3C) protease. The approach combines self-assembled monolayers of alkanethiolates on gold with matrix-assisted laser desorption ionization time-of-flight (MALDI TOF) mass spectrometry (MS), a technique termed SAMDI-ASMS. The primary screen of more than 100,000 compounds in pools of 8 compounds per well was completed in less than 8 h, and informs on the binding potential and selectivity of each compound. Initial hits were confirmed in follow-up SAMDI-ASMS experiments in single-concentration and dose-response curves. The ligands identified by SAMDI-ASMS were further validated using differential scanning fluorimetry (DSF) and in functional protease assays against HRV3C and the related SARS-CoV-2 3CLpro enzyme. SAMDI-ASMS offers key benefits for drug discovery over traditional ASMS approaches, including the high-throughput workflow and readout, minimizing compound misbehavior by using smaller compound pools, and up to a 50-fold reduction in reagent consumption. The flexibility of this novel technology opens avenues for high-throughput ASMS assays of any target, thereby accelerating drug discovery for diverse diseases.
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11
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Ratnayake AS, Flanagan ME, Foley TL, Hultgren SL, Bellenger J, Montgomery JI, Lall MS, Liu B, Ryder T, Kölmel DK, Shavnya A, Feng X, Lefker B, Byrnes LJ, Sahasrabudhe PV, Farley KA, Chen S, Wan J. Toward the assembly and characterization of an encoded library hit confirmation platform: Bead-Assisted Ligand Isolation Mass Spectrometry (BALI-MS). Bioorg Med Chem 2021; 41:116205. [PMID: 34000509 DOI: 10.1016/j.bmc.2021.116205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 12/15/2022]
Abstract
The ability to predict chemical structure from DNA sequence has to date been a necessary cornerstone of DNA-encoded library technology. DNA-encoded libraries (DELs) are typically screened by immobilized affinity selection and enriched library members are identified by counting the number of times an individual compound's sequence is observed in the resultant dataset. Those with high signal reads (DEL hits) are subsequently followed up through off-DNA synthesis of the predicted small molecule structures. However, hits followed-up in this manner often fail to translate to confirmed ligands. To address this low conversion rate of DEL hits to off-DNA ligands, we have developed an approach that eliminates the reliance on chemical structure prediction from DNA sequence. Here we describe our method of combining non-combinatorial resynthesis on-DNA following library procedures as a rapid means to assess the probable molecules attached to the DNA barcode. Furthermore, we apply our Bead-Assisted Ligand Isolation Mass Spectrometry (BALI-MS) technique to identify the true binders found within the mixtures of on-DNA synthesis products. Finally, we describe a Normalized Enrichment (NE) metric that allows for the quantitative assessment of affinity selection in these studies. We exemplify how this combined approach enables the identification of putative hit matter against a clinically relevant therapeutic target bisphosphoglycerate mutase, BPGM.
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Affiliation(s)
- Anokha S Ratnayake
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States.
| | - Mark E Flanagan
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States.
| | - Timothy L Foley
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States.
| | - Scott L Hultgren
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States.
| | - Justin Bellenger
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States.
| | - Justin I Montgomery
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States.
| | - Manjinder S Lall
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States.
| | - Bo Liu
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States.
| | - Tim Ryder
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States.
| | - Dominik K Kölmel
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States.
| | - Andre Shavnya
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States.
| | - Xidong Feng
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States.
| | - Bruce Lefker
- Lefker Biopharma Consulting LLC, Arlington, MA 02474 United States.
| | - Laura J Byrnes
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States.
| | - Parag V Sahasrabudhe
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States.
| | - Kathleen A Farley
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States.
| | - Shi Chen
- HitGen Inc., Shuangliu District, Chengdu, China.
| | - Jinqiao Wan
- HitGen Inc., Shuangliu District, Chengdu, China.
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12
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Motoyaji T. [High-throughput Screening Technology for Selective Inhibitors of Transporters and Its Application in Drug Discovery]. YAKUGAKU ZASSHI 2021; 141:511-515. [PMID: 33790118 DOI: 10.1248/yakushi.20-00204-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The first step in small-molecule drug discovery is the identification of hit compounds via high-throughput screening (HTS). In transporter drug discovery, most HTS assays are based on the uptake of labeled substrates, but such functional assays cannot be developed for many transporters, such as intracellular organelle transporters. These transporters remain unexplored in drug discovery despite their promise as drug targets. Affinity selection-mass spectrometry (AS-MS) is a label-free binding assay technology that has been developed as an HTS technology for analyzing interactions between targets and compounds. The use of AS-MS technology enables HTS against every type of drug target, in contrast to functional assays. AS-MS technology is usually used for soluble proteins, but we have developed this technology for application to membrane proteins as well. So far, we have used AS-MS for HTS of approximately 400000 compounds. In this review, the principles and application of AS-MS technology are introduced and an HTS campaign for solute carrier type 17A8 (SLC17A8) (vesicular glutamate transporter 3) is presented as an example.
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13
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Development of a target identification approach using native mass spectrometry. Sci Rep 2021; 11:2387. [PMID: 33504855 PMCID: PMC7840913 DOI: 10.1038/s41598-021-81859-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 01/07/2021] [Indexed: 02/06/2023] Open
Abstract
A key step in the development of new pharmaceutical drugs is the identification of the molecular target and distinguishing this from all other gene products that respond indirectly to the drug. Target identification remains a crucial process and a current bottleneck for advancing hits through the discovery pipeline. Here we report a method, that takes advantage of the specific detection of protein-ligand complexes by native mass spectrometry (MS) to probe the protein partner of a ligand in an untargeted method. The key advantage is that it uses unmodified small molecules for binding and, thereby, it does not require labelled ligands and is not limited by the chemistry required to tag the molecule. We demonstrate the use of native MS to identify known ligand-protein interactions in a protein mixture under various experimental conditions. A protein-ligand complex was successfully detected between parthenolide and thioredoxin (PfTrx) in a five-protein mixture, as well as when parthenolide was mixed in a bacterial cell lysate spiked with PfTrx. We provide preliminary data that native MS could be used to identify binding targets for any small molecule.
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14
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Yang D, Zhou Q, Labroska V, Qin S, Darbalaei S, Wu Y, Yuliantie E, Xie L, Tao H, Cheng J, Liu Q, Zhao S, Shui W, Jiang Y, Wang MW. G protein-coupled receptors: structure- and function-based drug discovery. Signal Transduct Target Ther 2021; 6:7. [PMID: 33414387 PMCID: PMC7790836 DOI: 10.1038/s41392-020-00435-w] [Citation(s) in RCA: 208] [Impact Index Per Article: 69.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/30/2020] [Accepted: 12/05/2020] [Indexed: 02/08/2023] Open
Abstract
As one of the most successful therapeutic target families, G protein-coupled receptors (GPCRs) have experienced a transformation from random ligand screening to knowledge-driven drug design. We are eye-witnessing tremendous progresses made recently in the understanding of their structure-function relationships that facilitated drug development at an unprecedented pace. This article intends to provide a comprehensive overview of this important field to a broader readership that shares some common interests in drug discovery.
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Affiliation(s)
- Dehua Yang
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China.,The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China
| | - Qingtong Zhou
- School of Basic Medical Sciences, Fudan University, 200032, Shanghai, China
| | - Viktorija Labroska
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Shanshan Qin
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China
| | - Sanaz Darbalaei
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yiran Wu
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China
| | - Elita Yuliantie
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Linshan Xie
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Houchao Tao
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China
| | - Jianjun Cheng
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China
| | - Qing Liu
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China.,The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China
| | - Suwen Zhao
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Wenqing Shui
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China. .,School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China.
| | - Yi Jiang
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China.
| | - Ming-Wei Wang
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China. .,The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China. .,School of Basic Medical Sciences, Fudan University, 200032, Shanghai, China. .,University of Chinese Academy of Sciences, 100049, Beijing, China. .,School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China. .,School of Pharmacy, Fudan University, 201203, Shanghai, China.
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15
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Foley TL, Burchett W, Chen Q, Flanagan ME, Kapinos B, Li X, Montgomery JI, Ratnayake AS, Zhu H, Peakman MC. Selecting Approaches for Hit Identification and Increasing Options by Building the Efficient Discovery of Actionable Chemical Matter from DNA-Encoded Libraries. SLAS DISCOVERY 2021; 26:263-280. [PMID: 33412987 DOI: 10.1177/2472555220979589] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Over the past 20 years, the toolbox for discovering small-molecule therapeutic starting points has expanded considerably. Pharmaceutical researchers can now choose from technologies that, in addition to traditional high-throughput knowledge-based and diversity screening, now include the screening of fragment and fragment-like libraries, affinity selection mass spectrometry, and selection against DNA-encoded libraries (DELs). Each of these techniques has its own unique combination of advantages and limitations that makes them more, or less, suitable for different target classes or discovery objectives, such as desired mechanism of action. Layered on top of this are the constraints of the drug-hunters themselves, including budgets, timelines, and available platform capacity; each of these can play a part in dictating the hit identification strategy for a discovery program. In this article, we discuss some of the factors that we use to govern our building of a hit identification roadmap for a program and describe the increasing role that DELs are playing in our discovery strategy. Furthermore, we share our learning during our initial exploration of DEL and highlight the approaches we have evolved to maximize the value returned from DEL selections. Topics addressed include the optimization of library design and production, reagent validation, data analysis, and hit confirmation. We describe how our thinking in these areas has led us to build a DEL platform that has begun to deliver tractable matter to our global discovery portfolio.
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Affiliation(s)
| | | | - Qiuxia Chen
- Lead Generation Unit, HitGen Inc., Chengdu, Shuangliu District, China
| | | | | | - Xianyang Li
- Lead Generation Unit, HitGen Inc., Chengdu, Shuangliu District, China
| | | | | | - Hongyao Zhu
- Simulation and Modelling Sciences, Pfizer Inc., Groton, CT, USA
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16
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Muchiri RN, van Breemen RB. Affinity selection-mass spectrometry for the discovery of pharmacologically active compounds from combinatorial libraries and natural products. JOURNAL OF MASS SPECTROMETRY : JMS 2021; 56:e4647. [PMID: 32955158 DOI: 10.1002/jms.4647] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/15/2020] [Accepted: 08/11/2020] [Indexed: 05/12/2023]
Abstract
Invented to address the high-throughput screening (HTS) demands of combinatorial chemistry, affinity selection-mass spectrometry (AS-MS) utilizes binding interactions between ligands and receptors to isolate pharmacologically active compounds from mixtures of small molecules and then relies on the selectivity, sensitivity, and speed of mass spectrometry to identify them. No radiolabels, fluorophores, or chromophores are required. Although many variations of AS-MS have been devised, three approaches have emerged as the most flexible, productive, and popular, and they differ primarily in how ligand-receptor complexes are separated from nonbinding compounds in the mixture. These are pulsed ultrafiltration (PUF) AS-MS, size exclusion chromatography (SEC) AS-MS, and magnetic microbead affinity selection screening (MagMASS). PUF and SEC AS-MS are solution-phase screening approaches, and MagMASS uses receptors immobilized on magnetic microbeads. Because pools of compounds are screened using AS-MS, each containing hundreds to thousands of potential ligands, hundreds of thousands of compounds can be screened per day. AS-MS is also compatible with complex mixtures of chemically diverse natural products in extracts of botanicals and fungi and microbial cultures, which often contain fluorophores and chromophores that can interfere with convention HTS. Unlike conventional HTS, AS-MS may be used to discover ligands binding to allosteric as well as orthosteric receptor sites, and AS-MS has been useful for discovering ligands to targets that are not easily incorporated into conventional HTS such as membrane-bound receptors.
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Affiliation(s)
- Ruth N Muchiri
- Linus Pauling Institute, Oregon State University, Corvallis, Oregon, 97331, USA
| | - Richard B van Breemen
- Linus Pauling Institute, Oregon State University, Corvallis, Oregon, 97331, USA
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, Oregon, 97331, USA
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17
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Tao Y, Yan J, Cai B. LABEL-FREE BIO-AFFINITY MASS SPECTROMETRY FOR SCREENING AND LOCATING BIOACTIVE MOLECULES. MASS SPECTROMETRY REVIEWS 2021; 40:53-71. [PMID: 31755145 DOI: 10.1002/mas.21613] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 11/04/2019] [Indexed: 06/10/2023]
Abstract
Despite the recent increase in the development of bioactive molecules in the drug industry, the enormous chemical space and lack of productivity are still important issues. Additional alternative approaches to screen and locate bioactive molecules are urgently needed. Label-free bio-affinity mass spectrometry (BA-MS) provides opportunities for the discovery and development of innovative drugs. This review provides a comprehensive portrayal of BA-MS techniques and of their applications in screening and locating bioactive molecules. After introducing the basic principles, alongside some application notes, the current state-of-the-art of BA-MS-assisted drug discovery is discussed, including native MS, size-exclusion chromatography-MS, ultrafiltration-MS, solid-phase micro-extraction-MS, and cell membrane chromatography-MS. Finally, several challenges and limitations of the current methods are summarized, with a view to potential future directions for BA-MS-assisted drug discovery. © 2019 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Yi Tao
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Jizhong Yan
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Baochang Cai
- Jiangsu Key Laboratory of Chinese Medicine Processing, Nanjing University of Chinese Medicine, Nanjing, 210023, PR China
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18
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Gopalsamy A, Aulabaugh AE, Barakat A, Beaumont KC, Cabral S, Canterbury DP, Casimiro-Garcia A, Chang JS, Chen MZ, Choi C, Dow RL, Fadeyi OO, Feng X, France SP, Howard RM, Janz JM, Jasti J, Jasuja R, Jones LH, King-Ahmad A, Knee KM, Kohrt JT, Limberakis C, Liras S, Martinez CA, McClure KF, Narayanan A, Narula J, Novak JJ, O'Connell TN, Parikh MD, Piotrowski DW, Plotnikova O, Robinson RP, Sahasrabudhe PV, Sharma R, Thuma BA, Vasa D, Wei L, Wenzel AZ, Withka JM, Xiao J, Yayla HG. PF-07059013: A Noncovalent Modulator of Hemoglobin for Treatment of Sickle Cell Disease. J Med Chem 2020; 64:326-342. [PMID: 33356244 DOI: 10.1021/acs.jmedchem.0c01518] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Sickle cell disease (SCD) is a genetic disorder caused by a single point mutation (β6 Glu → Val) on the β-chain of adult hemoglobin (HbA) that results in sickled hemoglobin (HbS). In the deoxygenated state, polymerization of HbS leads to sickling of red blood cells (RBC). Several downstream consequences of polymerization and RBC sickling include vaso-occlusion, hemolytic anemia, and stroke. We report the design of a noncovalent modulator of HbS, clinical candidate PF-07059013 (23). The seminal hit molecule was discovered by virtual screening and confirmed through a series of biochemical and biophysical studies. After a significant optimization effort, we arrived at 23, a compound that specifically binds to Hb with nanomolar affinity and displays strong partitioning into RBCs. In a 2-week multiple dose study using Townes SCD mice, 23 showed a 37.8% (±9.0%) reduction in sickling compared to vehicle treated mice. 23 (PF-07059013) has advanced to phase 1 clinical trials.
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Affiliation(s)
- Ariamala Gopalsamy
- Pfizer Medicine Design, Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Ann E Aulabaugh
- Pfizer Medicine Design, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Amey Barakat
- Rare Diseases Research Unit, Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Kevin C Beaumont
- Primary Pharmacology Group, Pharmacokinetics, Dynamics and Metabolism, Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Shawn Cabral
- Pfizer Medicine Design, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Daniel P Canterbury
- Pfizer Medicine Design, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Agustin Casimiro-Garcia
- Pfizer Medicine Design, Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Jeanne S Chang
- Pfizer Medicine Design, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Ming Z Chen
- Pfizer Medicine Design, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Chulho Choi
- Pfizer Medicine Design, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Robert L Dow
- Pfizer Medicine Design, Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Olugbeminiyi O Fadeyi
- Pfizer Medicine Design, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Xidong Feng
- Pfizer Medicine Design, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Scott P France
- Pfizer Medicine Design, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Roger M Howard
- Pfizer Medicine Design, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Jay M Janz
- Rare Diseases Research Unit, Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Jayasankar Jasti
- Pfizer Medicine Design, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Reema Jasuja
- Rare Diseases Research Unit, Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Lyn H Jones
- Pfizer Medicine Design, Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Amanda King-Ahmad
- Primary Pharmacology Group, Pharmacokinetics, Dynamics and Metabolism, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Kelly M Knee
- Rare Diseases Research Unit, Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Jeffrey T Kohrt
- Pfizer Medicine Design, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Chris Limberakis
- Pfizer Medicine Design, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Spiros Liras
- Pfizer Medicine Design, Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Carlos A Martinez
- Medicinal Sciences, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Kim F McClure
- Pfizer Medicine Design, Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Arjun Narayanan
- Pfizer Medicine Design, Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Jatin Narula
- Primary Pharmacology Group, Pharmacokinetics, Dynamics and Metabolism, Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Jonathan J Novak
- Primary Pharmacology Group, Pharmacokinetics, Dynamics and Metabolism, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Thomas N O'Connell
- Pfizer Medicine Design, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Mihir D Parikh
- Pfizer Medicine Design, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - David W Piotrowski
- Pfizer Medicine Design, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Olga Plotnikova
- Pfizer Medicine Design, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Ralph P Robinson
- Pfizer Medicine Design, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Parag V Sahasrabudhe
- Pfizer Medicine Design, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Raman Sharma
- Primary Pharmacology Group, Pharmacokinetics, Dynamics and Metabolism, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Benjamin A Thuma
- Pfizer Medicine Design, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Dipy Vasa
- Drug Product Design, Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Liuqing Wei
- Pfizer Medicine Design, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - A Zane Wenzel
- Pfizer Medicine Design, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Jane M Withka
- Pfizer Medicine Design, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Jun Xiao
- Pfizer Medicine Design, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Hatice G Yayla
- Pfizer Medicine Design, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
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19
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Sahasrabuddhe A, Oakley D, Chen K, McCarter JD. Development of a High-Throughput Affinity Mass Spectrometry (AMS) Platform Using Laser Diode Thermal Desorption Ionization Coupled to Mass Spectrometry (LDTD-MS). SLAS DISCOVERY 2020; 26:230-241. [PMID: 33334237 DOI: 10.1177/2472555220979596] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Affinity selection mass spectrometry (MS) or, simply, affinity mass spectrometry (AMS) is a label-free technology that has been used to identify high-affinity ligands of target proteins of interest by screening against small-molecule compound libraries and identifying molecules that are enriched in the presence of the target protein. We have previously applied Agilent Technology's (Santa Clara, CA) RapidFire solid-phase extraction (SPE)-based high-throughput MS technology to screen small-molecule libraries using AMS. However, SPE-based technologies rely on fluidics for desalting and separation prior to mass analysis with attendant high solvent consumption, relatively high sample volume requirements, risk of sample carryover, and frequent maintenance. To address these challenges, we have established an AMS platform using a laser diode thermal desorption-atmospheric pressure chemical ionization (LDTD-APCI) ionization source (Phytronix, Quebec, Canada) coupled with a SCIEX 5600+ TripleTOF MS (Framingham, MA). We also validated a data-independent acquisition (DIA) Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH-MS) method for the robust detection and analysis of small-molecule affinity hits. An informatics platform developed in-house has resulted in a streamlined data analysis workflow for high-throughput AMS screening campaigns and reduced data processing time without compromising data quality. Finally, 68,000 compounds were screened in a single plate and affinity selected hits were confirmed in an orthogonal enzyme activity assay.
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Affiliation(s)
| | - Dylan Oakley
- Research Automation Technologies, Thousand Oaks, CA, USA
| | - Kui Chen
- Discovery Technologies, Thousand Oaks, CA, USA
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20
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Ortiz-Meoz RF, Wang L, Matico R, Rutkowska-Klute A, De la Rosa M, Bedard S, Midgett R, Strohmer K, Thomson D, Zhang C, Mebrahtu M, Guss J, Totoritis R, Consler T, Campobasso N, Taylor D, Lewis T, Weaver K, Muelbaier M, Seal J, Dunham R, Kazmierski W, Favre D, Bergamini G, Shewchuk L, Rendina A, Zhang G. Characterization of Apo-Form Selective Inhibition of Indoleamine 2,3-Dioxygenase*. Chembiochem 2020; 22:516-522. [PMID: 32974990 DOI: 10.1002/cbic.202000298] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 09/23/2020] [Indexed: 01/01/2023]
Abstract
Indoleamine-2,3-dioxygenase 1 (IDO1) is a heme-containing enzyme that catalyzes the rate-limiting step in the kynurenine pathway of tryptophan (TRP) metabolism. As it is an inflammation-induced immunoregulatory enzyme, pharmacological inhibition of IDO1 activity is currently being pursued as a potential therapeutic tool for the treatment of cancer and other disease states. As such, a detailed understanding of the mechanism of action of IDO1 inhibitors with various mechanisms of inhibition is of great interest. Comparison of an apo-form-binding IDO1 inhibitor (GSK5628) to the heme-coordinating compound, epacadostat (Incyte), allows us to explore the details of the apo-binding inhibition of IDO1. Herein, we demonstrate that GSK5628 inhibits IDO1 by competing with heme for binding to a heme-free conformation of the enzyme (apo-IDO1), whereas epacadostat coordinates its binding with the iron atom of the IDO1 heme cofactor. Comparison of these two compounds in cellular systems reveals a long-lasting inhibitory effect of GSK5628, previously undescribed for other known IDO1 inhibitors. Detailed characterization of this apo-binding mechanism for IDO1 inhibition might help design superior inhibitors or could confer a unique competitive advantage over other IDO1 inhibitors vis-à-vis specificity and pharmacokinetic parameters.
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Affiliation(s)
- Rodrigo F Ortiz-Meoz
- Drug Design and Selection, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, PA, 19426, USA
| | - Liping Wang
- Drug Design and Selection, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, PA, 19426, USA
| | - Rosalie Matico
- Drug Design and Selection, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, PA, 19426, USA
| | | | - Martha De la Rosa
- Infectious Diseases TAU, GlaxoSmithKline Five Moore Drive, Research Triangle Park, NC 27709, USA
| | - Sabrina Bedard
- Drug Design and Selection, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, PA, 19426, USA
| | - Robert Midgett
- Drug Design and Selection, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, PA, 19426, USA
| | - Katrin Strohmer
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Douglas Thomson
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Cunyu Zhang
- Drug Design and Selection, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, PA, 19426, USA
| | - Makda Mebrahtu
- Drug Design and Selection, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, PA, 19426, USA
| | - Jeffrey Guss
- Drug Design and Selection, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, PA, 19426, USA
| | - Rachel Totoritis
- Drug Design and Selection, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, PA, 19426, USA
| | - Thomas Consler
- Drug Design and Selection, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, PA, 19426, USA
| | - Nino Campobasso
- Drug Design and Selection, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, PA, 19426, USA
| | - David Taylor
- Drug Design and Selection, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, PA, 19426, USA
| | - Tia Lewis
- Drug Design and Selection, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, PA, 19426, USA
| | - Kurt Weaver
- Drug Design and Selection, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, PA, 19426, USA
| | - Marcel Muelbaier
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - John Seal
- Drug Design and Selection, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, PA, 19426, USA
| | - Richard Dunham
- Infectious Diseases TAU, GlaxoSmithKline Five Moore Drive, Research Triangle Park, NC 27709, USA
| | - Wieslaw Kazmierski
- Infectious Diseases TAU, GlaxoSmithKline Five Moore Drive, Research Triangle Park, NC 27709, USA
| | - David Favre
- Infectious Diseases TAU, GlaxoSmithKline Five Moore Drive, Research Triangle Park, NC 27709, USA
| | - Giovanna Bergamini
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Lisa Shewchuk
- Drug Design and Selection, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, PA, 19426, USA
| | - Alan Rendina
- Drug Design and Selection, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, PA, 19426, USA
| | - Guofeng Zhang
- Drug Design and Selection, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, PA, 19426, USA
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21
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Simon RP, Winter M, Kleiner C, Wehrle L, Karnath M, Ries R, Zeeb M, Schnapp G, Fiegen D, Häbe TT, Runge F, Bretschneider T, Luippold AH, Bischoff D, Reindl W, Büttner FH. MALDI-TOF-Based Affinity Selection Mass Spectrometry for Automated Screening of Protein-Ligand Interactions at High Throughput. SLAS DISCOVERY 2020; 26:44-57. [PMID: 33073664 DOI: 10.1177/2472555220959266] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Demonstration of in vitro target engagement for small-molecule ligands by measuring binding to a molecular target is an established approach in early drug discovery and a pivotal step in high-throughput screening (HTS)-based compound triaging. We describe the setup, evaluation, and application of a ligand binding assay platform combining automated affinity selection (AS)-based sample preparation and label-free matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) analysis. The platform enables mass spectrometry (MS)-based HTS for small-molecule target interactions from single-compound incubation mixtures and is embedded into a regular assay automation environment. Efficient separation of target-ligand complexes is achieved by in-plate size exclusion chromatography (SEC), and small-molecule ligands are subsequently identified by MALDI-TOF analysis. In contrast to alternative HTS-capable binding assay formats, MALDI-TOF AS-MS is capable of identifying orthosteric and allosteric ligands, as shown for the model system protein tyrosine phosphatase 1B (PTP1B), irrespective of protein function. Furthermore, determining relative binding affinities (RBAs) enabled ligand ranking in accordance with functional inhibition and reference data for PTP1B and a number of diverse protein targets. Finally, we present a validation screen of more than 23,000 compounds within 24 h, demonstrating the general applicability of the platform for the HTS-compatible assessment of protein-ligand interactions.
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Affiliation(s)
- Roman P Simon
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Martin Winter
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Carola Kleiner
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Lucie Wehrle
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Michael Karnath
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Robert Ries
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Markus Zeeb
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Gisela Schnapp
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Dennis Fiegen
- Bioprocess Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Tim T Häbe
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Frank Runge
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Tom Bretschneider
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Andreas H Luippold
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Daniel Bischoff
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Wolfgang Reindl
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Frank H Büttner
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
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22
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Busby SA, Carbonneau S, Concannon J, Dumelin CE, Lee Y, Numao S, Renaud N, Smith TM, Auld DS. Advancements in Assay Technologies and Strategies to Enable Drug Discovery. ACS Chem Biol 2020; 15:2636-2648. [PMID: 32880443 DOI: 10.1021/acschembio.0c00495] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Assays drive drug discovery from the exploratory phases to the clinical testing of drug candidates. As such, numerous assay technologies and methodologies have arisen to support drug discovery efforts. Robust identification and characterization of tractable chemical matter requires biochemical, biophysical, and cellular approaches and often benefits from high-throughput methods. To increase throughput, efforts have been made to provide assays in miniaturized volumes which can be arrayed in microtiter plates to support the testing of as many as 100,000 samples/day. Alongside these efforts has been the growth of microtiter plate-free formats with encoded libraries that can support the screening of billions of compounds, a hunt for new drug modalities, as well as emphasis on more disease relevant formats using complex cell models of disease states. This review will focus on recent developments in high-throughput assay technologies applied to identify starting points for drug discovery. We also provide recommendations on strategies for implementing various assay types to select high quality leads for drug development.
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Affiliation(s)
- Scott A. Busby
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics, Cambridge, Massachusetts, United States
| | - Seth Carbonneau
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics, Cambridge, Massachusetts, United States
| | - John Concannon
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics, Cambridge, Massachusetts, United States
| | | | - YounKyoung Lee
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics, Cambridge, Massachusetts, United States
| | - Shin Numao
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Nicole Renaud
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics, Cambridge, Massachusetts, United States
| | - Thomas M. Smith
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics, Cambridge, Massachusetts, United States
| | - Douglas S. Auld
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics, Cambridge, Massachusetts, United States
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23
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Blay V, Otero-Muras I, Annis DA. Solving the Competitive Binding Equilibria between Many Ligands: Application to High-Throughput Screening and Affinity Optimization. Anal Chem 2020; 92:12630-12638. [PMID: 32812419 DOI: 10.1021/acs.analchem.0c02715] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Modern small-molecule drug discovery relies on the selective targeting of biological macromolecules by low-molecular weight compounds. Therefore, the binding affinities of candidate drugs to their targets are key for pharmacological activity and clinical use. For drug discovery methods where multiple drug candidates can simultaneously bind to the same target, a competition is established, and the resulting equilibrium depends on the dissociation constants and concentration of all the species present. Such coupling between all equilibrium-governing parameters complicates analysis and development of improved mixture-based, high-throughput drug discovery techniques. In this work, we present an iterative computational algorithm to solve coupled equilibria between an arbitrary number of ligands and a biomolecular target that is efficient and robust. The algorithm does not require the estimation of initial values to rapidly converge to the solution of interest. We explored binding equilibria under ligand/receptor conditions used in mixture-based library screening by affinity selection-mass spectrometry (AS-MS). Our studies support a facile method for affinity-ranking hits. The ranking method involves varying the receptor-to-ligand concentration ratio in a pool of candidate ligands in two sequential AS-MS analyses. The ranking is based on the relative change in bound ligand concentration. The method proposed does not require a known reference ligand and produces a ranking that is insensitive to variations in the concentration of individual compounds, thereby enabling the use of unpurified compounds generated by mixture-based combinatorial synthesis techniques.
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Affiliation(s)
- Vincent Blay
- Division of Biomaterials and Bioengineering, University of California San Francisco, San Francisco, California 94143, United States
| | - Irene Otero-Muras
- BioProcess Engineering Group, IIM-CSIC, Spanish National Research Council, Vigo 36208, Spain
| | - David Allen Annis
- Aileron Therapeutics, Inc., 490 Arsenal Way, Watertown, Massachusetts 02472, United States
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24
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Haniff HS, Knerr L, Chen JL, Disney MD, Lightfoot HL. Target-Directed Approaches for Screening Small Molecules against RNA Targets. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2020; 25:869-894. [PMID: 32419578 PMCID: PMC7442623 DOI: 10.1177/2472555220922802] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
RNA molecules have a variety of cellular functions that can drive disease pathologies. They are without a doubt one of the most intriguing yet controversial small-molecule drug targets. The ability to widely target RNA with small molecules could be revolutionary, once the right tools, assays, and targets are selected, thereby defining which biomolecules are targetable and what constitutes drug-like small molecules. Indeed, approaches developed over the past 5-10 years have changed the face of small molecule-RNA targeting by addressing historic concerns regarding affinity, selectivity, and structural dynamics. Presently, selective RNA-protein complex stabilizing drugs such as branaplam and risdiplam are in clinical trials for the modulation of SMN2 splicing, compounds identified from phenotypic screens with serendipitous outcomes. Fully developing RNA as a druggable target will require a target engagement-driven approach, and evolving chemical collections will be important for the industrial development of this class of target. In this review we discuss target-directed approaches that can be used to identify RNA-binding compounds and the chemical knowledge we have today of small-molecule RNA binders.
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Affiliation(s)
- Hafeez S. Haniff
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Laurent Knerr
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Jonathan L. Chen
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Matthew D. Disney
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
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25
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Li S, Shui W. Systematic mapping of protein–metabolite interactions with mass spectrometry-based techniques. Curr Opin Biotechnol 2020; 64:24-31. [DOI: 10.1016/j.copbio.2019.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 08/30/2019] [Accepted: 09/04/2019] [Indexed: 12/31/2022]
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26
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Motoyaji T. Revolution of Small Molecule Drug Discovery by Affinity Selection-Mass Spectrometry Technology. Chem Pharm Bull (Tokyo) 2020; 68:191-193. [DOI: 10.1248/cpb.c19-00832] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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27
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Wang J, Deng K, Zhou C, Fang Z, Meyer C, Deshpande KUA, Li Z, Mi X, Luo Q, Hammock BD, Tan C, Chen Y, Pan T. Microfluidic cap-to-dispense (μCD): a universal microfluidic-robotic interface for automated pipette-free high-precision liquid handling. LAB ON A CHIP 2019; 19:3405-3415. [PMID: 31501848 PMCID: PMC6785371 DOI: 10.1039/c9lc00622b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Microfluidic devices have been increasingly used for low-volume liquid handling operations. However, laboratory automation of such delicate devices has lagged behind due to the lack of world-to-chip (macro-to-micro) interfaces. In this paper, we have presented the first pipette-free robotic-microfluidic interface using a microfluidic-embedded container cap, referred to as a microfluidic cap-to-dispense (μCD), to achieve a seamless integration of liquid handling and robotic automation without any traditional pipetting steps. The μCD liquid handling platform offers a generic and modular way to connect the robotic device to standard liquid containers. It utilizes the high accuracy and high flexibility of the robotic system to recognize, capture and position; and then using microfluidic adaptive printing it can achieve high-precision on-demand volume distribution. With its modular connectivity, nanoliter processability, high adaptability, and multitask capacity, μCD shows great potential as a generic robotic-microfluidic interface for complete pipette-free liquid handling automation.
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Affiliation(s)
- Jingjing Wang
- Institute of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
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28
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Carter AJ, Kraemer O, Zwick M, Mueller-Fahrnow A, Arrowsmith CH, Edwards AM. Target 2035: probing the human proteome. Drug Discov Today 2019; 24:2111-2115. [PMID: 31278990 DOI: 10.1016/j.drudis.2019.06.020] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 06/11/2019] [Accepted: 06/27/2019] [Indexed: 11/29/2022]
Abstract
Biomedical scientists tend to focus on only a small fraction of the proteins encoded by the human genome despite overwhelming genetic evidence that many understudied proteins are important for human disease. One of the best ways to interrogate the function of a protein and to determine its relevance as a drug target is by using a pharmacological modulator, such as a chemical probe or an antibody. If these tools were available for most human proteins, it should be possible to translate the tremendous advances in genomics into a greater understanding of human health and disease, and catalyze the creation of innovative new medicines. Target 2035 is a global federation for developing and applying new technologies with the goal of creating chemogenomic libraries, chemical probes, and/or functional antibodies for the entire proteome.
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Affiliation(s)
- Adrian J Carter
- Discovery Research Coordination, Boehringer Ingelheim, 55216 Ingelheim am Rhein, Germany.
| | - Oliver Kraemer
- Discovery Research Coordination, Boehringer Ingelheim, 55216 Ingelheim am Rhein, Germany
| | - Matthias Zwick
- Computational Biology, Boehringer Ingelheim, 88400 Biberach an der Riß, Germany
| | | | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Canada; Princess Margaret Cancer Centre, Toronto, Ontario, M5G 1L7, Canada
| | - Aled M Edwards
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
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29
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Lu Y, Qin S, Zhang B, Dai A, Cai X, Ma M, Gao ZG, Yang D, Stevens RC, Jacobson KA, Wang MW, Shui W. Accelerating the Throughput of Affinity Mass Spectrometry-Based Ligand Screening toward a G Protein-Coupled Receptor. Anal Chem 2019; 91:8162-8169. [PMID: 31094506 PMCID: PMC6669887 DOI: 10.1021/acs.analchem.9b00477] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Affinity mass spectrometry (MS) enables rapid screening of compound mixtures for ligands bound to a specific protein target, yet its current throughput is limited to individually assay pools of 400-2000 compounds. Typical affinity MS screens implemented in pharmaceutical industry laboratories identify putative ligands based on qualitative analysis of compound binding to the target whereas no quantitative information is acquired to discriminate high- and low-affinity ligands in the screening phase. Furthermore, these screens require purification of a stabilized form of the protein target, which poses a great challenge for membrane receptor targets. Here, we describe a new, potentially general affinity MS strategy that allows screening of 20,000 compounds in one pool for highly efficient ligand discovery toward a G protein-coupled receptor (GPCR) target. Quantitative measurement of compound binding to the receptor enables high-affinity ligand selection using both the purified receptor and receptor-embedded cell membranes. This high-throughput, label-free and quantitative affinity MS screen resulted in discovery of three new antagonists of the A2A adenosine receptor.
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Affiliation(s)
- Yan Lu
- iHuman Institute, ShanghaiTech University, 201210 Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, 201210 Shanghai, China
- University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Shanshan Qin
- iHuman Institute, ShanghaiTech University, 201210 Shanghai, China
| | - Bingjie Zhang
- iHuman Institute, ShanghaiTech University, 201210 Shanghai, China
| | - Antao Dai
- The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203 Shanghai, China
| | - Xiaoqing Cai
- The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203 Shanghai, China
| | - Mengna Ma
- iHuman Institute, ShanghaiTech University, 201210 Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, 201210 Shanghai, China
- University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Zhan-Guo Gao
- National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, Maryland 20892 United States
| | - Dehua Yang
- The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203 Shanghai, China
| | - Raymond C. Stevens
- iHuman Institute, ShanghaiTech University, 201210 Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, 201210 Shanghai, China
| | - Kenneth A. Jacobson
- National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, Maryland 20892 United States
| | - Ming-Wei Wang
- University of Chinese Academy of Sciences, 100049 Beijing, China
- The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203 Shanghai, China
- School of Pharmacy, Fudan University, 201203 Shanghai, China
| | - Wenqing Shui
- iHuman Institute, ShanghaiTech University, 201210 Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, 201210 Shanghai, China
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30
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Rizvi NF, Nickbarg EB. RNA-ALIS: Methodology for screening soluble RNAs as small molecule targets using ALIS affinity-selection mass spectrometry. Methods 2019; 167:28-38. [PMID: 31059829 DOI: 10.1016/j.ymeth.2019.04.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 04/10/2019] [Accepted: 04/30/2019] [Indexed: 12/20/2022] Open
Abstract
Recent advances resulting from the completion of the human genome have shown that RNA has the promise to be a target for small molecule drugs, and therefore represents a previously unexploited class of targets for novel human therapeutics. We recently reported the adaptation of an affinity selection mass spectrometry screening technique, termed ALIS (Automatic Ligand Identification System), to screen and characterize a variety of RNA species from both prokaryotic and eukaryotic sources. We demonstrated that the ALIS technique, which had previously been used for protein targets, was also compatible for screening, ranking and characterizing small molecule ligands for RNA targets. We present here a detailed description of the use of ALIS for screening and characterizing ligands for RNA and discuss issues of validating and testing RNA for use in the ALIS system. We have also further elaborated on issues of RNA stability and testing in the ALIS system and demonstrate that the affinity-selection screening system has the potential to be a general solution for label-free screening and characterization of small molecule drug candidates for RNA targets.
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31
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In-solution enrichment identifies peptide inhibitors of protein-protein interactions. Nat Chem Biol 2019; 15:410-418. [PMID: 30886434 DOI: 10.1038/s41589-019-0245-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 02/13/2019] [Indexed: 12/14/2022]
Abstract
The use of competitive inhibitors to disrupt protein-protein interactions (PPIs) holds great promise for the treatment of disease. However, the discovery of high-affinity inhibitors can be a challenge. Here we report a platform for improving the affinity of peptide-based PPI inhibitors using non-canonical amino acids. The platform utilizes size exclusion-based enrichment from pools of synthetic peptides (1.5-4 kDa) and liquid chromatography-tandem mass spectrometry-based peptide sequencing to identify high-affinity binders to protein targets, without the need for 'reporter' or 'encoding' tags. Using this approach-which is inherently selective for high-affinity binders-we realized gains in affinity of up to ~100- or ~30-fold for binders to the oncogenic ubiquitin ligase MDM2 or HIV capsid protein C-terminal domain, which inhibit MDM2-p53 interaction or HIV capsid protein C-terminal domain dimerization, respectively. Subsequent macrocyclization of select MDM2 inhibitors rendered them cell permeable and cytotoxic toward cancer cells, demonstrating the utility of the identified compounds as functional PPI inhibitors.
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32
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Comess KM, McLoughlin SM, Oyer JA, Richardson PL, Stöckmann H, Vasudevan A, Warder SE. Emerging Approaches for the Identification of Protein Targets of Small Molecules - A Practitioners’ Perspective. J Med Chem 2018; 61:8504-8535. [DOI: 10.1021/acs.jmedchem.7b01921] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Kenneth M. Comess
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| | - Shaun M. McLoughlin
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| | - Jon A. Oyer
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| | - Paul L. Richardson
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| | - Henning Stöckmann
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| | - Anil Vasudevan
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| | - Scott E. Warder
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
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33
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34
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Qin S, Meng M, Yang D, Bai W, Lu Y, Peng Y, Song G, Wu Y, Zhou Q, Zhao S, Huang X, McCorvy JD, Cai X, Dai A, Roth BL, Hanson MA, Liu ZJ, Wang MW, Stevens RC, Shui W. High-throughput identification of G protein-coupled receptor modulators through affinity mass spectrometry screening. Chem Sci 2018; 9:3192-3199. [PMID: 29732102 PMCID: PMC5916221 DOI: 10.1039/c7sc04698g] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 02/19/2018] [Indexed: 12/24/2022] Open
Abstract
High-throughput identification of GPCR modulators through affinity MS screening.
G protein-coupled receptors (GPCRs) represent the largest class of cell surface proteins and thus constitute an important family of therapeutic targets. Therefore, significant effort has been put towards the identification of novel ligands that can modulate the activity of a GPCR target with high efficacy and selectivity. However, due to limitations inherent to the most common techniques for GPCR ligand discovery, there is a pressing need for more efficient and effective ligand screening methods especially for the identification of potential allosteric modulators. Here we present a high-throughput, label-free and unbiased screening approach for the identification of small molecule ligands towards GPCR targets based on affinity mass spectrometry. This new approach features the usage of target-expressing cell membranes rather than purified proteins for ligand screening and allows the detection of both orthosteric and allosteric ligands targeting specific GPCRs. Screening a small compound library with this approach led to the rapid discovery of an antagonist for the 5-HT receptor and four positive allosteric modulators for GLP-1 receptor that were not previously reported.
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Affiliation(s)
- Shanshan Qin
- iHuman Institute , ShanghaiTech University , 201210 , Shanghai , China .
| | - Mengmeng Meng
- College of Pharmacy , Nankai University , 300071 , Tianjin , China
| | - Dehua Yang
- The National Center for Drug Screening , The CAS Key Laboratory of Receptor Research , Shanghai Institute of Materia Medica , Chinese Academy of Sciences , 201203 , Shanghai , China .
| | - Wenwen Bai
- College of Pharmacy , Nankai University , 300071 , Tianjin , China
| | - Yan Lu
- iHuman Institute , ShanghaiTech University , 201210 , Shanghai , China . .,School of Life Science and Technology , ShanghaiTech University , 201202 , Shanghai , China
| | - Yao Peng
- iHuman Institute , ShanghaiTech University , 201210 , Shanghai , China .
| | - Gaojie Song
- iHuman Institute , ShanghaiTech University , 201210 , Shanghai , China .
| | - Yiran Wu
- iHuman Institute , ShanghaiTech University , 201210 , Shanghai , China .
| | - Qingtong Zhou
- iHuman Institute , ShanghaiTech University , 201210 , Shanghai , China .
| | - Suwen Zhao
- iHuman Institute , ShanghaiTech University , 201210 , Shanghai , China . .,School of Life Science and Technology , ShanghaiTech University , 201202 , Shanghai , China
| | - Xiping Huang
- Department of Pharmacology , Chapel Hill School of Medicine , University of North Carolina , NC 27599 Chapel Hill , USA
| | - John D McCorvy
- Department of Pharmacology , Chapel Hill School of Medicine , University of North Carolina , NC 27599 Chapel Hill , USA
| | - Xiaoqing Cai
- The National Center for Drug Screening , The CAS Key Laboratory of Receptor Research , Shanghai Institute of Materia Medica , Chinese Academy of Sciences , 201203 , Shanghai , China .
| | - Antao Dai
- The National Center for Drug Screening , The CAS Key Laboratory of Receptor Research , Shanghai Institute of Materia Medica , Chinese Academy of Sciences , 201203 , Shanghai , China .
| | - Bryan L Roth
- Department of Pharmacology , Chapel Hill School of Medicine , University of North Carolina , NC 27599 Chapel Hill , USA
| | | | - Zhi-Jie Liu
- iHuman Institute , ShanghaiTech University , 201210 , Shanghai , China . .,School of Life Science and Technology , ShanghaiTech University , 201202 , Shanghai , China
| | - Ming-Wei Wang
- The National Center for Drug Screening , The CAS Key Laboratory of Receptor Research , Shanghai Institute of Materia Medica , Chinese Academy of Sciences , 201203 , Shanghai , China . .,School of Life Science and Technology , ShanghaiTech University , 201202 , Shanghai , China.,School of Pharmacy , Fudan University , 201203 , Shanghai , China
| | - Raymond C Stevens
- iHuman Institute , ShanghaiTech University , 201210 , Shanghai , China . .,School of Life Science and Technology , ShanghaiTech University , 201202 , Shanghai , China
| | - Wenqing Shui
- iHuman Institute , ShanghaiTech University , 201210 , Shanghai , China . .,School of Life Science and Technology , ShanghaiTech University , 201202 , Shanghai , China
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35
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Brown KK, Hann MM, Lakdawala AS, Santos R, Thomas PJ, Todd K. Approaches to target tractability assessment - a practical perspective. MEDCHEMCOMM 2018; 9:606-613. [PMID: 30108951 DOI: 10.1039/c7md00633k] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 02/13/2018] [Indexed: 01/21/2023]
Abstract
The assessment of the suitability of novel targets to intervention by different modalities, e.g. small molecules or antibodies, is increasingly seen as important in helping to select the most progressable targets at the outset of a drug discovery project. This perspective considers differing aspects of tractability and how it can be assessed using in silico and experimental approaches. We also share some of our experiences in using these approaches.
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Affiliation(s)
- Kristin K Brown
- Computational and Modelling Sciences , Platform Technology and Sciences , GlaxoSmithKline , 1250 S. Collegeville Road , Collegeville , Pennsylvania 19426 , USA
| | - Michael M Hann
- NCE Molecular Discovery , Platform Technology and Sciences , GlaxoSmithKline Medicines Research Centre , Gunnels Wood Road, Stevenage , Hertfordshire , SG1 2NY , UK .
| | - Ami S Lakdawala
- In vitro/In vivo Translation Sciences , Platform Technology and Sciences , GlaxoSmithKline , 1250 S. Collegeville Road , Collegeville , Pennsylvania 19426 , USA
| | - Rita Santos
- Target Sciences Computational Biology , GlaxoSmithKline Medicines Research Centre , Gunnels Wood Road, Stevenage , Hertfordshire , SG1 2NY , UK
| | - Pamela J Thomas
- Computational and Modelling Sciences , Platform Technology and Sciences , GlaxoSmithKline Medicines Research Centre , Gunnels Wood Road, Stevenage , Hertfordshire , SG1 2NY , UK
| | - Kieran Todd
- Computational and Modelling Sciences , Platform Technology and Sciences , GlaxoSmithKline Medicines Research Centre , Gunnels Wood Road, Stevenage , Hertfordshire , SG1 2NY , UK
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36
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Musetti C, Bean MF, Quinque GT, Kwiatkowski C, Szewczuk LM, Baldoni J, Zajac MA. High-Throughput Assessment of Structural Continuity in Biologics. Anal Chem 2018; 90:2970-2975. [PMID: 29369625 PMCID: PMC6349355 DOI: 10.1021/acs.analchem.8b00180] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We demonstrate a high-throughput chemoprinting platform that confirms the consistency in the higher-order structure of protein biologics and is sensitive enough to detect single-point mutations. This method addresses the quality and consistency of the tertiary and quaternary structure of biologic drug products, which is arguably the most important, yet rarely examined, parameter. The method described uses specific small-molecule ligands as molecular probes to assess protein structure. Each library of probe molecules provides a "fingerprint" when taken holistically. After proof-of-concept experiments involving enzymes and antibodies, we were able to detect minor conformational perturbations between four 48 kDa protein mutants that only differ by one amino acid residue.
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Affiliation(s)
- Caterina Musetti
- Platform Technology and Science, GlaxoSmithKline , 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Mark F Bean
- Platform Technology and Science, GlaxoSmithKline , 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Geoffrey T Quinque
- Platform Technology and Science, GlaxoSmithKline , 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Christopher Kwiatkowski
- Platform Technology and Science, GlaxoSmithKline , 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Lawrence M Szewczuk
- Platform Technology and Science, GlaxoSmithKline , 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - John Baldoni
- Platform Technology and Science, GlaxoSmithKline , 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Matthew A Zajac
- Platform Technology and Science, GlaxoSmithKline , 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
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37
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Vinogradov AA, Gates ZP, Zhang C, Quartararo AJ, Halloran KH, Pentelute BL. Library Design-Facilitated High-Throughput Sequencing of Synthetic Peptide Libraries. ACS COMBINATORIAL SCIENCE 2017; 19:694-701. [PMID: 28892357 PMCID: PMC5818986 DOI: 10.1021/acscombsci.7b00109] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A methodology to achieve high-throughput de novo sequencing of synthetic peptide mixtures is reported. The approach leverages shotgun nanoliquid chromatography coupled with tandem mass spectrometry-based de novo sequencing of library mixtures (up to 2000 peptides) as well as automated data analysis protocols to filter away incorrect assignments, noise, and synthetic side-products. For increasing the confidence in the sequencing results, mass spectrometry-friendly library designs were developed that enabled unambiguous decoding of up to 600 peptide sequences per hour while maintaining greater than 85% sequence identification rates in most cases. The reliability of the reported decoding strategy was additionally confirmed by matching fragmentation spectra for select authentic peptides identified from library sequencing samples. The methods reported here are directly applicable to screening techniques that yield mixtures of active compounds, including particle sorting of one-bead one-compound libraries and affinity enrichment of synthetic library mixtures performed in solution.
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Affiliation(s)
| | - Zachary P. Gates
- Department of Chemistry, Massachusetts Institute of Technology, 18-563, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Chi Zhang
- Department of Chemistry, Massachusetts Institute of Technology, 18-563, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Anthony J. Quartararo
- Department of Chemistry, Massachusetts Institute of Technology, 18-563, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Kathryn H. Halloran
- Department of Chemistry, Massachusetts Institute of Technology, 18-563, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Bradley L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, 18-563, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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Rapid LC-MS Based High-Throughput Screening Method, Affording No False Positives or False Negatives, Identifies a New Inhibitor for Carbonic Anhydrase. Sci Rep 2017; 7:10324. [PMID: 28871149 PMCID: PMC5583356 DOI: 10.1038/s41598-017-08602-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 07/12/2017] [Indexed: 12/03/2022] Open
Abstract
Developing effective high-throughput screening (HTS) methods is of paramount importance in the early stage of drug discovery. While rugged and robust assays may be easily developed for certain enzymes, HTS assays designed to identify ligands that block protein binding are much more challenging to develop; attenuating the number of false positives and false negatives under high-throughput screening conditions is particularly difficult. We describe an MS-based HTS workflow that addresses these challenges. The assay mitigates false positives by selectively identifying positive hits exclusively when a ligand at the binding site of interest is displaced; it mitigates false negatives by detecting a reporter compound that ionizes well, not by detecting the ligand binder, which may not ionize. The method was validated by detecting known binders of three proteins, pepsin, maltose binding protein (MBP), and carbonic anhydrase (CA) in the presence of hundreds of non-binders. We also identified a novel CA binder, pifithrin-µ, which could not have been identified by any other MS-based assay because of its poor ionization efficiency. This new method addresses many of the challenges that are currently encountered during high-throughput screening.
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Genick CC, Wright SK. Biophysics: for HTS hit validation, chemical lead optimization, and beyond. Expert Opin Drug Discov 2017; 12:897-907. [DOI: 10.1080/17460441.2017.1349096] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Christine C. Genick
- Novartis Pharma AG, Novartis Institutes for BioMedical Research, Chemical Biology and Therapeutics, Protein Sciences, Basel, Switzerland
- Protein Sciences, Research Parkway Meriden, Cambridge, MA, USA
| | - S. Kirk Wright
- Protein Sciences, Research Parkway Meriden, Cambridge, MA, USA
- Protein Sciences, Novartis Pharma AG, Novartis Institutes for BioMedical Research, Chemical Biology and Therapeutics, Cambridge, MA, USA
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VanderPorten EC, Scholle MD, Sherrill J, Tran JC, Liu Y. Identification of Small-Molecule Noncovalent Binders Utilizing SAMDI Technology. SLAS DISCOVERY 2017; 22:1211-1217. [DOI: 10.1177/2472555217712761] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In recent years, the ability to unambiguously identify complex mixtures of analytes with high accuracy and resolving power in a label-free format continues to expand the application of mass spectrometry (MS) in the drug discovery process. This advantage combined with improved instrumentation makes MS suitable for targets with limited alternative assays for high-throughput screening (HTS). We describe a novel screening format using Self-Assembled Monolayers and matrix-assisted laser Desorption Ionization (SAMDI) technology. SAMDI enables affinity capture of a target protein for use in a small-molecule–binding assay format. Subsequent ionization enables the inferred identification of noncovalent compound interactions. SAMDI technology overcomes shot-to-shot variability by uniformly saturating the surface with captured protein, thereby minimizing matrix crystallization “hot spots.” Furthermore, the combination with high-resolution matrix-assisted laser desorption/ionization time of flight significantly reduces interference of small-molecule detection from salt, detergent, and matrix. By using a pooled library format, the SAMDI assay can significantly improve the throughput of MS-based screening irrespective of enzyme activity. Finally, we demonstrate binding affinity rank ordering from a pool of compounds that correlates with potency data from a biochemical assay.
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Affiliation(s)
- Erica C. VanderPorten
- Biochemical and Cellular Pharmacology Department, Genentech Inc., San Francisco, CA, USA
| | | | | | - John C. Tran
- Biochemical and Cellular Pharmacology Department, Genentech Inc., San Francisco, CA, USA
| | - Yichin Liu
- Biochemical and Cellular Pharmacology Department, Genentech Inc., San Francisco, CA, USA
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Wildey MJ, Haunso A, Tudor M, Webb M, Connick JH. High-Throughput Screening. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2017. [DOI: 10.1016/bs.armc.2017.08.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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A Small-Molecule Anti-secretagogue of PCSK9 Targets the 80S Ribosome to Inhibit PCSK9 Protein Translation. Cell Chem Biol 2016; 23:1362-1371. [DOI: 10.1016/j.chembiol.2016.08.016] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 08/06/2016] [Accepted: 08/10/2016] [Indexed: 01/25/2023]
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Imaduwage KP, Go EP, Zhu Z, Desaire H. HAMS: High-Affinity Mass Spectrometry Screening. A High-Throughput Screening Method for Identifying the Tightest-Binding Lead Compounds for Target Proteins with No False Positive Identifications. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1870-1877. [PMID: 27600575 PMCID: PMC5501305 DOI: 10.1007/s13361-016-1472-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 07/21/2016] [Accepted: 07/23/2016] [Indexed: 06/06/2023]
Abstract
A major challenge in drug discovery is the identification of high affinity lead compounds that bind a particular target protein; these leads are typically identified by high throughput screens. Mass spectrometry has become a detection method of choice in drug screening assays because the target and the ligand need not be modified. Label-free assays are advantageous because they can be developed more rapidly than assays requiring labels, and they eliminate the risk of the label interfering with the binding event. However, in commonly used MS-based screening methods, detection of false positives is a major challenge. Here, we describe a detection strategy designed to eliminate false positives. In this approach, the protein and the ligands are incubated together, and the non-binders are separated for detection. Hits (protein binders) are not detectable by MS after incubation with the protein, but readily identifiable by MS when the target protein is not present in the incubation media. The assay was demonstrated using three different proteins and hundreds of non-inhibitors; no false positive hits were identified in any experiment. The assay can be tuned to select for ligands of a particular binding affinity by varying the quantity of protein used and the immobilization method. As examples, the method selectively detected inhibitors that have Ki values of 0.2 μM, 50 pM, and 700 pM. These findings demonstrate that the approach described here compares favorably with traditional MS-based screening methods. Graphical Abstract ᅟ.
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Affiliation(s)
- Kasun P Imaduwage
- The Ralph N. Adams Institute for Bioanalytical Chemistry and Department of Chemistry, University of Kansas, 2030 Becker Drive, Lawrence, KS, 66047, USA
| | - Eden P Go
- The Ralph N. Adams Institute for Bioanalytical Chemistry and Department of Chemistry, University of Kansas, 2030 Becker Drive, Lawrence, KS, 66047, USA
| | - Zhikai Zhu
- The Ralph N. Adams Institute for Bioanalytical Chemistry and Department of Chemistry, University of Kansas, 2030 Becker Drive, Lawrence, KS, 66047, USA
| | - Heather Desaire
- The Ralph N. Adams Institute for Bioanalytical Chemistry and Department of Chemistry, University of Kansas, 2030 Becker Drive, Lawrence, KS, 66047, USA.
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Kutilek VD, Andrews CL, Richards MP, Xu Z, Sun T, Chen Y, Hashke A, Smotrov N, Fernandez R, Nickbarg EB, Chamberlin C, Sauvagnat B, Curran PJ, Boinay R, Saradjian P, Allen SJ, Byrne N, Elsen NL, Ford RE, Hall DL, Kornienko M, Rickert KW, Sharma S, Shipman JM, Lumb KJ, Coleman K, Dandliker PJ, Kariv I, Beutel B. Integration of Affinity Selection-Mass Spectrometry and Functional Cell-Based Assays to Rapidly Triage Druggable Target Space within the NF-κB Pathway. ACTA ACUST UNITED AC 2016; 21:608-19. [PMID: 26969322 DOI: 10.1177/1087057116637353] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 02/15/2016] [Indexed: 11/15/2022]
Abstract
The primary objective of early drug discovery is to associate druggable target space with a desired phenotype. The inability to efficiently associate these often leads to failure early in the drug discovery process. In this proof-of-concept study, the most tractable starting points for drug discovery within the NF-κB pathway model system were identified by integrating affinity selection-mass spectrometry (AS-MS) with functional cellular assays. The AS-MS platform Automated Ligand Identification System (ALIS) was used to rapidly screen 15 NF-κB proteins in parallel against large-compound libraries. ALIS identified 382 target-selective compounds binding to 14 of the 15 proteins. Without any chemical optimization, 22 of the 382 target-selective compounds exhibited a cellular phenotype consistent with the respective target associated in ALIS. Further studies on structurally related compounds distinguished two chemical series that exhibited a preliminary structure-activity relationship and confirmed target-driven cellular activity to NF-κB1/p105 and TRAF5, respectively. These two series represent new drug discovery opportunities for chemical optimization. The results described herein demonstrate the power of combining ALIS with cell functional assays in a high-throughput, target-based approach to determine the most tractable drug discovery opportunities within a pathway.
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Affiliation(s)
- Victoria D Kutilek
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Christine L Andrews
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Matthew P Richards
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Zangwei Xu
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Tianxiao Sun
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Yiping Chen
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Andrew Hashke
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Nadya Smotrov
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Rafael Fernandez
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Elliott B Nickbarg
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Chad Chamberlin
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Berengere Sauvagnat
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Patrick J Curran
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Ryan Boinay
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Peter Saradjian
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Samantha J Allen
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Noel Byrne
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Nathaniel L Elsen
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA Current address: AbbVie, North Chicago, IL USA
| | - Rachael E Ford
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Dawn L Hall
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Maria Kornienko
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Keith W Rickert
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA Current address: Medimmune, Gaithersburg, MD, USA
| | - Sujata Sharma
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Jennifer M Shipman
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Kevin J Lumb
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Kevin Coleman
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA Current address: Arvinas, New Haven, CT, USA
| | - Peter J Dandliker
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Ilona Kariv
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Bruce Beutel
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
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Klumpp M. Non-stoichiometric inhibition in integrated lead finding - a literature review. Expert Opin Drug Discov 2015; 11:149-62. [PMID: 26653534 DOI: 10.1517/17460441.2016.1128892] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
INTRODUCTION Non-stoichiometric inhibition summarizes different mechanisms by which low-molecular weight compounds can reproducibly inhibit high-throughput screening (HTS) and other lead finding assays without binding to a structurally defined site on their molecular target. This disqualifies such molecules from optimization by medicinal chemistry, and therefore their rapid elimination from screening hit lists is essential for productive and effective drug discovery. AREAS COVERED This review covers recent literature that either investigates the various mechanisms behind non-stoichiometric inhibition or suggests assays and readouts to identify them. In addition, combination of the various methods to distill promising molecules out of raw primary hit lists step-by-step is considered. Emerging technologies to demonstrate target engagement in cells are also discussed. EXPERT OPINION Over the last few years, awareness of non-stoichiometric inhibitors within screening libraries and HTS hit lists has considerably increased, not only in the pharmaceutical industry but also in the academic drug discovery community. This has resulted in a variety of methods to detect and handle such compounds. These range from in silico approaches to flag suspicious compounds, and counterassays to measure non-stoichiometric inhibition, to biophysical methods that positively demonstrate stoichiometric binding. In addition, novel technologies to verify target engagement within cells are becoming available. While still a time- and resource-consuming nuisance, non-stoichiometric inhibitors therefore do not fundamentally jeopardize the discovery of low molecular weight lead and drug candidates. Rather, they should be viewed as a manageable issue that with appropriate expertise can be overcome through integration of the above-mentioned approaches.
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Affiliation(s)
- Martin Klumpp
- a Novartis Institute of Biomedical Research Basel, Novartis Pharma AG , Basel , Switzerland
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Mass-spectrometry-based method for screening of new peptide ligands for G-protein-coupled receptors. Anal Bioanal Chem 2015; 407:5299-307. [DOI: 10.1007/s00216-015-8692-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 04/07/2015] [Accepted: 04/09/2015] [Indexed: 10/23/2022]
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