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Tan L, Hirte S, Palmacci V, Stork C, Kirchmair J. Tackling assay interference associated with small molecules. Nat Rev Chem 2024; 8:319-339. [PMID: 38622244 DOI: 10.1038/s41570-024-00593-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/29/2024] [Indexed: 04/17/2024]
Abstract
Biochemical and cell-based assays are essential to discovering and optimizing efficacious and safe drugs, agrochemicals and cosmetics. However, false assay readouts stemming from colloidal aggregation, chemical reactivity, chelation, light signal attenuation and emission, membrane disruption, and other interference mechanisms remain a considerable challenge in screening synthetic compounds and natural products. To address assay interference, a range of powerful experimental approaches are available and in silico methods are now gaining traction. This Review begins with an overview of the scope and limitations of experimental approaches for tackling assay interference. It then focuses on theoretical methods, discusses strategies for their integration with experimental approaches, and provides recommendations for best practices. The Review closes with a summary of the critical facts and an outlook on potential future developments.
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Affiliation(s)
- Lu Tan
- Drug Discovery Sciences, Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Steffen Hirte
- Department of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria
- Vienna Doctoral School of Pharmaceutical, Nutritional and Sport Sciences (PhaNuSpo), University of Vienna, Vienna, Austria
| | - Vincenzo Palmacci
- Department of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria
- Vienna Doctoral School of Pharmaceutical, Nutritional and Sport Sciences (PhaNuSpo), University of Vienna, Vienna, Austria
| | - Conrad Stork
- Department of Informatics, Center for Bioinformatics, Faculty of Mathematics, Informatics and Natural Sciences, Universität Hamburg, Hamburg, Germany
- BASF SE, Ludwigshafen am Rhein, Germany
| | - Johannes Kirchmair
- Department of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria.
- Christian Doppler Laboratory for Molecular Informatics in the Biosciences, Department for Pharmaceutical Sciences, University of Vienna, Vienna, Austria.
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2
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Di Marco CN, Terrell L, Sanchez R, Rueda L, Shuster L, Nartey EN, McHugh C, Mack JF, Shu A, Tian X, Medina JR, Rivero R, Manetsch R, Heerding D, Mangatt B. Design and synthesis of aminopyridine containing biaryls reducing c-MYC protein levels in cells. Bioorg Med Chem Lett 2023; 92:129385. [PMID: 37339719 DOI: 10.1016/j.bmcl.2023.129385] [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: 03/10/2023] [Accepted: 06/16/2023] [Indexed: 06/22/2023]
Abstract
The c-MYC oncogene transcription factor has been implicated in cell cycle regulation controlling cell growth and proliferation. It is tightly regulated in normal cells, but has been shown to be deregulated in cancer cells, and is thus an attractive target for oncogenic therapies. Building upon previous SAR, a series of analogues containing benzimidazole core replacements were prepared and evaluated, leading to the identification of imidazopyridazine compounds that were shown to possess equivalent or improved c-MYC HTRF pEC50 values, lipophilicity, solubility, and rat pharmacokinetics. The imidazopyridazine core was therefore determined to be superior to the original benzimidazole core and a viable alternate for continued lead optimization and medicinal chemistry campaigns.
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Affiliation(s)
- Christina N Di Marco
- Medicinal Science and Technology, GSK, Collegeville, PA 19426, USA; Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA.
| | - Lamont Terrell
- Medicinal Science and Technology, GSK, Collegeville, PA 19426, USA
| | - Robert Sanchez
- Medicinal Science and Technology, GSK, Collegeville, PA 19426, USA
| | - Lourdes Rueda
- Medicinal Science and Technology, GSK, Collegeville, PA 19426, USA
| | - Leanna Shuster
- Medicinal Science and Technology, GSK, Collegeville, PA 19426, USA
| | | | - Charles McHugh
- Drug Metabolism and Pharmacokinetics, Research In Vivo/In Vitro Translation, GSK, Collegeville, PA 19426, USA
| | - James F Mack
- Medicinal Science and Technology, GSK, Collegeville, PA 19426, USA
| | - Arthur Shu
- Medicinal Science and Technology, GSK, Collegeville, PA 19426, USA
| | - Xinrong Tian
- Medicinal Science and Technology, GSK, Collegeville, PA 19426, USA
| | - Jesus R Medina
- Medicinal Science and Technology, GSK, Collegeville, PA 19426, USA
| | - Ralph Rivero
- Medicinal Science and Technology, GSK, Collegeville, PA 19426, USA
| | - Roman Manetsch
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA; Department of Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA; Center for Drug Discovery, Northeastern University, Boston, MA 02115, USA; Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, MA 02115, USA
| | - Dirk Heerding
- Medicinal Science and Technology, GSK, Collegeville, PA 19426, USA
| | - Biju Mangatt
- Medicinal Science and Technology, GSK, Collegeville, PA 19426, USA
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3
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Lanne A, E J Usselmann L, Llowarch P, Michaelides IN, Fillmore M, Holdgate GA. A perspective on the changing landscape of HTS. Drug Discov Today 2023:103670. [PMID: 37328053 DOI: 10.1016/j.drudis.2023.103670] [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: 03/22/2023] [Revised: 05/14/2023] [Accepted: 06/09/2023] [Indexed: 06/18/2023]
Abstract
Recently, there has been a change in the types of drug target entering early drug discovery portfolios. A significant increase in the number of challenging targets or which would have historically been classed as intractable has been observed. Such targets often have shallow or non-existent ligand-binding sites, can have disordered structures or domains or can be involved in protein-protein or protein-DNA interactions. The nature of the screens required to identify useful hits has, by necessity, also changed. The range of drug modalities explored has also increased and the chemistry required to design and optimise these molecules has adapted. In this review, we discuss this changing landscape and provide insights into the future requirements for small-molecule hit and lead generation.
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Affiliation(s)
- Alice Lanne
- High Throughput Screening, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
| | - Laura E J Usselmann
- High Throughput Screening, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
| | - Poppy Llowarch
- High Throughput Screening, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
| | - Iacovos N Michaelides
- Fragment Based Lead Generation, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Martin Fillmore
- DNA Encoded Library, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
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4
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Tian X, Suarez D, Thomson D, Li W, King EA, LaFrance L, Boehm J, Barton L, Di Marco C, Martyr C, Thalji R, Medina J, Knight S, Heerding D, Gao E, Nartey E, Cecconie T, Nixon C, Zhang G, Berrodin TJ, Phelps C, Patel A, Bai X, Lind K, Prabhu N, Messer J, Zhu Z, Shewchuk L, Reid R, Graves AP, McHugh C, Mangatt B. Discovery of Proline-Based p300/CBP Inhibitors Using DNA-Encoded Library Technology in Combination with High-Throughput Screening. J Med Chem 2022; 65:14391-14408. [DOI: 10.1021/acs.jmedchem.2c00670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Xinrong Tian
- Research and Development, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Dominic Suarez
- Research and Development, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Douglas Thomson
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - William Li
- Research and Development, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Elizabeth A. King
- Research and Development, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Louis LaFrance
- Research and Development, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Jeffrey Boehm
- Research and Development, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Linda Barton
- Research and Development, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Christina Di Marco
- Research and Development, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Cuthbert Martyr
- Research and Development, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Reema Thalji
- Research and Development, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Jesus Medina
- Research and Development, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Steven Knight
- Research and Development, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Dirk Heerding
- Research and Development, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Enoch Gao
- Research and Development, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Eldridge Nartey
- Research and Development, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Ted Cecconie
- Research and Development, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Christopher Nixon
- Research and Development, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Guofeng Zhang
- Research and Development, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Thomas J. Berrodin
- Research and Development, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Christopher Phelps
- New Chemical Entity Molecular Discovery, GlaxoSmithKline, 200 Cambridgepark Drive, Cambridge, Massachusetts 02140, United States
| | - Amish Patel
- New Chemical Entity Molecular Discovery, GlaxoSmithKline, 200 Cambridgepark Drive, Cambridge, Massachusetts 02140, United States
| | - Xiaopeng Bai
- New Chemical Entity Molecular Discovery, GlaxoSmithKline, 200 Cambridgepark Drive, Cambridge, Massachusetts 02140, United States
| | - Ken Lind
- New Chemical Entity Molecular Discovery, GlaxoSmithKline, 200 Cambridgepark Drive, Cambridge, Massachusetts 02140, United States
| | - Ninad Prabhu
- New Chemical Entity Molecular Discovery, GlaxoSmithKline, 200 Cambridgepark Drive, Cambridge, Massachusetts 02140, United States
| | - Jeffrey Messer
- New Chemical Entity Molecular Discovery, GlaxoSmithKline, 200 Cambridgepark Drive, Cambridge, Massachusetts 02140, United States
| | - Zhengrong Zhu
- New Chemical Entity Molecular Discovery, GlaxoSmithKline, 200 Cambridgepark Drive, Cambridge, Massachusetts 02140, United States
| | - Lisa Shewchuk
- Research and Development, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Rob Reid
- Research and Development, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Alan P. Graves
- Research and Development, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Charles McHugh
- Research and Development, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Biju Mangatt
- Research and Development, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
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Medina JR, Tian X, Li WH, Suarez D, Mack JF, LaFrance L, Martyr C, Brackley J, Di Marco C, Rivero R, Heerding DA, McHugh C, Minthorn E, Bhaskar A, Rubin J, Butticello M, Carpenter C, Nartey EN, Berrodin TJ, Kallal LA, Mangatt B. Cell-Based Drug Discovery: Identification and Optimization of Small Molecules that Reduce c-MYC Protein Levels in Cells. J Med Chem 2021; 64:16056-16087. [PMID: 34669409 DOI: 10.1021/acs.jmedchem.1c01416] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Elevated expression of the c-MYC oncogene is one of the most common abnormalities in human cancers. Unfortunately, efforts to identify pharmacological inhibitors that directly target MYC have not yet yielded a drug-like molecule due to the lack of any known small molecule binding pocket in the protein, which could be exploited to disrupt MYC function. We have recently described a strategy to target MYC indirectly, where a screening effort designed to identify compounds that can rapidly decrease endogenous c-MYC protein levels in a MYC-amplified cell line led to the discovery of a compound series that phenocopies c-MYC knockdown by siRNA. Herein, we describe our medicinal chemistry program that led to the discovery of potent, orally bioavailable c-MYC-reducing compounds. The development of a minimum pharmacophore model based on empirical structure activity relationship as well as the property-based approach used to modulate pharmacokinetics properties will be highlighted.
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Affiliation(s)
- Jesús R Medina
- Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Xinrong Tian
- Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - William H Li
- Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Dominic Suarez
- Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - James F Mack
- Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Louis LaFrance
- Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Cuthbert Martyr
- Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - James Brackley
- Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Christina Di Marco
- Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Ralph Rivero
- Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Dirk A Heerding
- Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Charles McHugh
- Oncology Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Elisabeth Minthorn
- Oncology Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Aishwarya Bhaskar
- Oncology Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Jacob Rubin
- Oncology Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Michael Butticello
- Oncology Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | | | - Eldridge N Nartey
- Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Thomas J Berrodin
- Oncology Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Lorena A Kallal
- Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Biju Mangatt
- Oncology Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
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6
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Wigglesworth M, Hodder P. Hit Discovery Methodology. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2021; 26:165-167. [PMID: 33482072 DOI: 10.1177/2472555220982257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Affiliation(s)
- Mark Wigglesworth
- Director Hit Discovery, Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, Alderley Park, UK
| | - Peter Hodder
- Executive Director, Discovery Technologies, Amgen, Thousand Oaks, CA
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