1
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Hillebrand L, Liang XJ, Serafim RAM, Gehringer M. Emerging and Re-emerging Warheads for Targeted Covalent Inhibitors: An Update. J Med Chem 2024; 67:7668-7758. [PMID: 38711345 DOI: 10.1021/acs.jmedchem.3c01825] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Covalent inhibitors and other types of covalent modalities have seen a revival in the past two decades, with a variety of new targeted covalent drugs having been approved in recent years. A key feature of such molecules is an intrinsically reactive group, typically a weak electrophile, which enables the irreversible or reversible formation of a covalent bond with a specific amino acid of the target protein. This reactive group, often called the "warhead", is a critical determinant of the ligand's activity, selectivity, and general biological properties. In 2019, we summarized emerging and re-emerging warhead chemistries to target cysteine and other amino acids (Gehringer, M.; Laufer, S. A. J. Med. Chem. 2019, 62, 5673-5724; DOI: 10.1021/acs.jmedchem.8b01153). Since then, the field has rapidly evolved. Here we discuss the progress on covalent warheads made since our last Perspective and their application in medicinal chemistry and chemical biology.
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Affiliation(s)
- Laura Hillebrand
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Xiaojun Julia Liang
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
| | - Ricardo A M Serafim
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Matthias Gehringer
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
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2
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Machado-Neto JA, Cerqueira ARA, Veríssimo-Filho S, Muscará MN, Costa SKP, Lopes LR. Hydrogen Sulfide Signaling in the Tumor Microenvironment: Implications in Cancer Progression and Therapy. Antioxid Redox Signal 2024; 40:250-271. [PMID: 37597204 DOI: 10.1089/ars.2021.0256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 08/21/2023]
Abstract
Significance: Cancer is a complex and heterotypic structure with a spatial organization that contributes to challenges in therapeutics. Enzymes associated with producing the gasotransmitter hydrogen sulfide (H2S) are differentially expressed in tumors. Indeed, critical and paradoxical roles have been attributed to H2S in cancer-promoting characteristics by targeting both cancer cells and their milieu. This review focuses on the evidence and knowledge gaps of H2S on the tumor redox microenvironment and the pharmacological effects of H2S donors on cancer biology. Recent Advances: Endogenous and pharmacological concentrations of H2S evoke different effects on the same cell type: physiological H2S concentrations have been associated with tumor development and progression. In contrast, pharmacological concentrations have been associated with anticancer effects. Critical Issues: The exact threshold between the promotion and inhibition of tumorigenesis by H2S is largely unknown. The main issues covered in this review include H2S-modulated signaling pathways that are critical for cancer cells, the potential effects of H2S on cellular components of the tumor microenvironment, temporal modulation of H2S in promoting or inhibiting tumor progression (similar to observed for inflammation), and pharmacological agents that modulate H2S and which could play a role in antineoplastic therapy. Future Directions: Given the complexity and heterogeneity of tumor composition, mechanistic studies on context-dependent pharmacological effects of H2S donors for cancer therapy are necessary. These studies must determine the critical signaling pathways and the cellular components involved to allow advances in the rational use of H2S donors as antineoplastic agents. Antioxid. Redox Signal. 40, 250-271.
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Affiliation(s)
| | | | - Sidney Veríssimo-Filho
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Marcelo Nicolás Muscará
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Soraia Kátia Pereira Costa
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Lucia Rossetti Lopes
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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3
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Hoyt KW, Urul DA, Ogboo BC, Wittlinger F, Laufer SA, Schaefer EM, May EW, Heppner DE. Pitfalls and Considerations in Determining the Potency and Mutant Selectivity of Covalent Epidermal Growth Factor Receptor Inhibitors. J Med Chem 2024; 67:2-16. [PMID: 38134304 DOI: 10.1021/acs.jmedchem.3c01502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
Enzyme inhibitors that form covalent bonds with their targets are being increasingly pursued in drug development. Assessing their biochemical activity relies on time-dependent assays, which are distinct and more complex compared with methods commonly employed for reversible-binding inhibitors. To provide general guidance to the covalent inhibitor development community, we explored methods and reported kinetic values and experimental factors in determining the biochemical activity of various covalent epidermal growth factor receptor (EGFR) inhibitors. We showcase how liquid handling and assay reagents impact kinetic parameters and potency interpretations, which are critical for structure-kinetic relationships and covalent drug design. Additionally, we include benchmark kinetic values with reference inhibitors, which are imperative, as covalent EGFR inhibitor kinetic values are infrequently consistent in the literature. This overview seeks to inform best practices for developing new covalent inhibitors and highlight appropriate steps to address gaps in knowledge presently limiting assay reliability and reproducibility.
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Affiliation(s)
- Kristopher W Hoyt
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Daniel A Urul
- AssayQuant Technologies, Inc., Marlboro, Massachusetts 01752, United States
| | - Blessing C Ogboo
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Florian Wittlinger
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Stefan A Laufer
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
- Tübingen Center for Academic Drug Discovery & Development (TüCAD2), 72076 Tübingen, Germany
| | - Erik M Schaefer
- AssayQuant Technologies, Inc., Marlboro, Massachusetts 01752, United States
| | - Earl W May
- AssayQuant Technologies, Inc., Marlboro, Massachusetts 01752, United States
| | - David E Heppner
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14203, United States
- Department of Structural Biology, The State University of New York, Buffalo, New York 14203, United States
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4
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Punzalan C, Wang L, Bajrami B, Yao X. Measurement and utilization of the proteomic reactivity by mass spectrometry. MASS SPECTROMETRY REVIEWS 2024; 43:166-192. [PMID: 36924435 DOI: 10.1002/mas.21837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Chemical proteomics, which involves studying the covalent modifications of proteins by small molecules, has significantly contributed to our understanding of protein function and has become an essential tool in drug discovery. Mass spectrometry (MS) is the primary method for identifying and quantifying protein-small molecule adducts. In this review, we discuss various methods for measuring proteomic reactivity using MS and covalent proteomics probes that engage through reactivity-driven and proximity-driven mechanisms. We highlight the applications of these methods and probes in live-cell measurements, drug target identification and validation, and characterizing protein-small molecule interactions. We conclude the review with current developments and future opportunities in the field, providing our perspectives on analytical considerations for MS-based analysis of the proteomic reactivity landscape.
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Affiliation(s)
- Clodette Punzalan
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - Lei Wang
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
- AD Bio US, Takeda, Lexington, Massachusetts, 02421, USA
| | - Bekim Bajrami
- Chemical Biology & Proteomics, Biogen, Cambridge, Massachusetts, USA
| | - Xudong Yao
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
- Institute for Systems Biology, University of Connecticut, Storrs, Connecticut, USA
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5
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Niu ZX, Wang YT, Lu N, Sun JF, Nie P, Herdewijn P. Advances of clinically approved small-molecule drugs for the treatment of non-small cell lung cancer. Eur J Med Chem 2023; 261:115868. [PMID: 37844346 DOI: 10.1016/j.ejmech.2023.115868] [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: 07/25/2023] [Revised: 09/14/2023] [Accepted: 10/09/2023] [Indexed: 10/18/2023]
Abstract
Lung cancer continues to pose a significant challenge as a prominent contributor to global cancer-related mortality. Despite the considerable strides made in therapeutic interventions within the past decade, a substantial population of patients diagnosed with non-small cell lung cancer (NSCLC) still face the grim reality of an incurable condition. In the realm of optimal management strategies for individuals afflicted with locally advanced, yet amenable to surgical resection, NSCLC, a therapeutic approach encompassing chemoradiation stands as a fundamental component. Significant strides have been made in the therapeutic landscape of NSCLC during the preceding two decades, facilitating an enhanced comprehension of the underlying disease biology, and mechanisms governing tumor progression, as well as advancements in early detection modalities and multimodal therapeutic interventions. Nevertheless, the overall rates of curative interventions and survival outcomes for NSCLC continue to exhibit a discouragingly low trajectory, particularly in the context of metastatic disease. Hence, the imperative for sustained research endeavors in the realm of novel pharmaceutical agents and combinatorial therapeutic approaches remains paramount, with the overarching objective of broadening the scope of clinical advantages conferred upon a wider demographic of patients, thereby fostering tangible improvements in outcomes pertaining to NSCLC. The primary objective of this review is to provide an all-encompassing examination encompassing the clinical application and synthetic routes of specific drugs, with the explicit aim of disseminating invaluable knowledge that can inform future research and development endeavors focused on NSCLC.
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Affiliation(s)
- Zhen-Xi Niu
- Department of Pharmacy, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China
| | - Ya-Tao Wang
- Department of Pharmacy, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China; First People's Hospital of Shangqiu, Henan Province, Shangqiu, 476100, China
| | - Nan Lu
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark.
| | - Jin-Feng Sun
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, Yanbian University, College of Pharmacy, Yanji, Jilin, 133002, China.
| | - Peng Nie
- Rega Institute for Medical Research, Medicinal Chemistry, KU Leuven, Herestraat 49-Box 1041, 3000, Leuven, Belgium.
| | - Piet Herdewijn
- Rega Institute for Medical Research, Medicinal Chemistry, KU Leuven, Herestraat 49-Box 1041, 3000, Leuven, Belgium.
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6
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Li X, Zhou J, Wang X, Li C, Ma Z, Wan Q, Peng F. New advances in the research of clinical treatment and novel anticancer agents in tumor angiogenesis. Biomed Pharmacother 2023; 163:114806. [PMID: 37163782 DOI: 10.1016/j.biopha.2023.114806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/24/2023] [Accepted: 04/30/2023] [Indexed: 05/12/2023] Open
Abstract
In 1971, Folkman proposed that tumors could be limited to very small sizes by blocking angiogenesis. Angiogenesis is the generation of new blood vessels from pre-existing vessels, considered to be one of the important processes in tumor growth and metastasis. Angiogenesis is a complex process regulated by various factors and involves many secreted factors and signaling pathways. Angiogenesis is important in the transport of oxygen and nutrients to the tumor during tumor development. Therefore, inhibition of angiogenesis has become an important strategy in the clinical management of many solid tumors. Combination therapies of angiogenesis inhibitors with radiotherapy and chemotherapy are often used in clinical practice. In this article, we will review common targets against angiogenesis, the most common and up-to-date anti-angiogenic drugs and clinical treatments in recent years, including active ingredients from chemical and herbal medicines.
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Affiliation(s)
- Xin Li
- Department of Pharmacology, Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Jianbo Zhou
- Department of Pharmacology, Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Xue Wang
- Department of Pharmacology, Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Chunxi Li
- Department of Pharmacology, Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Zifan Ma
- Department of Pharmacology, Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Qiaoling Wan
- Department of Pharmacology, Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Fu Peng
- Department of Pharmacology, Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China.
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7
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bioTCIs: Middle-to-Macro Biomolecular Targeted Covalent Inhibitors Possessing Both Semi-Permanent Drug Action and Stringent Target Specificity as Potential Antibody Replacements. Int J Mol Sci 2023; 24:ijms24043525. [PMID: 36834935 PMCID: PMC9968108 DOI: 10.3390/ijms24043525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/30/2023] [Accepted: 02/03/2023] [Indexed: 02/12/2023] Open
Abstract
Monoclonal antibody therapies targeting immuno-modulatory targets such as checkpoint proteins, chemokines, and cytokines have made significant impact in several areas, including cancer, inflammatory disease, and infection. However, antibodies are complex biologics with well-known limitations, including high cost for development and production, immunogenicity, a limited shelf-life because of aggregation, denaturation, and fragmentation of the large protein. Drug modalities such as peptides and nucleic acid aptamers showing high-affinity and highly selective interaction with the target protein have been proposed alternatives to therapeutic antibodies. The fundamental limitation of short in vivo half-life has prevented the wide acceptance of these alternatives. Covalent drugs, also known as targeted covalent inhibitors (TCIs), form permanent bonds to target proteins and, in theory, eternally exert the drug action, circumventing the pharmacokinetic limitation of other antibody alternatives. The TCI drug platform, too, has been slow in gaining acceptance because of its potential prolonged side-effect from off-target covalent binding. To avoid the potential risks of irreversible adverse drug effects from off-target conjugation, the TCI modality is broadening from the conventional small molecules to larger biomolecules possessing desirable properties (e.g., hydrolysis resistance, drug-action reversal, unique pharmacokinetics, stringent target specificity, and inhibition of protein-protein interactions). Here, we review the historical development of the TCI made of bio-oligomers/polymers (i.e., peptide-, protein-, or nucleic-acid-type) obtained by rational design and combinatorial screening. The structural optimization of the reactive warheads and incorporation into the targeted biomolecules enabling a highly selective covalent interaction between the TCI and the target protein is discussed. Through this review, we hope to highlight the middle to macro-molecular TCI platform as a realistic replacement for the antibody.
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8
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Discovery of mobocertinib, a new irreversible tyrosine kinase inhibitor indicated for the treatment of non-small-cell lung cancer harboring EGFR exon 20 insertion mutations. Med Chem Res 2022; 31:1647-1662. [PMID: 36065226 PMCID: PMC9433531 DOI: 10.1007/s00044-022-02952-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/15/2022] [Indexed: 11/03/2022]
Abstract
Epidermal growth factor receptor (EGFR) is essential for normal cellular functions. Mutations of EGFR’s kinase domain can cause dysregulation leading to non-small cell lung cancer (NSCLC). Exon 20 insertion (ex20ins) mutations in EGFR are one of the leading contributors to oncogenesis and confer insensitivity to most available therapeutics. Mobocertinib is a novel tyrosine kinase inhibitor (TKI) recently approved by the US FDA as a first-in-class small molecule therapeutic for EGFR ex20ins-positive NSCLC. When compared to osimertinib, a TKI indicated for the treatment of EGFR T790M-positive NSCLC, mobocertinib differs only by the presence of an additional C5-carboxylate isopropyl ester group on the middle pyrimidine core. Together with the acrylamide side chain that is responsible for irreversible inhibition, this additional C5-substituent affords mobocertinib high anticancer potency and specificity to EGFR ex20ins-positive lung cancer that is resistant to other EGFR TKIs. This review article provides an overview of the discovery of mobocertinib from osimertinib including their structure-activity relationships, mechanisms of action, preclinical pharmacology, pharmacokinetics, and clinical applications. The discovery and use of mobocertinib and other EGFR TKIs demonstrate the power of structure-based drug design and promising therapeutic outcomes of using precision medicine approaches in the management of molecularly defined tumors. Graphical abstract ![]()
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Abstract
Covalent drugs have made a major impact on human health but until recently were shunned by the pharmaceutical industry over concerns about the potential for toxicity. A resurgence has occurred driven by the clinical success of targeted covalent inhibitors (TCIs), with eight drugs approved over the past decade. The opportunity to create unique drugs by exploiting the covalent mechanism of action has enabled clinically decisive target product profiles to be achieved. TCIs have revolutionized the treatment paradigm for non-small-cell lung cancer and chronic lymphocytic leukemia. This Perspective will highlight the clinical and financial success of this class of drugs and provide early insight into toxicity, a key factor that had hindered progress in the field. Further innovation in the TCI approach, including expanding beyond cysteine-directed electrophiles, kinases, and cancer, highlights the broad opportunity to deliver a new generation of breakthrough therapies.
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Affiliation(s)
- Juswinder Singh
- Ankaa Therapeutics, M2D2 Incubator, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, Massachusetts 01655, United States
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10
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Lu X, Smaill JB, Patterson AV, Ding K. Discovery of Cysteine-targeting Covalent Protein Kinase Inhibitors. J Med Chem 2021; 65:58-83. [PMID: 34962782 DOI: 10.1021/acs.jmedchem.1c01719] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Small molecule covalent kinase inhibitors (CKIs) have entered a new era in drug discovery, which have the advantage for sustained target inhibition and high selectivity. An increased understanding of binding kinetics of CKIs and discovery of additional irreversible and reversible-covalent cysteine-targeted warheads has inspired the development of this area. Herein, we summarize the major medicinal chemistry strategies employed in the discovery of these representative CKIs, which are categorized by the location of the target cysteine within seven main regions of the kinase: the front region, the glycine rich loop (P-loop), the hinge region, the DFG region, the activation loop (A-loop), the catalytic loop (C-loop), and the remote loop. The emphasis is placed on the design and optimization strategies of CKIs that are generated by addition of a warhead to a reversible lead/inhibitor scaffold. In addition, we address the challenges facing this area of drug discovery.
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Affiliation(s)
- Xiaoyun Lu
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Jeff B Smaill
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland, Private Bag 92019, Auckland, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Adam V Patterson
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland, Private Bag 92019, Auckland, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Ke Ding
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
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11
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Serafim RAM, Elkins JM, Zuercher WJ, Laufer SA, Gehringer M. Chemical Probes for Understudied Kinases: Challenges and Opportunities. J Med Chem 2021; 65:1132-1170. [PMID: 34477374 DOI: 10.1021/acs.jmedchem.1c00980] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Over 20 years after the approval of the first-in-class protein kinase inhibitor imatinib, the biological function of a significant fraction of the human kinome remains poorly understood while most research continues to be focused on few well-validated targets. Given the strong genetic evidence for involvement of many kinases in health and disease, the understudied fraction of the kinome holds a large and unexplored potential for future therapies. Specific chemical probes are indispensable tools to interrogate biology enabling proper preclinical validation of novel kinase targets. In this Perspective, we highlight recent case studies illustrating the development of high-quality chemical probes for less-studied kinases and their application in target validation. We spotlight emerging techniques and approaches employed in the generation of chemical probes for protein kinases and beyond and discuss the associated challenges and opportunities.
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Affiliation(s)
- Ricardo A M Serafim
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Jonathan M Elkins
- Centre for Medicines Discovery, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - William J Zuercher
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Stefan A Laufer
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.,Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany.,Tübingen Center for Academic Drug Discovery, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Matthias Gehringer
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.,Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
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12
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Heppner DE, Eck MJ. A structural perspective on targeting the RTK/Ras/MAP kinase pathway in cancer. Protein Sci 2021; 30:1535-1553. [PMID: 34008902 PMCID: PMC8284588 DOI: 10.1002/pro.4125] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 02/06/2023]
Abstract
Precision oncology is premised on identifying and drugging proteins and pathways that drive tumorigenesis or are required for survival of tumor cells. Across diverse cancer types, the signaling pathway emanating from receptor tyrosine kinases on the cell surface to RAS and the MAP kinase pathway is the most frequent target of oncogenic mutations, and key proteins in this signaling axis including EGFR, SHP2, RAS, BRAF, and MEK have long been a focus in cancer drug discovery. In this review, we provide an overview of historical and recent efforts to develop inhibitors targeting these nodes with an emphasis on the role that an understanding of protein structure and regulation has played in inhibitor discovery and characterization. Beyond its well-established role in structure-based drug design, structural biology has revealed mechanisms of allosteric regulation, distinct effects of activating oncogenic mutations, and other vulnerabilities that have opened new avenues in precision cancer drug discovery.
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Affiliation(s)
- David E. Heppner
- Department of ChemistryUniversity at Buffalo, State University of New YorkBuffaloNew YorkUSA
- Department of Pharmacology and TherapeuticsRoswell Park Comprehensive Cancer CenterBuffaloNew YorkUSA
| | - Michael J. Eck
- Department of Cancer BiologyDana‐Farber Cancer InstituteBostonMassachusettsUSA
- Department of Biological Chemistry and Molecular PharmacologyHarvard Medical SchoolBostonMassachusettsUSA
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13
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Li XF, Liu CF, Rao GW. Monoclonal Antibodies, Small Molecule Inhibitors and Antibody-drug Conjugates as HER2 Inhibitors. Curr Med Chem 2021; 28:3339-3360. [PMID: 32900344 DOI: 10.2174/0929867327666200908112847] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/30/2020] [Accepted: 08/04/2020] [Indexed: 11/22/2022]
Abstract
Overexpression of human epidermal growth factor receptor (HER)-2 is found in a variety of cancers, often portending poor clinical outcomes. Therefore, HER2 is an attractive target for treatment. This review describes the research progress of HER2 targeted inhibitors in recent years. Excellent reviews are available, so we focus on the development, mechanisms of action, and structure-activity relationships of different types of inhibitors, including monoclonal antibodies, small molecule inhibitors, and antibody-drug conjugates (ADCs). In addition, the differences among them are compared.
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Affiliation(s)
- Xiu-Fang Li
- College of Pharmaceutical Science, Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou 310014, China
| | - Chen-Fu Liu
- School of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, China
| | - Guo-Wu Rao
- College of Pharmaceutical Science, Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou 310014, China
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14
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Massip-Copiz MM, Valdivieso ÁG, Clauzure M, Mori C, Asensio CJA, Aguilar MÁ, Santa-Coloma TA. Epidermal growth factor receptor activity upregulates lactate dehydrogenase A expression, lactate dehydrogenase activity, and lactate secretion in cultured IB3-1 cystic fibrosis lung epithelial cells. Biochem Cell Biol 2021; 99:476-487. [PMID: 33481676 DOI: 10.1139/bcb-2020-0522] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Cystic fibrosis (CF) is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. It has been postulated that reduced HCO3- transport through CFTR may lead to a decreased airway surface liquid pH. In contrast, others have reported no changes in the extracellular pH (pHe). We have recently reported that in carcinoma Caco-2/pRS26 cells (transfected with short hairpin RNA for CFTR) or CF lung epithelial IB3-1 cells, the mutation in CFTR decreased mitochondrial complex I activity and increased lactic acid production, owing to an autocrine IL-1β loop. The secreted lactate accounted for the reduced pHe, because oxamate fully restored the pHe. These effects were attributed to the IL-1β autocrine loop and the downstream signaling kinases c-Src and JNK. Here we show that the pHe of IB3-1 cells can be restored to normal values (∼7.4) by incubation with the epidermal growth factor receptor (EGFR, HER1, ErbB1) inhibitors AG1478 and PD168393. PD168393 fully restored the pHe values of IB3-1 cells, suggesting that the reduced pHe is mainly due to increased EGFR activity and lactate. Also, in IB3-1 cells, lactate dehydrogenase A mRNA, protein expression, and activity are downregulated when EGFR is inhibited. Thus, a constitutive EGFR activation seems to be responsible for the reduced pHe in IB3-1 cells.
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Affiliation(s)
- María Macarena Massip-Copiz
- Laboratory of Cellular and Molecular Biology, Institute for Biomedical Research, School of Medical Sciences, Pontifical Catholic University of Argentina, and the Pontifical Catholic University of Argentina, Buenos Aires, Argentina.,Laboratory of Cellular and Molecular Biology, Institute for Biomedical Research, School of Medical Sciences, Pontifical Catholic University of Argentina, and the Pontifical Catholic University of Argentina, Buenos Aires, Argentina
| | - Ángel G Valdivieso
- Laboratory of Cellular and Molecular Biology, Institute for Biomedical Research, School of Medical Sciences, Pontifical Catholic University of Argentina, and the Pontifical Catholic University of Argentina, Buenos Aires, Argentina.,Laboratory of Cellular and Molecular Biology, Institute for Biomedical Research, School of Medical Sciences, Pontifical Catholic University of Argentina, and the Pontifical Catholic University of Argentina, Buenos Aires, Argentina
| | - Mariángeles Clauzure
- Laboratory of Cellular and Molecular Biology, Institute for Biomedical Research, School of Medical Sciences, Pontifical Catholic University of Argentina, and the Pontifical Catholic University of Argentina, Buenos Aires, Argentina.,Laboratory of Cellular and Molecular Biology, Institute for Biomedical Research, School of Medical Sciences, Pontifical Catholic University of Argentina, and the Pontifical Catholic University of Argentina, Buenos Aires, Argentina
| | - Consuelo Mori
- Laboratory of Cellular and Molecular Biology, Institute for Biomedical Research, School of Medical Sciences, Pontifical Catholic University of Argentina, and the Pontifical Catholic University of Argentina, Buenos Aires, Argentina.,Laboratory of Cellular and Molecular Biology, Institute for Biomedical Research, School of Medical Sciences, Pontifical Catholic University of Argentina, and the Pontifical Catholic University of Argentina, Buenos Aires, Argentina
| | - Cristian J A Asensio
- Laboratory of Cellular and Molecular Biology, Institute for Biomedical Research, School of Medical Sciences, Pontifical Catholic University of Argentina, and the Pontifical Catholic University of Argentina, Buenos Aires, Argentina.,Laboratory of Cellular and Molecular Biology, Institute for Biomedical Research, School of Medical Sciences, Pontifical Catholic University of Argentina, and the Pontifical Catholic University of Argentina, Buenos Aires, Argentina
| | - María Á Aguilar
- Laboratory of Cellular and Molecular Biology, Institute for Biomedical Research, School of Medical Sciences, Pontifical Catholic University of Argentina, and the Pontifical Catholic University of Argentina, Buenos Aires, Argentina.,Laboratory of Cellular and Molecular Biology, Institute for Biomedical Research, School of Medical Sciences, Pontifical Catholic University of Argentina, and the Pontifical Catholic University of Argentina, Buenos Aires, Argentina
| | - Tomás A Santa-Coloma
- Laboratory of Cellular and Molecular Biology, Institute for Biomedical Research, School of Medical Sciences, Pontifical Catholic University of Argentina, and the Pontifical Catholic University of Argentina, Buenos Aires, Argentina.,Laboratory of Cellular and Molecular Biology, Institute for Biomedical Research, School of Medical Sciences, Pontifical Catholic University of Argentina, and the Pontifical Catholic University of Argentina, Buenos Aires, Argentina
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15
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Sabbah DA, Hajjo R, Sweidan K. Review on Epidermal Growth Factor Receptor (EGFR) Structure, Signaling Pathways, Interactions, and Recent Updates of EGFR Inhibitors. Curr Top Med Chem 2021; 20:815-834. [PMID: 32124699 DOI: 10.2174/1568026620666200303123102] [Citation(s) in RCA: 208] [Impact Index Per Article: 69.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 11/21/2019] [Accepted: 12/10/2019] [Indexed: 12/13/2022]
Abstract
The epidermal growth factor receptor (EGFR) belongs to the ERBB family of tyrosine kinase receptors. EGFR signaling cascade is a key regulator in cell proliferation, differentiation, division, survival, and cancer development. In this review, the EGFR structure and its mutations, signaling pathway, ligand binding and EGFR dimerization, EGF/EGFR interaction, and the progress in the development of EGFR inhibitors have been explored.
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Affiliation(s)
- Dima A Sabbah
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, P.O. Box 130, Amman 11733, Jordan
| | - Rima Hajjo
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, P.O. Box 130, Amman 11733, Jordan
| | - Kamal Sweidan
- Department of Chemistry, The University of Jordan, Amman 11942, Jordan
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16
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Chan WC, Sharifzadeh S, Buhrlage SJ, Marto JA. Chemoproteomic methods for covalent drug discovery. Chem Soc Rev 2021; 50:8361-8381. [PMID: 34143170 DOI: 10.1039/d1cs00231g] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Covalent drugs constitute cornerstones of modern medicine. The past decade has witnessed growing enthusiasm for development of covalent inhibitors, fueled by clinical successes as well as advances in analytical techniques associated with the drug discovery pipeline. Among these, mass spectrometry-based chemoproteomic methods stand out due to their broad applicability from focused analysis of electrophile-containing compounds to surveying proteome-wide inhibitor targets. Here, we review applications of both foundational and cutting-edge chemoproteomic techniques across target identification, hit discovery, and lead characterization/optimization in covalent drug discovery. We focus on the practical aspects necessary for the general drug discovery scientist to design, interpret, and evaluate chemoproteomic experiments. We also present three case studies on clinical stage molecules to further showcase the real world significance and future opportunities of these methodologies.
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Affiliation(s)
- Wai Cheung Chan
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA. and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Shabnam Sharifzadeh
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA. and Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Sara J Buhrlage
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA. and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Jarrod A Marto
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA. and Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA, USA
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17
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Pathak P, Rimac H, Grishina M, Verma A, Potemkin V. Hybrid Quinazoline 1,3,5-Triazines as Epidermal Growth Factor Receptor (EGFR) Inhibitors with Anticancer Activity: Design, Synthesis, and Computational Study. ChemMedChem 2020; 16:822-838. [PMID: 33155373 DOI: 10.1002/cmdc.202000646] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/08/2020] [Indexed: 11/07/2022]
Abstract
We report a series of hybrid quinazoline-1,3,5-triazine derivatives as EGFR inhibitors, which were synthesised and tested by using a variety of in vitro, in silico, and in vivo techniques. The derivatives were found to be active against different cancer cell lines and nontoxic against normal ones, with compounds 7 c, 7 d, 7 e, and 7 j being the most potent ones. The derivatives were also evaluated for angiogenesis inhibition potency in chicken eggs, and molecular docking and dynamics simulation studies were carried out to elucidate the fundamental substituent groups essential for their bioactivity. Additionally, a SAR study of the derivatives was performed for future compound optimisation. These studies suggested that the derivatives have a high affinity towards EGFR with favourable pharmacological properties. The most active compound (7 e) was further evaluated for in vivo anticancer activity against DMBA-induced tumours in female Sprague-Dawley rats as well as its effects on plasma antioxidant status, biotransformation enzymes, and lipid profile. The study suggested that 7 e has lead properties against breast cancer and can serve as a starting compound for further development of anti-EGFR compounds.
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MESH Headings
- 9,10-Dimethyl-1,2-benzanthracene
- Animals
- Antineoplastic Agents/chemical synthesis
- Antineoplastic Agents/chemistry
- Antineoplastic Agents/pharmacology
- Cell Proliferation/drug effects
- Cell Survival/drug effects
- Dose-Response Relationship, Drug
- Drug Design
- Drug Screening Assays, Antitumor
- ErbB Receptors/antagonists & inhibitors
- ErbB Receptors/metabolism
- Female
- Humans
- Mammary Neoplasms, Experimental/chemically induced
- Mammary Neoplasms, Experimental/drug therapy
- Mammary Neoplasms, Experimental/pathology
- Models, Molecular
- Molecular Structure
- Protein Kinase Inhibitors/chemical synthesis
- Protein Kinase Inhibitors/chemistry
- Protein Kinase Inhibitors/pharmacology
- Quinazolines/chemistry
- Quinazolines/pharmacology
- Rats
- Rats, Sprague-Dawley
- Structure-Activity Relationship
- Triazines/chemistry
- Triazines/pharmacology
- Tumor Cells, Cultured
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Affiliation(s)
- Prateek Pathak
- Laboratory of Computational Modelling of Drugs, South Ural State University, Chaikovskogo 20A, Chelyabinsk, 454008, Russia
| | - Hrvoje Rimac
- Laboratory of Computational Modelling of Drugs, South Ural State University, Chaikovskogo 20A, Chelyabinsk, 454008, Russia
- Department of Medicinal Chemistry, University of Zagreb Faculty of Pharmacy and Biochemistry, Ante Kovacica 1, Zagreb, 10000, Croatia
| | - Maria Grishina
- Laboratory of Computational Modelling of Drugs, South Ural State University, Chaikovskogo 20A, Chelyabinsk, 454008, Russia
| | - Amita Verma
- Bioorganic and Medicinal Chemistry Research Laboratory, Department of Pharmaceutical Sciences, Sam Higginbottom University of Agriculture, Technology & Sciences Naini, Prayagraj, Uttar Pradesh, 211007, India
| | - Vladimir Potemkin
- Laboratory of Computational Modelling of Drugs, South Ural State University, Chaikovskogo 20A, Chelyabinsk, 454008, Russia
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18
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Bian Y, Jun JJ, Cuyler J, Xie XQ. Covalent allosteric modulation: An emerging strategy for GPCRs drug discovery. Eur J Med Chem 2020; 206:112690. [PMID: 32818870 PMCID: PMC9948676 DOI: 10.1016/j.ejmech.2020.112690] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/10/2020] [Accepted: 07/24/2020] [Indexed: 12/13/2022]
Abstract
Designing covalent allosteric modulators brings new opportunities to the field of drug discovery towards G-protein-coupled receptors (GPCRs). Targeting an allosteric binding pocket can allow a modulator to have protein subtype selectivity and low drug resistance. Utilizing covalent warheads further enables the modulator to increase the binding potency and extend the duration of action. This review starts with GPCR allosteric modulation to discuss the structural biology of allosteric binding pockets, the different types of allosteric modulators, as well as the advantages of employing allosteric modulation. This is followed by a discussion on covalent modulators to clarify how covalent ligands can benefit the receptor modulation and to illustrate moieties that can commonly be used as covalent warheads. Finally, case studies are presented on designing class A, B, and C GPCR covalent allosteric modulators to demonstrate successful stories on combining allosteric modulation and covalent binding. Limitations and future perspectives are also covered.
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Affiliation(s)
- Yuemin Bian
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy,NIH National Center of Excellence for Computational Drug Abuse Research
| | - Jaden Jungho Jun
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy,NIH National Center of Excellence for Computational Drug Abuse Research
| | - Jacob Cuyler
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy,NIH National Center of Excellence for Computational Drug Abuse Research
| | - Xiang-Qun Xie
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, Pittsburgh, PA, 15261, United States; NIH National Center of Excellence for Computational Drug Abuse Research, Pittsburgh, PA, 15261, United States; Drug Discovery Institute, Pittsburgh, PA, 15261, United States; Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, United States.
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19
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Seetaha S, Boonyarit B, Tongsima S, Songtawee N, Choowongkomon K. Potential tripeptides against the tyrosine kinase domain of human epidermal growth factor receptor (HER) 2 through computational and kinase assay approaches. J Mol Graph Model 2020; 97:107564. [DOI: 10.1016/j.jmgm.2020.107564] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 02/03/2020] [Accepted: 02/03/2020] [Indexed: 01/21/2023]
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20
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Schmitt J, Goodfellow E, Huang S, Williams C, Gomes IN, Rosa MN, Reis RM, Yang R, Titi HM, Jean-Claude BJ. Comparative analysis of the dual EGFR-DNA targeting and growth inhibitory properties of 6-mono-alkylamino- and 6,6-dialkylaminoquinazoline-based type II combi-molecules. Eur J Med Chem 2020; 192:112185. [DOI: 10.1016/j.ejmech.2020.112185] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/12/2020] [Accepted: 02/23/2020] [Indexed: 01/03/2023]
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21
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Khattri RB, Morris DL, Bilinovich SM, Manandhar E, Napper KR, Sweet JW, Modarelli DA, Leeper TC. Identifying Ortholog Selective Fragment Molecules for Bacterial Glutaredoxins by NMR and Affinity Enhancement by Modification with an Acrylamide Warhead. Molecules 2019; 25:E147. [PMID: 31905878 PMCID: PMC6983068 DOI: 10.3390/molecules25010147] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/20/2019] [Accepted: 12/23/2019] [Indexed: 12/30/2022] Open
Abstract
Illustrated here is the development of a new class of antibiotic lead molecules targeted at Pseudomonas aeruginosa glutaredoxin (PaGRX). This lead was produced to (a) circumvent efflux-mediated resistance mechanisms via covalent inhibition while (b) taking advantage of species selectivity to target a fundamental metabolic pathway. This work involved four components: a novel workflow for generating protein specific fragment hits via independent nuclear magnetic resonance (NMR) measurements, NMR-based modeling of the target protein structure, NMR guided docking of hits, and synthetic modification of the fragment hit with a vinyl cysteine trap moiety, i.e., acrylamide warhead, to generate the chimeric lead. Reactivity of the top warhead-fragment lead suggests that the ortholog selectivity observed for a fragment hit can translate into a substantial kinetic advantage in the mature warhead lead, which bodes well for future work to identify potent, species specific drug molecules targeted against proteins heretofore deemed undruggable.
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Affiliation(s)
- Ram B. Khattri
- Department of Physiology and Functional genomics, University of Florida, Gainesville, FL 32610, USA;
| | - Daniel L. Morris
- Department of Chemistry and Biochemistry, The University of Akron, Akron, OH 44325, USA; (D.L.M.); (K.R.N.); (J.W.S.); (D.A.M.)
| | - Stephanie M. Bilinovich
- Department of Pediatrics and Human Development, Michigan State University, East Lansing, MI 48824, USA;
| | | | - Kahlilah R. Napper
- Department of Chemistry and Biochemistry, The University of Akron, Akron, OH 44325, USA; (D.L.M.); (K.R.N.); (J.W.S.); (D.A.M.)
| | - Jacob W. Sweet
- Department of Chemistry and Biochemistry, The University of Akron, Akron, OH 44325, USA; (D.L.M.); (K.R.N.); (J.W.S.); (D.A.M.)
| | - David A. Modarelli
- Department of Chemistry and Biochemistry, The University of Akron, Akron, OH 44325, USA; (D.L.M.); (K.R.N.); (J.W.S.); (D.A.M.)
| | - Thomas C. Leeper
- Department of Chemistry and Biochemistry, Kennesaw State University, GA 30144, USA
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22
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Aran V, Omerovic J. Current Approaches in NSCLC Targeting K-RAS and EGFR. Int J Mol Sci 2019; 20:E5701. [PMID: 31739412 PMCID: PMC6888213 DOI: 10.3390/ijms20225701] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 11/12/2019] [Accepted: 11/12/2019] [Indexed: 12/24/2022] Open
Abstract
The research and treatment of non-small cell lung cancer (NSCLC) have achieved some important advances in recent years. Nonetheless, the overall survival rates for NSCLC remain low, indicating the importance to effectively develop new therapies and improve current approaches. The understanding of the function of different biomarkers involved in NSCLC progression, survival and response to therapy are important for the development of early detection tools and treatment options. Epidermal growth factor receptor (EGFR) and Kirsten rat sarcoma viral oncogene homolog (K-RAS) are two of the main significant biomarkers for the management of NSCLC. Mutations in these genes were associated with development and response to therapies. For example, the use of small molecule tyrosine kinase (TK) inhibitors and immunotherapy has led to benefits in some, but not all patients with altered EGFR. In contrast, there is still no effective approved drug to act upon patients harbouring K-RAS mutations. In addition, K-RAS mutations have been associated with lack of activity of TK inhibitors. However, promising approaches aimed to inhibit mutant K-RAS are currently under study. Therefore, this review will discuss these approaches and also EGFR therapies, and hopefully, it will draw attention to the need of continued research in the field in order to improve the outcomes in NSCLC patients.
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Affiliation(s)
- Veronica Aran
- Research Division, National Institute of Traumatology and Orthopedics, Av. Brasil 500, 20940-070 Rio de Janeiro, Brazil
| | - Jasminka Omerovic
- School of Medicine, University of Split, Šoltanska 2, 21000 Split, Croatia;
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23
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Nishiya N, Murai M, Hosoda A, Yonezawa H, Omori N. Bucillamine Prevents Afatinib-Mediated Inhibition of Epidermal Growth Factor Receptor Signaling. Pharmaceuticals (Basel) 2019; 12:ph12040165. [PMID: 31703435 PMCID: PMC6958386 DOI: 10.3390/ph12040165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/29/2019] [Accepted: 11/05/2019] [Indexed: 11/16/2022] Open
Abstract
Molecular targeting therapies often cause characteristic adverse effects, such as skin rash during anti-epidermal growth factor receptor (EGFR) therapies, making treatment continuation difficult. In contrast, skin symptoms induced by EGFR inhibition are strongly correlated with the overall survival of the therapies. Therefore, controlling adverse effects not only facilitates treatment continuation but also increases clinical benefits. In this study, we proposed a novel strategy for reducing EGFR–tyrosine kinase inhibitor (TKI)-induced adverse effects in nontumorous organs by repositioning approved medicines using a zebrafish model. We developed a model system for evaluating chemical quenchers of afatinib, a clinically available irreversible EGFR-TKI, by scoring the inhibition of afatinib-induced hyperformation of lateral line neuromasts in zebrafish larvae. Bucillamine, an antirheumatic drug, was identified as an afatinib quencher in the zebrafish system and inhibited TKI activity in vitro. In addition, bucillamine restored EGFR autophosphorylation and downstream signaling in afatinib-treated A431 cells. Thus, topical bucillamine is a potential reliever of irreversible EGFR-TKI-induced skin rash. The zebrafish model can be applied to a screening for quenchers of other anti-EGFR-targeting therapies, including reversible TKIs and biologics.
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Affiliation(s)
- Naoyuki Nishiya
- Division of Integrated Information for Pharmaceutical Sciences, Department of Clinical Pharmacy, Iwate Medical University School of Pharmacy, 1-1-1 Idaidori, Yahaba-cho, Shiwa-gun, Iwate 028-3694, Japan; (M.M.); (A.H.); (H.Y.); (N.O.)
- Correspondence:
| | - Moeka Murai
- Division of Integrated Information for Pharmaceutical Sciences, Department of Clinical Pharmacy, Iwate Medical University School of Pharmacy, 1-1-1 Idaidori, Yahaba-cho, Shiwa-gun, Iwate 028-3694, Japan; (M.M.); (A.H.); (H.Y.); (N.O.)
| | - Ayumi Hosoda
- Division of Integrated Information for Pharmaceutical Sciences, Department of Clinical Pharmacy, Iwate Medical University School of Pharmacy, 1-1-1 Idaidori, Yahaba-cho, Shiwa-gun, Iwate 028-3694, Japan; (M.M.); (A.H.); (H.Y.); (N.O.)
| | - Honami Yonezawa
- Division of Integrated Information for Pharmaceutical Sciences, Department of Clinical Pharmacy, Iwate Medical University School of Pharmacy, 1-1-1 Idaidori, Yahaba-cho, Shiwa-gun, Iwate 028-3694, Japan; (M.M.); (A.H.); (H.Y.); (N.O.)
| | - Norikazu Omori
- Division of Integrated Information for Pharmaceutical Sciences, Department of Clinical Pharmacy, Iwate Medical University School of Pharmacy, 1-1-1 Idaidori, Yahaba-cho, Shiwa-gun, Iwate 028-3694, Japan; (M.M.); (A.H.); (H.Y.); (N.O.)
- Department of Pharmacy, Iwate Medical University Hospital, 2-1-1 Idaidori, Yahaba-cho, Shiwa-gun, Iwate 028-3695, Japan
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24
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Shipman WD, Chyou S, Ramanathan A, Izmirly PM, Sharma S, Pannellini T, Dasoveanu DC, Qing X, Magro CM, Granstein RD, Lowes MA, Pamer EG, Kaplan DH, Salmon JE, Mehrara BJ, Young JW, Clancy RM, Blobel CP, Lu TT. A protective Langerhans cell-keratinocyte axis that is dysfunctional in photosensitivity. Sci Transl Med 2019; 10:10/454/eaap9527. [PMID: 30111646 DOI: 10.1126/scitranslmed.aap9527] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 07/13/2018] [Indexed: 12/14/2022]
Abstract
Photosensitivity, or skin sensitivity to ultraviolet radiation (UVR), is a feature of lupus erythematosus and other autoimmune and dermatologic conditions, but the mechanistic underpinnings are poorly understood. We identify a Langerhans cell (LC)-keratinocyte axis that limits UVR-induced keratinocyte apoptosis and skin injury via keratinocyte epidermal growth factor receptor (EGFR) stimulation. We show that the absence of LCs in Langerin-diphtheria toxin subunit A (DTA) mice leads to photosensitivity and that, in vitro, mouse and human LCs can directly protect keratinocytes from UVR-induced apoptosis. LCs express EGFR ligands and a disintegrin and metalloprotease 17 (ADAM17), the metalloprotease that activates EGFR ligands. Deletion of ADAM17 from LCs leads to photosensitivity, and UVR induces LC ADAM17 activation and generation of soluble active EGFR ligands, suggesting that LCs protect by providing activated EGFR ligands to keratinocytes. Photosensitive systemic lupus erythematosus (SLE) models and human SLE skin show reduced epidermal EGFR phosphorylation and LC defects, and a topical EGFR ligand reduces photosensitivity. Together, our data establish a direct tissue-protective function for LCs, reveal a mechanistic basis for photosensitivity, and suggest EGFR stimulation as a treatment for photosensitivity in lupus erythematosus and potentially other autoimmune and dermatologic conditions.
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Affiliation(s)
- William D Shipman
- Weill Cornell/Rockefeller/Sloan-Kettering Tri-Institutional MD-PhD Program, New York, NY 10065, USA.,Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA.,Autoimmunity and Inflammation Program, Hospital for Special Surgery, New York, NY 10021, USA
| | - Susan Chyou
- Autoimmunity and Inflammation Program, Hospital for Special Surgery, New York, NY 10021, USA
| | - Anusha Ramanathan
- Autoimmunity and Inflammation Program, Hospital for Special Surgery, New York, NY 10021, USA
| | - Peter M Izmirly
- Department of Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Sneh Sharma
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Tania Pannellini
- Autoimmunity and Inflammation Program, Hospital for Special Surgery, New York, NY 10021, USA
| | - Dragos C Dasoveanu
- Autoimmunity and Inflammation Program, Hospital for Special Surgery, New York, NY 10021, USA.,Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Xiaoping Qing
- Autoimmunity and Inflammation Program, Hospital for Special Surgery, New York, NY 10021, USA
| | - Cynthia M Magro
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | | | | | - Eric G Pamer
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Daniel H Kaplan
- Department of Dermatology, University of Pittsburgh, PA 15260, USA.,Department of Immunology, University of Pittsburgh, PA 15260, USA
| | - Jane E Salmon
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA.,Autoimmunity and Inflammation Program, Hospital for Special Surgery, New York, NY 10021, USA.,Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA.,Division of Rheumatology and Pediatric Rheumatology, Hospital for Special Surgery, New York, NY 10021, USA
| | - Babak J Mehrara
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - James W Young
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Rockefeller University, New York, NY 10065, USA.,Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA.,Adult Bone Marrow Transplantation Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Robert M Clancy
- Department of Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Carl P Blobel
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY 10065, USA.,Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA.,Arthritis and Tissue Degeneration Program, Hospital for Special Surgery, New York, NY 10021, USA.,Institute for Advanced Studies, Technical University Munich, Munich, Germany
| | - Theresa T Lu
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA. .,Autoimmunity and Inflammation Program, Hospital for Special Surgery, New York, NY 10021, USA.,Division of Rheumatology and Pediatric Rheumatology, Hospital for Special Surgery, New York, NY 10021, USA.,Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
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25
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Groppe JC. Induced degradation of protein kinases by bifunctional small molecules: a next-generation strategy. Expert Opin Drug Discov 2019; 14:1237-1253. [DOI: 10.1080/17460441.2019.1660641] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jay C. Groppe
- Department of Biomedical Sciences, Texas A&M University College of Dentistry, Dallas, TX, USA
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26
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Niggenaber J, Hardick J, Lategahn J, Rauh D. Structure Defines Function: Clinically Relevant Mutations in ErbB Kinases. J Med Chem 2019; 63:40-51. [DOI: 10.1021/acs.jmedchem.9b00964] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Janina Niggenaber
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227 Dortmund, (Germany)
- Drug Discovery Hub Dortmund (DDHD) am Zentrum für Integrierte Wirkstoffforschung (ZIW), TU Dortmund University, 44227 Dortmund (Germany)
| | - Julia Hardick
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227 Dortmund, (Germany)
- Drug Discovery Hub Dortmund (DDHD) am Zentrum für Integrierte Wirkstoffforschung (ZIW), TU Dortmund University, 44227 Dortmund (Germany)
| | - Jonas Lategahn
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227 Dortmund, (Germany)
- Drug Discovery Hub Dortmund (DDHD) am Zentrum für Integrierte Wirkstoffforschung (ZIW), TU Dortmund University, 44227 Dortmund (Germany)
| | - Daniel Rauh
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227 Dortmund, (Germany)
- Drug Discovery Hub Dortmund (DDHD) am Zentrum für Integrierte Wirkstoffforschung (ZIW), TU Dortmund University, 44227 Dortmund (Germany)
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27
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Ghosh AK, Samanta I, Mondal A, Liu WR. Covalent Inhibition in Drug Discovery. ChemMedChem 2019; 14:889-906. [PMID: 30816012 DOI: 10.1002/cmdc.201900107] [Citation(s) in RCA: 148] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Indexed: 12/11/2022]
Abstract
Although covalent inhibitors have been used as therapeutics for more than a century, there has been general resistance in the pharmaceutical industry against their further development due to safety concerns. This inclination has recently been reverted after the development of a wide variety of covalent inhibitors to address human health conditions along with the US Food and Drug Administration (FDA) approval of several covalent therapeutics for use in humans. Along with this exciting resurrection of an old drug discovery concept, this review surveys enzymes that can be targeted by covalent inhibitors for the treatment of human diseases. We focus on protein kinases, RAS proteins, and a few other enzymes that have been studied extensively as targets for covalent inhibition, with the aim to address challenges in designing effective covalent drugs and to provide suggestions in the area that have yet to be explored.
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Affiliation(s)
- Avick Kumar Ghosh
- Department of Chemistry, Texas A&M University, Corner of Ross and Spence Streets, College Station, TX, 77843, USA
| | - Indranil Samanta
- Department of Chemistry, Texas A&M University, Corner of Ross and Spence Streets, College Station, TX, 77843, USA
| | - Anushree Mondal
- Department of Chemistry, Texas A&M University, Corner of Ross and Spence Streets, College Station, TX, 77843, USA
| | - Wenshe Ray Liu
- Department of Chemistry, Texas A&M University, Corner of Ross and Spence Streets, College Station, TX, 77843, USA
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A novel scaffold for EGFR inhibition: Introducing N-(3-(3-phenylureido)quinoxalin-6-yl) acrylamide derivatives. Sci Rep 2019; 9:14. [PMID: 30626888 PMCID: PMC6327040 DOI: 10.1038/s41598-018-36846-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 11/29/2018] [Indexed: 11/08/2022] Open
Abstract
Clinical data acquired over the last decade on non-small cell lung cancer (NSCLC) treatment with small molecular weight Epidermal Growth Factor Receptor (EGFR) inhibitors have shown significant influence of EGFR point mutations and in-frame deletions on clinical efficacy. Identification of small molecules capable of inhibiting the clinically relevant EGFR mutant forms is desirable, and novel chemical scaffolds might provide knowledge regarding selectivity among EGFR forms and shed light on new strategies to overcome current clinical limitations. Design, synthesis, docking studies and in vitro evaluation of N-(3-(3-phenylureido)quinoxalin-6-yl) acrylamide derivatives (7a-m) against EGFR mutant forms are described. Compounds 7h and 7l were biochemically active in the nanomolar range against EGFRwt and EGFRL858R. Molecular docking and reaction enthalpy calculations have shown the influence of the combination of reversible and covalent binding modes with EGFR on the inhibitory activity. The inhibitory profile of 7h against a panel of patient-derived tumor cell lines was established, demonstrating selective growth inhibition of EGFR related cells at 10 μM among a panel of 30 cell lines derived from colon, melanoma, breast, bladder, kidney, prostate, pancreas and ovary tumors.
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Castelli R, Bozza N, Cavazzoni A, Bonelli M, Vacondio F, Ferlenghi F, Callegari D, Silva C, Rivara S, Lodola A, Digiacomo G, Fumarola C, Alfieri R, Petronini PG, Mor M. Balancing reactivity and antitumor activity: heteroarylthioacetamide derivatives as potent and time-dependent inhibitors of EGFR. Eur J Med Chem 2019; 162:507-524. [DOI: 10.1016/j.ejmech.2018.11.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 11/08/2018] [Accepted: 11/09/2018] [Indexed: 01/04/2023]
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Maneiro M, Lence E, Sanz-Gaitero M, Otero JM, van Raaij MJ, Thompson P, Hawkins AR, González-Bello C. Hydroxylammonium derivatives for selective active-site lysine modification in the anti-virulence bacterial target DHQ1 enzyme. Org Chem Front 2019. [DOI: 10.1039/c9qo00453j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The first example of a hydroxylammonium derivative that causes a specific covalent modification of the active-site lysine residue of an aldolase enzyme, which is a promising target for anti-bacterial drug discovery, is reported.
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Affiliation(s)
- María Maneiro
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS)
- Departamento de Química Orgánica
- Universidade de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - Emilio Lence
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS)
- Departamento de Química Orgánica
- Universidade de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - Marta Sanz-Gaitero
- Departamento de Estructura de Macromoléculas
- Centro Nacional de Biotecnología (CSIC)
- 28049 Madrid
- Spain
| | - José M. Otero
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS)
- Departamento de Química Orgánica
- Universidade de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - Mark J. van Raaij
- Departamento de Estructura de Macromoléculas
- Centro Nacional de Biotecnología (CSIC)
- 28049 Madrid
- Spain
| | - Paul Thompson
- Institute of Cell and Molecular Biosciences
- Medical School
- University of Newcastle upon Tyne
- Newcastle upon Tyne NE2 4HH
- UK
| | - Alastair R. Hawkins
- Institute of Cell and Molecular Biosciences
- Medical School
- University of Newcastle upon Tyne
- Newcastle upon Tyne NE2 4HH
- UK
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS)
- Departamento de Química Orgánica
- Universidade de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
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Castro-Falcón G, Seiler GS, Demir Ö, Rathinaswamy MK, Hamelin D, Hoffmann RM, Makowski SL, Letzel AC, Field SJ, Burke JE, Amaro RE, Hughes CC. Neolymphostin A Is a Covalent Phosphoinositide 3-Kinase (PI3K)/Mammalian Target of Rapamycin (mTOR) Dual Inhibitor That Employs an Unusual Electrophilic Vinylogous Ester. J Med Chem 2018; 61:10463-10472. [PMID: 30380865 PMCID: PMC6688905 DOI: 10.1021/acs.jmedchem.8b00975] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Using a novel chemistry-based assay for identifying electrophilic natural products in unprocessed extracts, we identified the PI3-kinase/mTOR dual inhibitor neolymphostin A from Salinispora arenicola CNY-486. The method further showed that the vinylogous ester substituent on the neolymphostin core was the exact site for enzyme conjugation. Tandem MS/MS experiments on PI3Kα treated with the inhibitor revealed that neolymphostin covalently modified Lys802 with a shift in mass of +306 amu, corresponding to addition of the inhibitor and elimination of methanol. The binding pose of the inhibitor bound to PI3Kα was modeled, and hydrogen-deuterium exchange mass spectrometry experiments supported this model. Against a panel of kinases, neolymphostin showed good selectivity for PI3-kinase and mTOR. In addition, the natural product blocked AKT phosphorylation in live cells with an IC50 of ∼3 nM. Taken together, neolymphostin is the first reported example of a covalent kinase inhibitor from the bacterial domain of life.
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Affiliation(s)
- Gabriel Castro-Falcón
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, USA, 92093
- These authors contributed equally to this work
| | - Grant S. Seiler
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, USA, 92093
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA, 92093
- These authors contributed equally to this work
| | - Özlem Demir
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA, 92093
| | - Manoj K. Rathinaswamy
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada, V8W 2Y2
| | - David Hamelin
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada, V8W 2Y2
| | - Reece M. Hoffmann
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada, V8W 2Y2
| | - Stefanie L. Makowski
- School of Medicine, University of California, San Diego, La Jolla, California, USA, 92093
| | - Anne-Catrin Letzel
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, USA, 92093
| | - Seth J. Field
- School of Medicine, University of California, San Diego, La Jolla, California, USA, 92093
| | - John E. Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada, V8W 2Y2
| | - Rommie E. Amaro
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA, 92093
| | - Chambers C. Hughes
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, USA, 92093
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The Effect of Canertinib on Sensitivity of Cytotoxic Drugs in Tamoxifen-Resistant Breast Cancer Cells In Vitro. Int J Genomics 2018; 2018:7628734. [PMID: 30425998 PMCID: PMC6218737 DOI: 10.1155/2018/7628734] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 07/18/2018] [Accepted: 07/31/2018] [Indexed: 01/05/2023] Open
Abstract
Aims and Objectives To investigate and examine the reversal effects of canertinib on the activity of EGFR and tamoxifen resistance in drug-resistant human breast carcinoma cells (MCF-7/TamR). Materials and Methods The antiproliferative activity of canertinib alone or in combination with a conventional EGFR-targeting chemotherapies cytotoxic drugs differing in the mechanism(s) of action, such as paclitaxel, carboplatin, etoposide, vinorelbine, and daunorubicin as well as resistance mechanisms of EGFR targeting, have been investigated. Results With an elevated dosage of canertinib, a significant decrease in proliferation and increase in apoptosis was observed. The treatment with higher doses of canertinib resulted in a 2-3-fold increase in apoptosis. In the combined treatment, it had been noticed a significant developed apoptotic cell death rather induced by single agent treatment. A significant downregulation of the antiapoptotic protein bcl-2 was exposed by immunocytochemistry investigation. Sensitivity to paclitaxel was also measured and was found to inversely correlate to bcl-2 status. Conclusion Proliferation inhibition and apoptosis in MCF-7/TAM-R cells increase with increasing dosage of canertinib. This suggests that canertinib can reverse tamoxifen resistance in breast cancer cells. The antitumor effect of this EGFR-irreversible tyrosine kinase inhibitor provides a rationale for its clinical evaluation in combination with other cytotoxic drugs.
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Discovery of 4,5-Dihydro-1 H-thieno[2',3':2,3]thiepino [4,5-c]pyrazole-3-carboxamide Derivatives as the Potential Epidermal Growth Factor Receptors for Tyrosine Kinase Inhibitors. Molecules 2018; 23:molecules23081980. [PMID: 30096806 PMCID: PMC6222878 DOI: 10.3390/molecules23081980] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 06/25/2018] [Accepted: 07/17/2018] [Indexed: 12/15/2022] Open
Abstract
The epidermal growth factor receptors (EGFRs), in which overexpression (known as upregulation) or overactivity have been associated with a number of cancers, has become an attractive molecular target for the treatment of selective cancers. We report here the design and synthesis of a novel series of 4,5-dihydro-1H-thieno [2′,3′:2,3]thiepino[4,5-c]pyrazole-3-carboxamide derivatives and the screening for their inhibitory activity on the EGFR high-expressing human A549 cell line using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT). A Docking simulation was performed to fit compound 6g and gifitinib into the EGFR to determine the probable binding models, and the binding sites and modes conformation of 6g and gifitinib were exactly similar, the two compounds were stabilized by hydrogen bond interactions with MET769. Combining with the biological activity evaluation, compound 6g demonstrated the most potent inhibitory activity (IC50 = 9.68 ± 1.95 μmol·L–1 for A549). Conclusively, 4,5-dihydro-1H-thieno[2′,3′:2,3]thiepino[4,5-c]pyrazole-3-carboxamide derivatives as the EGFR tyrosine kinase inhibitors were discovered, and could be used as potential lead compounds against cancer cells.
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Niazi S, Purohit M, Sonawani A, Niazi JH. Revealing the molecular interactions of aptamers that specifically bind to the extracellular domain of HER2 cancer biomarker protein: An in silico assessment. J Mol Graph Model 2018; 83:112-121. [DOI: 10.1016/j.jmgm.2018.06.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 06/03/2018] [Accepted: 06/04/2018] [Indexed: 12/16/2022]
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35
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Wang C, Xu P, Zhang L, Huang J, Zhu K, Luo C. Current Strategies and Applications for Precision Drug Design. Front Pharmacol 2018; 9:787. [PMID: 30072901 PMCID: PMC6060444 DOI: 10.3389/fphar.2018.00787] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Accepted: 06/28/2018] [Indexed: 12/23/2022] Open
Abstract
Since Human Genome Project (HGP) revealed the heterogeneity of individuals, precision medicine that proposes the customized healthcare has become an intractable and hot research. Meanwhile, as the Precision Medicine Initiative launched, precision drug design which aims at maximizing therapeutic effects while minimizing undesired side effects for an individual patient has entered a new stage. One of the key strategies of precision drug design is target based drug design. Once a key pathogenic target is identified, rational drug design which constitutes the major part of precision drug design can be performed. Examples of rational drug design on novel druggable targets and protein-protein interaction surfaces are summarized in this review. Besides, various kinds of computational modeling and simulation approaches increasingly benefit for the drug discovery progress. Molecular dynamic simulation, drug target prediction and in silico clinical trials are discussed. Moreover, due to the powerful ability in handling high-dimensional data and complex system, deep learning has efficiently promoted the applications of artificial intelligence in drug discovery and design. In this review, deep learning methods that tailor to precision drug design are carefully discussed. When a drug molecule is discovered, the development of specific targeted drug delivery system becomes another key aspect of precision drug design. Therefore, state-of-the-art techniques of drug delivery system including antibody-drug conjugates (ADCs), and ligand-targeted conjugates are also included in this review.
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Affiliation(s)
- Chen Wang
- School of Biological Science and Technology, University of Jinan, Jinan, China
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Pan Xu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Luyu Zhang
- School of Pharmacy, Fudan University, Shanghai, China
| | - Jing Huang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Kongkai Zhu
- School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Cheng Luo
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
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36
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MS methods to study macromolecule-ligand interaction: Applications in drug discovery. Methods 2018; 144:152-174. [PMID: 29890284 DOI: 10.1016/j.ymeth.2018.06.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 06/01/2018] [Accepted: 06/03/2018] [Indexed: 12/12/2022] Open
Abstract
The interaction of small compounds (i.e. ligands) with macromolecules or macromolecule assemblies (i.e. targets) is the mechanism of action of most of the drugs available today. Mass spectrometry is a popular technique for the interrogation of macromolecule-ligand interactions and therefore is also widely used in drug discovery and development. Thanks to its versatility, mass spectrometry is used for multiple purposes such as biomarker screening, identification of the mechanism of action, ligand structure optimization or toxicity assessment. The evolution and automation of the instruments now allows the development of high throughput methods with high sensitivity and a minimized false discovery rate. Herein, all these approaches are described with a focus on the methods for studying macromolecule-ligand interaction aimed at defining the structure-activity relationships of drug candidates, along with their mechanism of action, metabolism and toxicity.
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Abstract
Covalent inhibition is a rapidly growing discipline within drug discovery. Many historical covalent inhibitors were discovered by serendipity, with such a mechanism of action often regarded as undesirable due to potential toxicity issues. Recent progress has seen a major shift in this outlook, as covalent inhibition shows promise for targets where previous efforts to identify non-covalent small molecule inhibitors have failed. Targeted covalent inhibitors (TCIs) can offer drug discovery scientists the ability to increase the potency and/or selectivity of small molecule inhibitors, by attachment of reactive functional groups designed to covalently bind to specific sites in a target. In this tutorial review we introduce the broader concept of covalent inhibition, discuss the potential benefits and challenges of such an approach, and provide an overview of the current status of the field. We also describe some strategies and computational tools to enable successful covalent drug discovery.
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Affiliation(s)
- Richard Lonsdale
- Chemistry, Oncology, IMED Biotech Unit, AstraZeneca, Cambridge, CB4 0WG, UK.
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Zheng D, Hu M, Bai Y, Zhu X, Lu X, Wu C, Wang J, Liu L, Wang Z, Ni J, Yang Z, Xu J. EGFR G796D mutation mediates resistance to osimertinib. Oncotarget 2018; 8:49671-49679. [PMID: 28572531 PMCID: PMC5564797 DOI: 10.18632/oncotarget.17913] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 05/04/2017] [Indexed: 12/29/2022] Open
Abstract
Osimertinib is an effective third-generation epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI) approved in multiple countries and regions for patients with EGFR T790M mutation-positive non-small cell lung cancer (NSCLC). Despite impressive initial tumor responses, development of drug resistance ultimately limits the benefit of this compound. Mechanisms of resistance to osimertinib are just beginning to emerge, such as EGFR C797S and L718Q mutations, BRAF V600E and PIK3CA E545K mutations, as well as ERBB2 and MET amplification. However, a comprehensive view is still missing. In this study, we presented the first case of Chinese NSCLC patient who developed resistance to osimertinib, and discovered de novo EGFR G796D mutation as a potential mechanism. Our findings provided insights into mechanisms of resistance to osimertinib and highlighted tumor heterogeneity and clonal evolution during the development of drug resistance.
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Affiliation(s)
- Di Zheng
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School, Shanghai, China
| | - Min Hu
- IMED Asia, AstraZeneca, Shanghai, China
| | - Yu Bai
- IMED Asia, AstraZeneca, Shanghai, China
| | | | - Xuesong Lu
- Research and Development Information, AstraZeneca, Shanghai, China
| | - Chunyan Wu
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University Medical School, Shanghai, China
| | - Jiying Wang
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School, Shanghai, China
| | - Li Liu
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School, Shanghai, China
| | - Zheng Wang
- Research and Development Information, AstraZeneca, Shanghai, China
| | - Jian Ni
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School, Shanghai, China
| | | | - Jianfang Xu
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School, Shanghai, China
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39
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Yin DM, Hammler D, Peter MF, Marx A, Schmitz A, Hagelueken G. Inhibitor-Directed Spin Labelling-A High Precision and Minimally Invasive Technique to Study the Conformation of Proteins in Solution. Chemistry 2018; 24:6665-6671. [DOI: 10.1002/chem.201706047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Indexed: 01/29/2023]
Affiliation(s)
- Dongsheng M. Yin
- Max Planck Fellow Chemical Biology; Center of Advanced European Studies and Research (caesar); Ludwig-Erhard-Allee 2 53175 Bonn Germany
- LIMES Chemical Biology Unit; Rheinische Friedrich-Wilhelms-Universität Bonn; Gerhard-Domagk-Strasse 1 53121 Bonn Germany
| | - Daniel Hammler
- Department of Chemistry; University of Konstanz; Universitaetsstraße 10 78457 Konstanz Germany
| | - Martin F. Peter
- Institute of Physical and Theoretical Chemistry; Rheinische Friedrich-Wilhelms-Universität Bonn; Wegelerstrasse 12 53115 Bonn Germany
| | - Andreas Marx
- Department of Chemistry; University of Konstanz; Universitaetsstraße 10 78457 Konstanz Germany
| | - Anton Schmitz
- Max Planck Fellow Chemical Biology; Center of Advanced European Studies and Research (caesar); Ludwig-Erhard-Allee 2 53175 Bonn Germany
- LIMES Chemical Biology Unit; Rheinische Friedrich-Wilhelms-Universität Bonn; Gerhard-Domagk-Strasse 1 53121 Bonn Germany
| | - Gregor Hagelueken
- Institute of Physical and Theoretical Chemistry; Rheinische Friedrich-Wilhelms-Universität Bonn; Wegelerstrasse 12 53115 Bonn Germany
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40
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Chaikuad A, Koch P, Laufer SA, Knapp S. The Cysteinome of Protein Kinases as a Target in Drug Development. Angew Chem Int Ed Engl 2018; 57:4372-4385. [DOI: 10.1002/anie.201707875] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 09/20/2017] [Indexed: 01/04/2023]
Affiliation(s)
- Apirat Chaikuad
- Nuffield Department of Clinical Medicine; Structural Genomics Consortium and Target Discovery Institute; University of Oxford, Old Road Campus Research Building; Roosevelt Drive Oxford OX3 7DQ UK
- Institute for Pharmaceutical Chemistry; Goethe-University; Max-von-Laue-Strasse 9 60438 Frankfurt am Main Germany
| | - Pierre Koch
- Department of Pharmaceutical/Medicinal Chemistry; Eberhard-Karls-University Tübingen; Auf der Morgenstelle 8 72076 Tübingen Germany
| | - Stefan A. Laufer
- Department of Pharmaceutical/Medicinal Chemistry; Eberhard-Karls-University Tübingen; Auf der Morgenstelle 8 72076 Tübingen Germany
- German Cancer Consortium DKTK, Standort Tübingen; Germany
| | - Stefan Knapp
- Nuffield Department of Clinical Medicine; Structural Genomics Consortium and Target Discovery Institute; University of Oxford, Old Road Campus Research Building; Roosevelt Drive Oxford OX3 7DQ UK
- German Cancer Consortium DKTK, Standort Frankfurt/Mainz; Germany
- Institute for Pharmaceutical Chemistry; Goethe-University; Max-von-Laue-Strasse 9 60438 Frankfurt am Main Germany
- Structural Genomics Consortium and Buchmann Institute for Molecular Life Sciences; Johann Wolfgang Goethe-University; Max-von-Laue-Strasse 15 60438 Frankfurt am Main Germany
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41
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Chaikuad A, Koch P, Laufer SA, Knapp S. Das Cysteinom der Proteinkinasen als Zielstruktur in der Arzneistoffentwicklung. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201707875] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Apirat Chaikuad
- Nuffield Department of Clinical Medicine; Structural Genomics Consortium and Target Discovery Institute; Universität Oxford, Old Road Campus Research Building; Roosevelt Drive Oxford OX3 7DQ Großbritannien
- Institut für pharmazeutische Chemie; Johann Wolfgang Goethe-Universität; Max-von-Laue-Straße 9 60438 Frankfurt am Main Deutschland
| | - Pierre Koch
- Institut für pharmazeutische und medizinische Chemie; Eberhard-Karls-Universität Tübingen; Auf der Morgenstelle 8 72076 Tübingen Deutschland
| | - Stefan A. Laufer
- Institut für pharmazeutische und medizinische Chemie; Eberhard-Karls-Universität Tübingen; Auf der Morgenstelle 8 72076 Tübingen Deutschland
- Deutsches Zentrum für translationale Krebsforschung, Standort; Tübingen Deutschland
| | - Stefan Knapp
- Nuffield Department of Clinical Medicine; Structural Genomics Consortium and Target Discovery Institute; Universität Oxford, Old Road Campus Research Building; Roosevelt Drive Oxford OX3 7DQ Großbritannien
- Deutsches Zentrum für translationale Krebsforschung, Standort Frankfurt/Mainz; Deutschland
- Institut für pharmazeutische Chemie; Johann Wolfgang Goethe-Universität; Max-von-Laue-Straße 9 60438 Frankfurt am Main Deutschland
- Structural Genomics Consortium and Buchmann Institute for Molecular Life Sciences; Johann Wolfgang Goethe-Universität; Max-von-Laue-Straße 15 60438 Frankfurt am Main Deutschland
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42
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Ainsley J, Lodola A, Mulholland AJ, Christov CZ, Karabencheva-Christova TG. Combined Quantum Mechanics and Molecular Mechanics Studies of Enzymatic Reaction Mechanisms. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2018; 113:1-32. [PMID: 30149903 DOI: 10.1016/bs.apcsb.2018.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The combined quantum mechanics/molecular mechanics (QM/MM) methods have become a valuable tool in computational biochemistry and received versatile applications for studying the reaction mechanisms of enzymes. The approach combines the calculations of the electronic structure of the active site by QM, with modeling of the protein environment using MM force field, which allows the long-range electrostatics and steric effects on the enzyme reactivity to be accounted for. In this review, we review some key theoretical and computational aspects of the method and we also present some applications to particular enzymatic reactions such as tryptophan-7-halogenase, cyclooxygenase-1, and the epidermal growth factor receptor.
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Affiliation(s)
- Jon Ainsley
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | | | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, United Kingdom
| | - Christo Z Christov
- Department of Chemistry, Michigan Technological University, Houghton, MI, United States.
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43
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Chang CH, Liu WT, Hung HC, Gean CY, Tsai HM, Su CL, Gean PW. Synergistic inhibition of tumor growth by combination treatment with drugs against different subpopulations of glioblastoma cells. BMC Cancer 2017; 17:905. [PMID: 29284440 PMCID: PMC5747127 DOI: 10.1186/s12885-017-3924-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 12/14/2017] [Indexed: 12/28/2022] Open
Abstract
Background Glioma stem cells (GSCs) contribute to tumor recurrence and drug resistance. This study characterizes the tumorigenesis of CD133+ cells and their sensitivity to pharmacological inhibition. Methods GSCs from human U87 and rat C6 glioblastoma cell lines were isolated via magnetic cell sorting using CD133 as a cancer stem cell marker. Cell proliferation was determined using the WST-1 assay. An intracranial mouse model and bioluminescence imaging were used to assess the effects of drugs on tumor growth in vivo. Results CD133+ cells expressed stem cell markers and exhibited self-renewal and enhanced tumor formation. Minocycline (Mino) was more effective in reducing the survival rate of CD133+ cells, whereas CD133− cells were more sensitive to inhibition by the signal transducer and activator of transcription 3 (STAT3) inhibitor. Inhibition of STAT3 decreased the expression of CD133+ stem cell markers. The combination of Mino and STAT3 inhibitor synergistically reduced the cell viability of glioma cells. Furthermore, this combination synergistically suppressed tumor growth in nude mice. Conclusion The results suggest that concurrent targeting of different subpopulations of glioblastoma cells may be an effective therapeutic strategy for patients with malignant glioma.
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Affiliation(s)
- Chia-Hsin Chang
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Wei-Ting Liu
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Hui-Chi Hung
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chia-Yu Gean
- Department of Diagnostic Radiology, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Hong-Ming Tsai
- Department of Diagnostic Radiology, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Chun-Lin Su
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Po-Wu Gean
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, Taiwan. .,Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan.
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44
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Heppner DE, Hristova M, Ida T, Mijuskovic A, Dustin CM, Bogdándi V, Fukuto JM, Dick TP, Nagy P, Li J, Akaike T, van der Vliet A. Cysteine perthiosulfenic acid (Cys-SSOH): A novel intermediate in thiol-based redox signaling? Redox Biol 2017; 14:379-385. [PMID: 29054072 PMCID: PMC5647513 DOI: 10.1016/j.redox.2017.10.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 10/05/2017] [Accepted: 10/07/2017] [Indexed: 01/08/2023] Open
Abstract
The reversible oxidation of protein cysteine residues (Cys-SH) is a key reaction in cellular redox signaling involving initial formation of sulfenic acids (Cys-SOH), which are commonly detected using selective dimedone-based probes. Here, we report that significant portions of dimedone-tagged proteins are susceptible to cleavage by DTT reflecting the presence of perthiosulfenic acid species (Cys-SSOH) due to similar oxidation of hydropersulfides (Cys-SSH), since Cys-S-dimedone adducts are stable toward DTT. Combined studies using molecular modeling, mass spectrometry, and cell-based experiments indicate that Cys-SSH are readily oxidized to Cys-SSOH, which forms stable adducts with dimedone-based probes. We additionally confirm the presence of Cys-SSH within protein tyrosine kinases such as EGFR, and their apparent oxidation to Cys-SSOH in response NADPH oxidase activation, suggesting that such Cys-SSH oxidation may represent a novel, as yet uncharacterized, event in redox-based signaling.
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Affiliation(s)
- David E Heppner
- Department of Pathology and Laboratory Medicine, Robert Larner M.D., College of Medicine, University of Vermont, Burlington, VT, USA
| | - Milena Hristova
- Department of Pathology and Laboratory Medicine, Robert Larner M.D., College of Medicine, University of Vermont, Burlington, VT, USA
| | - Tomoaki Ida
- Department of Environmental Health Sciences and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Ana Mijuskovic
- Division of Redox Regulation, DKFZ-ZMBH Alliance, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christopher M Dustin
- Department of Pathology and Laboratory Medicine, Robert Larner M.D., College of Medicine, University of Vermont, Burlington, VT, USA
| | - Virág Bogdándi
- Department of Molecular Immunology and Toxicology, National Institute of Oncology, Budapest, Hungary
| | - Jon M Fukuto
- Department of Chemistry, Sonoma State University, Rohnert Park, CA, USA
| | - Tobias P Dick
- Division of Redox Regulation, DKFZ-ZMBH Alliance, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Péter Nagy
- Department of Molecular Immunology and Toxicology, National Institute of Oncology, Budapest, Hungary
| | - Jianing Li
- Department of Chemistry, University of Vermont, Burlington, VT, USA
| | - Takaaki Akaike
- Department of Environmental Health Sciences and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai, Japan.
| | - Albert van der Vliet
- Department of Pathology and Laboratory Medicine, Robert Larner M.D., College of Medicine, University of Vermont, Burlington, VT, USA.
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45
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Allimuthu D, Adams DJ. 2-Chloropropionamide As a Low-Reactivity Electrophile for Irreversible Small-Molecule Probe Identification. ACS Chem Biol 2017; 12:2124-2131. [PMID: 28613814 DOI: 10.1021/acschembio.7b00424] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Resurgent interest in covalent target engagement in drug discovery has demonstrated that small molecules containing weakly reactive electrophiles can be safe and effective therapies. Several recently FDA-approved drugs feature an acrylamide functionality to selectively engage cysteine side chains of kinases (Ibrutinib, Afatinib, and Neratinib). Additional electrophilic functionalities whose reactivity is compatible with highly selective target engagement and in vivo application could open new avenues in covalent small molecule discovery. Here, we report the synthesis and evaluation of a library of small molecules containing the 2-chloropropionamide functionality, which we demonstrate is less reactive than typical acrylamide electrophiles. Although many library members do not appear to label proteins in cells, we identified S-CW3554 as selectively labeling protein disulfide isomerase and inhibiting its enzymatic activity. Subsequent profiling of the library against five diverse cancer cell lines showed unique cytotoxicity for S-CW3554 in cells derived from multiple myeloma, a cancer recently reported to be sensitive to PDI inhibition. Our novel PDI inhibitor highlights the potential of 2-chloropropionamides as weak and stereochemically tunable electrophiles for covalent drug discovery.
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Affiliation(s)
- Dharmaraja Allimuthu
- Department of Genetics and
Genome Sciences and Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Drew J. Adams
- Department of Genetics and
Genome Sciences and Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States
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46
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Lagoutte R, Patouret R, Winssinger N. Covalent inhibitors: an opportunity for rational target selectivity. Curr Opin Chem Biol 2017; 39:54-63. [DOI: 10.1016/j.cbpa.2017.05.008] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 05/16/2017] [Accepted: 05/23/2017] [Indexed: 10/19/2022]
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47
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Weitsman G, Mitchell NJ, Evans R, Cheung A, Kalber TL, Bofinger R, Fruhwirth GO, Keppler M, Wright ZVF, Barber PR, Gordon P, de Koning T, Wulaningsih W, Sander K, Vojnovic B, Ameer-Beg S, Lythgoe M, Arnold JN, Årstad E, Festy F, Hailes HC, Tabor AB, Ng T. Detecting intratumoral heterogeneity of EGFR activity by liposome-based in vivo transfection of a fluorescent biosensor. Oncogene 2017; 36:3618-3628. [PMID: 28166195 PMCID: PMC5421598 DOI: 10.1038/onc.2016.522] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 11/12/2016] [Accepted: 12/21/2016] [Indexed: 12/20/2022]
Abstract
Despite decades of research in the epidermal growth factor receptor (EGFR) signalling field, and many targeted anti-cancer drugs that have been tested clinically, the success rate for these agents in the clinic is low, particularly in terms of the improvement of overall survival. Intratumoral heterogeneity is proposed as a major mechanism underlying treatment failure of these molecule-targeted agents. Here we highlight the application of fluorescence lifetime microscopy (FLIM)-based biosensing to demonstrate intratumoral heterogeneity of EGFR activity. For sensing EGFR activity in cells, we used a genetically encoded CrkII-based biosensor which undergoes conformational changes upon tyrosine-221 phosphorylation by EGFR. We transfected this biosensor into EGFR-positive tumour cells using targeted lipopolyplexes bearing EGFR-binding peptides at their surfaces. In a murine model of basal-like breast cancer, we demonstrated a significant degree of intratumoral heterogeneity in EGFR activity, as well as the pharmacodynamic effect of a radionuclide-labeled EGFR inhibitor in situ. Furthermore, a significant correlation between high EGFR activity in tumour cells and macrophage-tumour cell proximity was found to in part account for the intratumoral heterogeneity in EGFR activity observed. The same effect of macrophage infiltrate on EGFR activation was also seen in a colorectal cancer xenograft. In contrast, a non-small cell lung cancer xenograft expressing a constitutively active EGFR conformational mutant exhibited macrophage proximity-independent EGFR activity. Our study validates the use of this methodology to monitor therapeutic response in terms of EGFR activity. In addition, we found iNOS gene induction in macrophages that are cultured in tumour cell-conditioned media as well as an iNOS activity-dependent increase in EGFR activity in tumour cells. These findings point towards an immune microenvironment-mediated regulation that gives rise to the observed intratumoral heterogeneity of EGFR signalling activity in tumour cells in vivo.
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Affiliation(s)
- G Weitsman
- Richard Dimbleby Department of Cancer Research, Randall Division & Division of Cancer Studies, Kings College London, Guy’s Medical School Campus, London, UK
| | - N J Mitchell
- Department of Chemistry, University College London, London, UK
| | - R Evans
- Richard Dimbleby Department of Cancer Research, Randall Division & Division of Cancer Studies, Kings College London, Guy’s Medical School Campus, London, UK
| | - A Cheung
- Richard Dimbleby Department of Cancer Research, Randall Division & Division of Cancer Studies, Kings College London, Guy’s Medical School Campus, London, UK
- Breast Cancer Now Research Unit, King’s College London, London, UK
| | - T L Kalber
- UCL Centre for Advanced Biomedical Imaging, Division of Medicine, University College London, London, UK
| | - R Bofinger
- Department of Chemistry, University College London, London, UK
| | - G O Fruhwirth
- Richard Dimbleby Department of Cancer Research, Randall Division & Division of Cancer Studies, Kings College London, Guy’s Medical School Campus, London, UK
| | - M Keppler
- Richard Dimbleby Department of Cancer Research, Randall Division & Division of Cancer Studies, Kings College London, Guy’s Medical School Campus, London, UK
| | - Z V F Wright
- Department of Chemistry, University College London, London, UK
| | - P R Barber
- Gray Laboratories, Department of Oncology, Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Oxford, UK
| | - P Gordon
- Breast Cancer Now Research Unit, King’s College London, London, UK
| | - T de Koning
- Division of Cancer Studies, Kings College London, Guy’s Medical School Campus, London, UK
| | - W Wulaningsih
- Cancer Epidemiology Group, Division of Cancer Studies, King’s College London, London, UK
| | - K Sander
- Institute of Nuclear Medicine, University College London, London, UK
| | - B Vojnovic
- Gray Laboratories, Department of Oncology, Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Oxford, UK
| | - S Ameer-Beg
- Richard Dimbleby Department of Cancer Research, Randall Division & Division of Cancer Studies, Kings College London, Guy’s Medical School Campus, London, UK
| | - M Lythgoe
- UCL Centre for Advanced Biomedical Imaging, Division of Medicine, University College London, London, UK
| | - J N Arnold
- Division of Cancer Studies, Kings College London, Guy’s Medical School Campus, London, UK
| | - E Årstad
- Institute of Nuclear Medicine, University College London, London, UK
| | - F Festy
- King’s College London Dental Institute, Tissue Engineering and Biophotonics, Guy’s Hospital Campus, London, UK
| | - H C Hailes
- Department of Chemistry, University College London, London, UK
| | - A B Tabor
- Department of Chemistry, University College London, London, UK
| | - T Ng
- Richard Dimbleby Department of Cancer Research, Randall Division & Division of Cancer Studies, Kings College London, Guy’s Medical School Campus, London, UK
- Breast Cancer Now Research Unit, King’s College London, London, UK
- UCL Cancer Institute, Paul O’Gorman Building, University College London, London, UK
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48
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Yin DM, Hannam JS, Schmitz A, Schiemann O, Hagelueken G, Famulok M. Studying the Conformation of a Receptor Tyrosine Kinase in Solution by Inhibitor-Based Spin Labeling. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201703154] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Dongsheng M. Yin
- Max Planck Fellow Chemical Biology; Center of Advanced European Studies and Research (caesar); Ludwig-Erhard-Allee 2 53175 Bonn Germany
- LIMES Chemical Biology Unit; Rheinische Friedrich-Wilhelms-Universität Bonn; Gerhard-Domagk-Strasse 1 53121 Bonn Germany
| | - Jeffrey S. Hannam
- LIMES Chemical Biology Unit; Rheinische Friedrich-Wilhelms-Universität Bonn; Gerhard-Domagk-Strasse 1 53121 Bonn Germany
| | - Anton Schmitz
- Max Planck Fellow Chemical Biology; Center of Advanced European Studies and Research (caesar); Ludwig-Erhard-Allee 2 53175 Bonn Germany
- LIMES Chemical Biology Unit; Rheinische Friedrich-Wilhelms-Universität Bonn; Gerhard-Domagk-Strasse 1 53121 Bonn Germany
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry; Rheinische Friedrich-Wilhelms-Universität Bonn; Wegelerstrasse 12 53115 Bonn Germany
| | - Gregor Hagelueken
- Institute of Physical and Theoretical Chemistry; Rheinische Friedrich-Wilhelms-Universität Bonn; Wegelerstrasse 12 53115 Bonn Germany
| | - Michael Famulok
- Max Planck Fellow Chemical Biology; Center of Advanced European Studies and Research (caesar); Ludwig-Erhard-Allee 2 53175 Bonn Germany
- LIMES Chemical Biology Unit; Rheinische Friedrich-Wilhelms-Universität Bonn; Gerhard-Domagk-Strasse 1 53121 Bonn Germany
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49
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Yin DM, Hannam JS, Schmitz A, Schiemann O, Hagelueken G, Famulok M. Studying the Conformation of a Receptor Tyrosine Kinase in Solution by Inhibitor-Based Spin Labeling. Angew Chem Int Ed Engl 2017. [PMID: 28628261 PMCID: PMC5575716 DOI: 10.1002/anie.201703154] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The synthesis of a spin label based on PD168393, a covalent inhibitor of a major anticancer drug target, the epidermal growth factor receptor (EGFR), is reported. The label facilitates the analysis of the EGFR structure in solution by pulsed electron paramagnetic resonance (EPR) spectroscopy. For various EGFR constructs, including near-full-length EGFR, we determined defined distance distributions between the two spin labels bound to the ATP binding sites of the EGFR dimer. The distances are in excellent agreement with an asymmetric dimer of the EGFR. Based on crystal structures, this dimer had previously been proposed to reflect the active conformation of the receptor but structural data demonstrating its existence in solution have been lacking. More generally, our study provides proof-of-concept that inhibitor-based spin labeling enables the convenient introduction of site-specific spin labels into kinases for which covalent or tight-binding small-molecule modulators are available.
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Affiliation(s)
- Dongsheng M Yin
- Max Planck Fellow Chemical Biology, Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175, Bonn, Germany.,LIMES Chemical Biology Unit, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| | - Jeffrey S Hannam
- LIMES Chemical Biology Unit, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| | - Anton Schmitz
- Max Planck Fellow Chemical Biology, Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175, Bonn, Germany.,LIMES Chemical Biology Unit, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-Universität Bonn, Wegelerstrasse 12, 53115, Bonn, Germany
| | - Gregor Hagelueken
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-Universität Bonn, Wegelerstrasse 12, 53115, Bonn, Germany
| | - Michael Famulok
- Max Planck Fellow Chemical Biology, Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175, Bonn, Germany.,LIMES Chemical Biology Unit, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
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50
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Punthasee P, Laciak AR, Cummings AH, Ruddraraju KV, Lewis SM, Hillebrand R, Singh H, Tanner JJ, Gates KS. Covalent Allosteric Inactivation of Protein Tyrosine Phosphatase 1B (PTP1B) by an Inhibitor–Electrophile Conjugate. Biochemistry 2017; 56:2051-2060. [DOI: 10.1021/acs.biochem.7b00151] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Puminan Punthasee
- Department
of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| | - Adrian R. Laciak
- Department
of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| | - Andrea H. Cummings
- Department
of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| | | | - Sarah M. Lewis
- Department
of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| | - Roman Hillebrand
- Department
of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| | - Harkewal Singh
- Department
of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| | - John J. Tanner
- Department
of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
- Department
of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, Missouri 65211, United States
| | - Kent S. Gates
- Department
of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
- Department
of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, Missouri 65211, United States
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