1
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Ozgencil F, Gunindi HB, Eren G. Dual-targeted NAMPT inhibitors as a progressive strategy for cancer therapy. Bioorg Chem 2024; 149:107509. [PMID: 38824699 DOI: 10.1016/j.bioorg.2024.107509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 04/29/2024] [Accepted: 05/28/2024] [Indexed: 06/04/2024]
Abstract
In mammals, nicotinamide phosphoribosyltransferase (NAMPT) is a crucial enzyme in the nicotinamide adenine dinucleotide (NAD+) synthesis pathway catalyzing the condensation of nicotinamide (NAM) with 5-phosphoribosyl-1-pyrophosphate (PRPP) to produce nicotinamide mononucleotide (NMN). Given the pivotal role of NAD+ in a range of cellular functions, including DNA synthesis, redox reactions, cytokine generation, metabolism, and aging, NAMPT has become a promising target for many diseases, notably cancer. Therefore, various NAMPT inhibitors have been reported and classified as first and second-generation based on their chemical structures and design strategies, dual-targeted being one. However, most NAMPT inhibitors suffer from several limitations, such as dose-dependent toxicity and poor pharmacokinetic properties. Consequently, there is no clinically approved NAMPT inhibitor. Hence, research on discovering more effective and less toxic dual-targeted NAMPT inhibitors with desirable pharmacokinetic properties has drawn attention recently. This review summarizes the previously reported dual-targeted NAMPT inhibitors, focusing on their design strategies and advantages over the single-targeted therapies.
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Affiliation(s)
- Fikriye Ozgencil
- SIRTeam Group, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Gazi University, 06330 Ankara, Türkiye
| | - Habibe Beyza Gunindi
- SIRTeam Group, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Gazi University, 06330 Ankara, Türkiye
| | - Gokcen Eren
- SIRTeam Group, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Gazi University, 06330 Ankara, Türkiye.
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2
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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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3
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Compain G, Monsarrat C, Blagojevic J, Brillet K, Dumas P, Hammann P, Kuhn L, Martiel I, Engilberge S, Oliéric V, Wolff P, Burnouf DY, Wagner J, Guichard G. Peptide-Based Covalent Inhibitors Bearing Mild Electrophiles to Target a Conserved His Residue of the Bacterial Sliding Clamp. JACS AU 2024; 4:432-440. [PMID: 38425897 PMCID: PMC10900491 DOI: 10.1021/jacsau.3c00572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/20/2023] [Accepted: 01/04/2024] [Indexed: 03/02/2024]
Abstract
Peptide-based covalent inhibitors targeted to nucleophilic protein residues have recently emerged as new modalities to target protein-protein interactions (PPIs) as they may provide some benefits over more classic competitive inhibitors. Covalent inhibitors are generally targeted to cysteine, the most intrinsically reactive amino acid residue, and to lysine, which is more abundant at the surface of proteins but much less frequently to histidine. Herein, we report the structure-guided design of targeted covalent inhibitors (TCIs) able to bind covalently and selectively to the bacterial sliding clamp (SC), by reacting with a well-conserved histidine residue located on the edge of the peptide-binding pocket. SC is an essential component of the bacterial DNA replication machinery, identified as a promising target for the development of new antibacterial compounds. Thermodynamic and kinetic analyses of ligands bearing different mild electrophilic warheads confirmed the higher efficiency of the chloroacetamide compared to Michael acceptors. Two high-resolution X-ray structures of covalent inhibitor-SC adducts were obtained, revealing the canonical orientation of the ligand and details of covalent bond formation with histidine. Proteomic studies were consistent with a selective SC engagement by the chloroacetamide-based TCI. Finally, the TCI of SC was substantially more active than the parent noncovalent inhibitor in an in vitro SC-dependent DNA synthesis assay, validating the potential of the approach to design covalent inhibitors of protein-protein interactions targeted to histidine.
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Affiliation(s)
- Guillaume Compain
- Univ.
Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, 2 Rue Robert Escarpit, F-33607 Pessac, France
| | - Clément Monsarrat
- Univ.
Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, 2 Rue Robert Escarpit, F-33607 Pessac, France
| | - Julie Blagojevic
- Université
de Strasbourg, CNRS, FR1589, Plateforme Protéomique Strasbourg
Esplanade, 2 Allée K. Roentgen, 67084 Strasbourg, France
| | - Karl Brillet
- Université
de Strasbourg, CNRS, Architecture et Réactivité de l’ARN,
UPR 9002, Institut de Biologie Moléculaire et Cellulaire du
CNRS, 2 Allée
K. Roentgen, 67084 Strasbourg, France
| | - Philippe Dumas
- Department
of Integrative Structural Biology, IGBMC, Strasbourg University, ESBS, 1 Rue Laurent Fries, 67404 Illkirch, Cedex, France
| | - Philippe Hammann
- Université
de Strasbourg, CNRS, FR1589, Plateforme Protéomique Strasbourg
Esplanade, 2 Allée K. Roentgen, 67084 Strasbourg, France
| | - Lauriane Kuhn
- Université
de Strasbourg, CNRS, FR1589, Plateforme Protéomique Strasbourg
Esplanade, 2 Allée K. Roentgen, 67084 Strasbourg, France
| | - Isabelle Martiel
- Swiss
Light Source (SLS), Paul Scherrer Institute
(PSI), 5232 Villigen-PSI, Switzerland
| | - Sylvain Engilberge
- Swiss
Light Source (SLS), Paul Scherrer Institute
(PSI), 5232 Villigen-PSI, Switzerland
| | - Vincent Oliéric
- Swiss
Light Source (SLS), Paul Scherrer Institute
(PSI), 5232 Villigen-PSI, Switzerland
| | - Philippe Wolff
- Université
de Strasbourg, CNRS, Architecture et Réactivité de l’ARN,
UPR 9002, Institut de Biologie Moléculaire et Cellulaire du
CNRS, 2 Allée
K. Roentgen, 67084 Strasbourg, France
| | - Dominique Y. Burnouf
- Université
de Strasbourg, CNRS, Architecture et Réactivité de l’ARN,
UPR 9002, Institut de Biologie Moléculaire et Cellulaire du
CNRS, 2 Allée
K. Roentgen, 67084 Strasbourg, France
| | - Jérôme Wagner
- Université
de Strasbourg, CNRS, Architecture et Réactivité de l’ARN,
UPR 9002, Institut de Biologie Moléculaire et Cellulaire du
CNRS, 2 Allée
K. Roentgen, 67084 Strasbourg, France
| | - Gilles Guichard
- Univ.
Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, 2 Rue Robert Escarpit, F-33607 Pessac, France
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Anas E, Hoover E, Ille AL, Ille AM, Amico-Ruvio S. Towards multi-target glioblastoma therapy: Structural, distribution, and functional insights into protein target candidates. Brain Res 2024; 1822:148623. [PMID: 37820848 DOI: 10.1016/j.brainres.2023.148623] [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: 07/24/2023] [Revised: 09/25/2023] [Accepted: 10/07/2023] [Indexed: 10/13/2023]
Abstract
Glioblastoma is the most commonly occurring and most lethal primary brain tumor. Treatment options are limited in number and therapeutic development remains a major challenge. However, substantial progress has been made in better understanding the underlying biology of the disease. A recent proteomic meta-analysis revealed that 270 proteins were commonly dysregulated in glioblastoma, highlighting the complexity of the disease. This motivated us to explore potential protein targets which may be collectively inhibited, based on common upregulation, as part of a multi-target therapeutic strategy. Herein, we identify and characterize structural attributes relevant to the druggability of six protein target candidates. Computational analysis of crystal structures revealed druggable cavities in each of these proteins, and various parameters of these cavities were determined. For proteins with inhibitor-bound structures available, inhibitor compounds were found to overlap with the computationally determined cavities upon structural alignment. We also performed bioinformatic analysis for normal transcriptional expression distribution of these proteins across various brain regions and various tissues, as well as gene ontology curation to gain functional insights, as this information is useful for understanding the potential for off-target adverse effects. Our findings represent initial steps towards the development of multi-target glioblastoma therapy and may aid future work exploring similar therapeutic strategies.
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Affiliation(s)
- Emily Anas
- STEM Biomedical, Kitchener, Ontario, Canada
| | | | - Anetta L Ille
- STEM Biomedical, Kitchener, Ontario, Canada; Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Alexander M Ille
- STEM Biomedical, Kitchener, Ontario, Canada; School of Graduate Studies, Rutgers University, Newark, NJ, USA
| | - Stacy Amico-Ruvio
- Department of Natural Sciences and Mathematics, D'Youville University, Buffalo, NY, USA.
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5
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Mehta NV, Degani MS. The expanding repertoire of covalent warheads for drug discovery. Drug Discov Today 2023; 28:103799. [PMID: 37839776 DOI: 10.1016/j.drudis.2023.103799] [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: 07/22/2023] [Revised: 10/04/2023] [Accepted: 10/10/2023] [Indexed: 10/17/2023]
Abstract
The reactive functionalities of drugs that engage in covalent interactions with the enzyme/receptor residue in either a reversible or an irreversible manner are called 'warheads'. Covalent warheads that were previously neglected because of safety concerns have recently gained center stage as a result of their various advantages over noncovalent drugs, including increased selectivity, increased residence time, and higher potency. With the approval of several covalent inhibitors over the past decade, research in this area has accelerated. Various strategies are being continuously developed to tune the characteristics of warheads to improve their potency and mitigate toxicity. Here, we review research progress in warhead discovery over the past 5 years to provide valuable insights for future drug discovery.
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Affiliation(s)
- Namrashee V Mehta
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Nathalal Parekh Marg, Matunga, Mumbai 400019, Maharashtra, India.
| | - Mariam S Degani
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Nathalal Parekh Marg, Matunga, Mumbai 400019, Maharashtra, India.
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6
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Murnan KM, Horbinski C, Stegh AH. Redox Homeostasis and Beyond: The Role of Wild-Type Isocitrate Dehydrogenases for the Pathogenesis of Glioblastoma. Antioxid Redox Signal 2023; 39:923-941. [PMID: 37132598 PMCID: PMC10654994 DOI: 10.1089/ars.2023.0262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 03/06/2023] [Indexed: 05/04/2023]
Abstract
Significance: Glioblastoma is an aggressive and devastating brain tumor characterized by a dismal prognosis and resistance to therapeutic intervention. To support catabolic processes critical for unabated cellular growth and defend against harmful reactive oxygen species, glioblastoma tumors upregulate the expression of wild-type isocitrate dehydrogenases (IDHs). IDH enzymes catalyze the oxidative decarboxylation of isocitrate to α-ketoglutarate (α-KG), NAD(P)H, and CO2. On molecular levels, IDHs epigenetically control gene expression through effects on α-KG-dependent dioxygenases, maintain redox balance, and promote anaplerosis by providing cells with NADPH and precursor substrates for macromolecular synthesis. Recent Advances: While gain-of-function mutations in IDH1 and IDH2 represent one of the most comprehensively studied mechanisms of IDH pathogenic effects, recent studies identified wild-type IDHs as critical regulators of normal organ physiology and, when transcriptionally induced or down regulated, as contributing to glioblastoma progression. Critical Issues: Here, we will discuss molecular mechanisms of how wild-type IDHs control glioma pathogenesis, including the regulation of oxidative stress and de novo lipid biosynthesis, and provide an overview of current and future research directives that aim to fully characterize wild-type IDH-driven metabolic reprogramming and its contribution to the pathogenesis of glioblastoma. Future Directions: Future studies are required to further dissect mechanisms of metabolic and epigenomic reprogramming in tumors and the tumor microenvironment, and to develop pharmacological approaches to inhibit wild-type IDH function. Antioxid. Redox Signal. 39, 923-941.
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Affiliation(s)
- Kevin M. Murnan
- Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, The Robert H. Lurie Comprehensive Cancer Center, Malnati Brain Tumor Institute, Northwestern University, Chicago, Illinois, USA
| | - Craig Horbinski
- Department of Pathology, Feinberg School of Medicine, Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois, USA
- Department of Neurological Surgery, Feinberg School of Medicine, Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois, USA
| | - Alexander H. Stegh
- Department of Neurological Surgery, The Brain Tumor Center, Alvin J. Siteman Comprehensive Cancer Center, Washington University School of Medicine, St. Louis, Missouri, USA
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Ng R, Zhang G, Li JJ. An update on the discovery and development of reversible covalent inhibitors. Med Chem Res 2023; 32:1039-1062. [PMID: 37305209 PMCID: PMC10148018 DOI: 10.1007/s00044-023-03065-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 04/18/2023] [Indexed: 06/13/2023]
Abstract
Small molecule drugs that covalently bind irreversibly to their target proteins have several advantages over conventional reversible inhibitors. They include increased duration of action, less-frequent drug dosing, reduced pharmacokinetic sensitivity, and the potential to target intractable shallow binding sites. Despite these advantages, the key challenges of irreversible covalent drugs are their potential for off-target toxicities and immunogenicity risks. Incorporating reversibility into covalent drugs would lead to less off-target toxicity by forming reversible adducts with off-target proteins and thus reducing the risk of idiosyncratic toxicities caused by the permanent modification of proteins, which leads to higher levels of potential haptens. Herein, we systematically review electrophilic warheads employed during the development of reversible covalent drugs. We hope the structural insights of electrophilic warheads would provide helpful information to medicinal chemists and aid in designing covalent drugs with better on-target selectivity and improved safety. Graphical Abstract
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Affiliation(s)
- Raymond Ng
- Olema Oncology, 512 2nd St., 4th Floor, San Francisco, 94107 CA USA
| | - Guiping Zhang
- Genhouse Bio, No.1 Xinze Road, Suzhou Industrial Park, Suzhou, Jiangsu Province 215123 PR China
| | - Jie Jack Li
- Genhouse Bio, No.1 Xinze Road, Suzhou Industrial Park, Suzhou, Jiangsu Province 215123 PR China
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Zarei M, Hajihassani O, Hue JJ, Graor HJ, Rothermel LD, Winter JM. Targeting wild-type IDH1 enhances chemosensitivity in pancreatic cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.29.534596. [PMID: 37034685 PMCID: PMC10081181 DOI: 10.1101/2023.03.29.534596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Pancreatic cancer (PC) is one of the most aggressive types of cancer, with a five-year overall survival rate of 11% among all-comers. Current systemic therapeutic options are limited to cytotoxic chemotherapies which have limited clinical efficacy and are often associated with development of drug resistance. Analysis of The Cancer Genome Atlas showed that wild-type isocitrate dehydrogenase (wtIDH1) is overexpressed in pancreatic tumors. In this study, we focus on the potential roles of wtIDH1 in pancreatic cancer chemoresistance. We found that treatment of pancreatic cancer cells with chemotherapy induced expression of wtIDH1, and this serves as a key resistance factor. The enzyme is protective to cancer cells under chemotherapy-induced oxidative stress by producing NADPH and alpha-ketoglutarate to maintain redox balance and mitochondrial function. An FDA-approved mutant IDH1 inhibitor, ivosidenib (AG-120), is actually a potent wtDH1 inhibitor under a nutrient-deprived microenvironment, reflective of the pancreatic cancer microenvironment. Suppression of wtIDH1 impairs redox balance, results in increased ROS levels, and enhances chemotherapy induced apoptosis in pancreatic cancer vis ROS damage in vitro. In vivo experiments further revealed that inhibiting wtIDH1 enhances chemotherapy anti-tumor effects in patient-derived xenografts and murine models of pancreatic cancer. Pharmacologic wtIDH1 inhibition with ivosidenib represents an attractive option for combination therapies with cytotoxic chemotherapy for patients with pancreatic cancer. Based on these data, we have initiated phase Ib trial combining ivosidenib and multi-agent chemotherapy in patients with pancreatic cancer (NCT05209074).
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Affiliation(s)
- Mehrdad Zarei
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH
- Department of Surgery, Division of Surgical Oncology, University Hospitals Cleveland Medical Center, Cleveland, OH
| | - Omid Hajihassani
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH
| | - Jonathan J. Hue
- Department of Surgery, Division of Surgical Oncology, University Hospitals Cleveland Medical Center, Cleveland, OH
| | - Hallie J. Graor
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH
| | - Luke D. Rothermel
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH
- Department of Surgery, Division of Surgical Oncology, University Hospitals Cleveland Medical Center, Cleveland, OH
| | - Jordan M. Winter
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH
- Department of Surgery, Division of Surgical Oncology, University Hospitals Cleveland Medical Center, Cleveland, OH
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Epigenetic Abnormalities in Chondrosarcoma. Int J Mol Sci 2023; 24:ijms24054539. [PMID: 36901967 PMCID: PMC10003547 DOI: 10.3390/ijms24054539] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/19/2023] [Accepted: 02/22/2023] [Indexed: 03/03/2023] Open
Abstract
In recent years, our understanding of the epigenetic mechanisms involved in tumor pathology has improved greatly. DNA and histone modifications, such as methylation, demethylation, acetylation, and deacetylation, can lead to the up-regulation of oncogenic genes, as well as the suppression of tumor suppressor genes. Gene expression can also be modified on a post-transcriptional level by microRNAs that contribute to carcinogenesis. The role of these modifications has been already described in many tumors, e.g., colorectal, breast, and prostate cancers. These mechanisms have also begun to be investigated in less common tumors, such as sarcomas. Chondrosarcoma (CS) is a rare type of tumor that belongs to sarcomas and is the second most common malignant bone tumor after osteosarcoma. Due to unknown pathogenesis and resistance to chemo- and radiotherapies of these tumors, there is a need to develop new potential therapies against CS. In this review, we summarize current knowledge on the influence of epigenetic alterations in the pathogenesis of CS by discussing potential candidates for future therapies. We also emphasize ongoing clinical trials that use drugs targeting epigenetic modifications in CS treatment.
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Che J, Jones LH. Covalent drugs targeting histidine - an unexploited opportunity? RSC Med Chem 2022; 13:1121-1126. [PMID: 36325394 PMCID: PMC9579939 DOI: 10.1039/d2md00258b] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/26/2022] [Indexed: 09/30/2023] Open
Abstract
Covalent drugs and chemical probes often possess pharmacological advantages over reversible binding ligands, such as enhanced potency and pharmacodynamic duration. The highly nucleophilic cysteine thiol is commonly targeted using acrylamide electrophiles, but the amino acid is rarely present in protein binding sites. Sulfonyl exchange chemistry has expanded the covalent drug discovery toolkit by enabling the rational design of irreversible inhibitors targeting tyrosine, lysine, serine and threonine. Probes containing the sulfonyl fluoride warhead have also been shown to serendipitously label histidine residues in proteins. Histidine targeting is an attractive prospect because the residue is frequently proximal to protein small molecule ligands and the imidazole side chain possesses desirable nucleophilicity. We recently reported the design of cereblon molecular glues to site-selectively modify a histidine in the thalidomide binding site using sulfonyl exchange chemistry. We believe that histidine targeting holds great promise for future covalent drug development and this Opinion highlights these opportunities.
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Affiliation(s)
- Jianwei Che
- Center for Protein Degradation, Dana-Farber Cancer Institute 360 Longwood Avenue Boston MA USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School Boston MA USA
| | - Lyn H Jones
- Center for Protein Degradation, Dana-Farber Cancer Institute 360 Longwood Avenue Boston MA USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School Boston MA USA
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Zarei M, Hajihassani O, Hue JJ, Graor HJ, Loftus AW, Rathore M, Vaziri-Gohar A, Asara JM, Winter JM, Rothermel LD. Wild-type IDH1 inhibition enhances chemotherapy response in melanoma. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2022; 41:283. [PMID: 36153582 PMCID: PMC9509573 DOI: 10.1186/s13046-022-02489-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 09/06/2022] [Indexed: 12/31/2022]
Abstract
BACKGROUND Alternative treatment strategies in melanoma beyond immunotherapy and mutation-targeted therapy are urgently needed. Wild-type isocitrate dehydrogenase 1 (wtIDH1) has recently been implicated as a metabolic dependency in cancer. The enzyme protects cancer cells under metabolic stress, including nutrient limited conditions in the tumor microenvironment. Specifically, IDH1 generates NADPH to maintain redox homeostasis and produces α-ketoglutarate to support mitochondrial function through anaplerosis. Herein, the role of wtIDH1 in melanoma is further explored. METHODS The expression of wtIDH1 was determined by qRT-PCR, and Western blot in melanoma cell lines and the effect of wtIDH1 on metabolic reprogramming in melanoma was interrogated by LC-MS. The impact of wtIDH1 inhibition alone and in combination with chemotherapy was determined in cell culture and mouse melanoma models. RESULTS Melanoma patients express higher levels of the wtIDH1 enzyme compared to normal skin tissue, and elevated wtIDH1 expression portends poor patient survival. Knockdown of IDH1 by RNA interference inhibited cell proliferation and migration under low nutrient levels. Suppression of IDH1 expression in melanoma also decreased NADPH and glutathione levels, resulting in increased reactive oxygen species. An FDA-approved inhibitor of mutant IDH1, ivosidenib (AG-120), exhibited potent anti-wtIDH1 properties under low magnesium and nutrient levels, reflective of the tumor microenvironment in natura. Thus, similar findings were replicated in murine models of melanoma. In light of the impact of wtIDH1 inhibition on oxidative stress, enzyme blockade was synergistic with conventional anti-melanoma chemotherapy in pre-clinical models. CONCLUSIONS These results demonstrate the clinical potential of wtIDH1 inhibition as a novel and readily available combination treatment strategy for patients with advanced and refractory melanoma. Schematic shows increased wild-type IDH1 expression and activity as an adaptive response to metabolic stress induced by chemotherapy.
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Affiliation(s)
- Mehrdad Zarei
- grid.67105.350000 0001 2164 3847Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH USA ,grid.443867.a0000 0000 9149 4843Department of Surgery, Division of Surgical Oncology, University Hospitals Cleveland Medical Center, 11100 Euclid Ave., Cleveland, OH 44106 USA
| | - Omid Hajihassani
- grid.67105.350000 0001 2164 3847Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH USA
| | - Jonathan J. Hue
- grid.443867.a0000 0000 9149 4843Department of Surgery, Division of Surgical Oncology, University Hospitals Cleveland Medical Center, 11100 Euclid Ave., Cleveland, OH 44106 USA
| | - Hallie J. Graor
- grid.67105.350000 0001 2164 3847Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH USA
| | - Alexander W. Loftus
- grid.443867.a0000 0000 9149 4843Department of Surgery, Division of Surgical Oncology, University Hospitals Cleveland Medical Center, 11100 Euclid Ave., Cleveland, OH 44106 USA
| | - Moeez Rathore
- grid.67105.350000 0001 2164 3847Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH USA
| | - Ali Vaziri-Gohar
- grid.67105.350000 0001 2164 3847Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH USA
| | - John M. Asara
- grid.239395.70000 0000 9011 8547Division of Signal Transduction and Mass Spectrometry Core, Beth Israel Deaconess Medical Center, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Medicine, Harvard Medical School, Boston, MA USA
| | - Jordan M. Winter
- grid.67105.350000 0001 2164 3847Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH USA ,grid.443867.a0000 0000 9149 4843Department of Surgery, Division of Surgical Oncology, University Hospitals Cleveland Medical Center, 11100 Euclid Ave., Cleveland, OH 44106 USA
| | - Luke D. Rothermel
- grid.67105.350000 0001 2164 3847Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH USA ,grid.443867.a0000 0000 9149 4843Department of Surgery, Division of Surgical Oncology, University Hospitals Cleveland Medical Center, 11100 Euclid Ave., Cleveland, OH 44106 USA
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12
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Yun J, Jeong D, Xie Z, Lee S, Kim J, Surmeier DJ, Silverman RB, Kang S. Palladium-Catalyzed α-Arylation of Cyclic β-Dicarbonyl Compounds for the Synthesis of Ca V1.3 Inhibitors. ACS OMEGA 2022; 7:14252-14263. [PMID: 35559207 PMCID: PMC9089348 DOI: 10.1021/acsomega.2c00889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 03/31/2022] [Indexed: 06/15/2023]
Abstract
Cyclic α-aryl β-dicarbonyl derivatives are important scaffolds in medicinal chemistry. Palladium-catalyzed coupling reactions of haloarenes were conducted with diverse five- to seven-membered cyclic β-dicarbonyl derivatives including barbiturate, pyrazolidine-3,5-dione, and 1,4-diazepane-5,7-dione. The coupling reactions of various para- or meta-substituted aryl halides occurred efficiently when Pd(t-Bu3P)2, Xphos, and Cs2CO3 were used under 1,4-dioxane reflux conditions. Although the couplings of ortho-substituted aryl halides with pyrazolidine-3,5-dione and 1,4-diazepane-5,7-dione were moderate, the coupling with barbiturate was limited. Using the optimized reaction conditions, we synthesized several 5-aryl barbiturates as new scaffolds of CaV1.3 Ca2+ channel inhibitors. Among the synthesized molecules, 14e was the most potent CaV1.3 inhibitor with an IC50 of 1.42 μM.
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Affiliation(s)
- Jisu Yun
- College
of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic
of Korea
| | - Dayeon Jeong
- College
of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic
of Korea
| | - Zhong Xie
- Department
of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, United States
| | - Sol Lee
- College
of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic
of Korea
| | - Jiho Kim
- College
of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic
of Korea
| | - D. James Surmeier
- Department
of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, United States
| | - Richard B. Silverman
- Department
of Chemistry, Chemistry of Life Processes Institute, Center for Developmental
Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
| | - Soosung Kang
- College
of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic
of Korea
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13
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Shindo N, Ojida A. Recent progress in covalent warheads for in vivo targeting of endogenous proteins. Bioorg Med Chem 2021; 47:116386. [PMID: 34509863 DOI: 10.1016/j.bmc.2021.116386] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 08/18/2021] [Accepted: 08/23/2021] [Indexed: 01/21/2023]
Abstract
Covalent drugs exert potent and durable activity by chemical modification of the endogenous target protein in vivo. To maximize the pharmacological efficacy while alleviating the risk of toxicity due to nonspecific off-target reactions, current covalent drug discovery focuses on the development of targeted covalent inhibitors (TCIs), wherein a reactive group (warhead) is strategically incorporated onto a reversible ligand of the target protein to facilitate specific covalent engagement. Various aspects of warheads, such as intrinsic reactivity, chemoselectivity, mode of reaction, and reversibility of the covalent engagement, would affect the target selectivity of TCIs. Although TCIs clinically approved to date largely rely on Michael acceptor-type electrophiles for cysteine targeting, a wide array of novel warheads have been devised and tested in TCI development in recent years. In this short review, we provide an overview of recent progress in chemistry for selective covalent targeting of proteins and their applications in TCI designs.
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Affiliation(s)
- Naoya Shindo
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku Fukuoka, Japan
| | - Akio Ojida
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku Fukuoka, Japan.
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14
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Aljoundi A, El Rashedy A, Soliman MES. Comparison of irreversible inhibition targeting HSP72 protein: the resurgence of covalent drug developments. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.1949457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Aimen Aljoundi
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Ahmed El Rashedy
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Mahmoud E. S. Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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15
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Sun J, Guo Y, Fan Y, Wang Q, Zhang Q, Lai D. Decreased expression of IDH1 by chronic unpredictable stress suppresses proliferation and accelerates senescence of granulosa cells through ROS activated MAPK signaling pathways. Free Radic Biol Med 2021; 169:122-136. [PMID: 33865962 DOI: 10.1016/j.freeradbiomed.2021.04.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/09/2021] [Accepted: 04/10/2021] [Indexed: 12/20/2022]
Abstract
Studies suggested that psychosocial stress was associated with female fertility decline, but the underlying mechanisms remained unclear. Granulosa cells (GCs) are important somatic cells to support follicular development and oocyte maturation. Herein, by using a mouse model of chronic unpredictable stress (CUS), we found that CUS induced oxidative stress damage in mouse ovaries, also inhibited GCs proliferation and accelerated GCs senescence. Isocitrate dehydrogenase-1 (IDH1), an antioxidant related gene by generating NADPH, was shown to be downregulated in GCs of CUS mice. Consistently, IDH1 knockdown inhibited cell proliferation and accelerated cellular senescence in KGN cells in vitro. In addition, IDH1 knockdown increased ROS content, induced autophagy activation and triggered cell cycle arrest in S and G2/M phases in KGN cells, which could be rescued by N-acetyl-l-cysteine (NAC), a ROS scavenger in these cells. Besides, IDH1 knockdown activated MAPK signaling pathways, including ERK, JNK and p38 signaling pathways in KGN cells, while NAC could suppress the activation. Through using inhibitors of MAPK signaling pathways, we showed that the activation of ERK pathway participated in autophagy related cell proliferation inhibition and cellular senescence, whereas JNK and p38 MAPK signaling pathways took part in regulation cell cycle arrest associated cell proliferation inhibitory and senescence in IDH1 knockdown KGN cells. Our findings suggested that downregulated expression of IDH1 induced by CUS has a physiological function in GCs proliferation and senescence through ROS activated MAPK signaling pathways, and improvement of IDH1 activity might be a beneficial therapeutic strategy for ovarian dysfunction.
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Affiliation(s)
- Junyan Sun
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China; Shanghai Municipal Key Clinical Speciality, Shanghai, 200030, China
| | - Ying Guo
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China; Shanghai Municipal Key Clinical Speciality, Shanghai, 200030, China
| | - Yihui Fan
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China; Shanghai Municipal Key Clinical Speciality, Shanghai, 200030, China
| | - Qian Wang
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China; Shanghai Municipal Key Clinical Speciality, Shanghai, 200030, China
| | - Qiuwan Zhang
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China; Shanghai Municipal Key Clinical Speciality, Shanghai, 200030, China
| | - Dongmei Lai
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China; Shanghai Municipal Key Clinical Speciality, Shanghai, 200030, China.
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16
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Pu F, Radosevich AJ, Sawicki JW, Chang-Yen D, Talaty NN, Gopalakrishnan SM, Williams JD, Elsen NL. High-Throughput Label-Free Biochemical Assays Using Infrared Matrix-Assisted Desorption Electrospray Ionization Mass Spectrometry. Anal Chem 2021; 93:6792-6800. [PMID: 33885291 DOI: 10.1021/acs.analchem.1c00737] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Mass spectrometry (MS) can provide high sensitivity and specificity for biochemical assays without the requirement of labels, eliminating the risk of assay interference. However, its use had been limited to lower-throughput assays due to the need for chromatography to overcome ion suppression from the sample matrix. Direct analysis without chromatography has the potential for high throughput if sensitivity is sufficient despite the presence of a matrix. Here, we report and demonstrate a novel direct analysis high-throughput MS system based on infrared matrix-assisted desorption electrospray ionization (IR-MALDESI) that has a potential acquisition rate of 33 spectra/s. We show the development of biochemical assays in standard buffers for wild-type isocitrate dehydrogenase 1 (IDH1), diacylglycerol kinase zeta (DGKζ), and p300 histone acetyltransferase (P300) to demonstrate the suitability of this system for a broad range of high-throughput lead discovery assays. A proof-of-concept pilot screen of ∼3k compounds is also shown for IDH1 and compared to a previously reported fluorescence-based assay. We were able to obtain reliable data at a speed amenable for high-throughput screening of large-scale compound libraries.
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Affiliation(s)
- Fan Pu
- Drug Discovery Science and Technology, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Andrew J Radosevich
- Drug Discovery Science and Technology, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - James W Sawicki
- Drug Discovery Science and Technology, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - David Chang-Yen
- Drug Discovery Science and Technology, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Nari N Talaty
- Drug Discovery Science and Technology, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Sujatha M Gopalakrishnan
- Drug Discovery Science and Technology, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Jon D Williams
- Drug Discovery Science and Technology, AbbVie Inc., North Chicago, Illinois 60064, United States
| | - Nathaniel L Elsen
- Drug Discovery Science and Technology, AbbVie Inc., North Chicago, Illinois 60064, United States
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17
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Oltvai ZN, Harley SE, Koes D, Michel S, Warlick ED, Nelson AC, Yohe S, Mroz P. Assessing acquired resistance to IDH1 inhibitor therapy by full-exon IDH1 sequencing and structural modeling. Cold Spring Harb Mol Case Stud 2021; 7:mcs.a006007. [PMID: 33832922 PMCID: PMC8040736 DOI: 10.1101/mcs.a006007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 01/26/2021] [Indexed: 12/14/2022] Open
Abstract
Somatic mutations in hotspot regions of the cytosolic or mitochondrial isoforms of the isocitrate dehydrogenase gene (IDH1 and IDH2, respectively) contribute to the pathogenesis of acute myeloid leukemia (AML) by producing the oncometabolite 2-hydroxyglutarate (2-HG). The allosteric IDH1 inhibitor, ivosidenib, suppresses 2-HG production and induces clinical responses in relapsed/refractory IDH1-mutant AML. Herein, we describe a clinical case of AML in which we detected the neomorphic IDH1 p.R132C mutation in consecutive patient samples with a mutational hotspot targeted next-generation sequencing (NGS) assay. The patient had a clinical response to ivosidenib, followed by relapse and disease progression. Subsequent sequencing of the relapsed sample using a newly developed all-exon, hybrid-capture-based NGS panel identified an additional IDH1 p.S280F mutation known to cause renewed 2-HG production and drug resistance. Structural modeling confirmed that serine-to-phenylalanine substitution at this codon sterically hinders ivosidenib from binding to the mutant IDH1 dimer interface and predicted a similar effect on the pan-IDH inhibitor AG-881. Joint full-exon NGS and structural modeling enables monitoring IDH1 inhibitor-treated AML patients for acquired drug resistance and choosing follow-up therapy.
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Affiliation(s)
- Zoltán N Oltvai
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA.,Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA.,Department of Pathology and Laboratory Medicine, University of Rochester, Rochester, New York 14642, USA
| | - Susan E Harley
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Division of Hematology, Oncology, and Transplantation, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - David Koes
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Stephen Michel
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Erica D Warlick
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Andrew C Nelson
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Sophia Yohe
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Pawel Mroz
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota 55455, USA
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18
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Chung C, Sweha SR, Pratt D, Tamrazi B, Panwalkar P, Banda A, Bayliss J, Hawes D, Yang F, Lee HJ, Shan M, Cieslik M, Qin T, Werner CK, Wahl DR, Lyssiotis CA, Bian Z, Shotwell JB, Yadav VN, Koschmann C, Chinnaiyan AM, Blüml S, Judkins AR, Venneti S. Integrated Metabolic and Epigenomic Reprograming by H3K27M Mutations in Diffuse Intrinsic Pontine Gliomas. Cancer Cell 2020; 38:334-349.e9. [PMID: 32795401 PMCID: PMC7494613 DOI: 10.1016/j.ccell.2020.07.008] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 05/28/2020] [Accepted: 07/15/2020] [Indexed: 01/08/2023]
Abstract
H3K27M diffuse intrinsic pontine gliomas (DIPGs) are fatal and lack treatments. They mainly harbor H3.3K27M mutations resulting in H3K27me3 reduction. Integrated analysis in H3.3K27M cells, tumors, and in vivo imaging in patients showed enhanced glycolysis, glutaminolysis, and tricarboxylic acid cycle metabolism with high alpha-ketoglutarate (α-KG) production. Glucose and/or glutamine-derived α-KG maintained low H3K27me3 in H3.3K27M cells, and inhibition of key enzymes in glycolysis or glutaminolysis increased H3K27me3, altered chromatin accessibility, and prolonged survival in animal models. Previous studies have shown that mutant isocitrate-dehydrogenase (mIDH)1/2 glioma cells convert α-KG to D-2-hydroxyglutarate (D-2HG) to increase H3K27me3. Here, we show that H3K27M and IDH1 mutations are mutually exclusive and experimentally synthetic lethal. Overall, we demonstrate that H3.3K27M and mIDH1 hijack a conserved and critical metabolic pathway in opposing ways to maintain their preferred epigenetic state. Consequently, interruption of this metabolic/epigenetic pathway showed potent efficacy in preclinical models, suggesting key therapeutic targets for much needed treatments.
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Affiliation(s)
- Chan Chung
- Laboratory of Brain Tumor Metabolism and Epigenetics, Department of Pathology, University of Michigan Medical School, Michigan Medicine, University of Michigan, 3520E MSRB 1, 1150 West Medical Center Drive, Ann Arbor, MI 48109-41804, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Stefan R Sweha
- Laboratory of Brain Tumor Metabolism and Epigenetics, Department of Pathology, University of Michigan Medical School, Michigan Medicine, University of Michigan, 3520E MSRB 1, 1150 West Medical Center Drive, Ann Arbor, MI 48109-41804, USA; Neuroscience Graduate Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Drew Pratt
- Laboratory of Brain Tumor Metabolism and Epigenetics, Department of Pathology, University of Michigan Medical School, Michigan Medicine, University of Michigan, 3520E MSRB 1, 1150 West Medical Center Drive, Ann Arbor, MI 48109-41804, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Benita Tamrazi
- Department of Radiology, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA 90027, USA
| | - Pooja Panwalkar
- Laboratory of Brain Tumor Metabolism and Epigenetics, Department of Pathology, University of Michigan Medical School, Michigan Medicine, University of Michigan, 3520E MSRB 1, 1150 West Medical Center Drive, Ann Arbor, MI 48109-41804, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Adam Banda
- Laboratory of Brain Tumor Metabolism and Epigenetics, Department of Pathology, University of Michigan Medical School, Michigan Medicine, University of Michigan, 3520E MSRB 1, 1150 West Medical Center Drive, Ann Arbor, MI 48109-41804, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Jill Bayliss
- Laboratory of Brain Tumor Metabolism and Epigenetics, Department of Pathology, University of Michigan Medical School, Michigan Medicine, University of Michigan, 3520E MSRB 1, 1150 West Medical Center Drive, Ann Arbor, MI 48109-41804, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Debra Hawes
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Fusheng Yang
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Ho-Joon Lee
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Mengrou Shan
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Marcin Cieslik
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Tingting Qin
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Christian K Werner
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Daniel R Wahl
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Costas A Lyssiotis
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Zhiguo Bian
- Centralized Medicinal Chemistry, AbbVie, 1 North Waukegan Road, North Chicago, IL 60064, USA
| | - J Brad Shotwell
- Centralized Medicinal Chemistry, AbbVie, 1 North Waukegan Road, North Chicago, IL 60064, USA
| | - Viveka Nand Yadav
- Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Carl Koschmann
- Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Arul M Chinnaiyan
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Stefan Blüml
- Department of Radiology, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA 90027, USA
| | - Alexander R Judkins
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Sriram Venneti
- Laboratory of Brain Tumor Metabolism and Epigenetics, Department of Pathology, University of Michigan Medical School, Michigan Medicine, University of Michigan, 3520E MSRB 1, 1150 West Medical Center Drive, Ann Arbor, MI 48109-41804, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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19
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Moose JE, Leets KA, Mate NA, Chisholm JD, Hougland JL. An overview of ghrelin O-acyltransferase inhibitors: a literature and patent review for 2010-2019. Expert Opin Ther Pat 2020; 30:581-593. [PMID: 32564644 DOI: 10.1080/13543776.2020.1776263] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
INTRODUCTION The peptide hormone ghrelin regulates physiological processes associated with energy homeostasis such as appetite, insulin signaling, glucose metabolism, and adiposity. Ghrelin has also been implicated in a growing number of neurological pathways involved in stress response and addiction behavior. For ghrelin to bind the growth hormone secretagogue receptor 1a (GHS-R1a) and activate signaling, the hormone must first be octanoylated on a specific serine side chain. This key transformation is performed by the enzyme ghrelin O-acyltransferase (GOAT), and therefore GOAT inhibitors may be useful in treating disorders related to ghrelin signaling such as diabetes, obesity, and related metabolic syndromes. AREAS COVERED This report covers ghrelin and GOAT as potential therapeutic targets and summarizes work on GOAT inhibitors through the end of 2019, highlighting recent successes with both peptidomimetics and small molecule GOAT inhibitors as potent modulators of GOAT-catalyzed ghrelin octanoylation. EXPERT OPINION A growing body of biochemical and structural knowledge regarding the ghrelin/GOAT system now enables multiple avenues for identifying and optimizing GOAT inhibitors. We are at the beginning of a new era with increased opportunities for leveraging ghrelin and GOAT in the understanding and treatment of multiple health conditions including diabetes, obesity, and addiction.
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Affiliation(s)
- Jacob E Moose
- Department of Chemistry and BioInspired Syracuse, Syracuse University , Syracuse, NY, USA
| | - Katelyn A Leets
- Department of Chemistry and BioInspired Syracuse, Syracuse University , Syracuse, NY, USA
| | - Nilamber A Mate
- Department of Chemistry and BioInspired Syracuse, Syracuse University , Syracuse, NY, USA
| | - John D Chisholm
- Department of Chemistry and BioInspired Syracuse, Syracuse University , Syracuse, NY, USA
| | - James L Hougland
- Department of Chemistry and BioInspired Syracuse, Syracuse University , Syracuse, NY, USA
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20
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Affiliation(s)
- Matthew D. Lloyd
- Drug & Target Development, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, U.K
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21
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Chambers JM, Miller W, Quichocho G, Upadhye V, Matteo DA, Bobkov AA, Sohl CD, Schiffer JM. Water Networks and Correlated Motions in Mutant Isocitrate Dehydrogenase 1 (IDH1) Are Critical for Allosteric Inhibitor Binding and Activity. Biochemistry 2020; 59:479-490. [PMID: 31869219 DOI: 10.1021/acs.biochem.9b01023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Point mutations in human isocitrate dehydrogenase 1 (IDH1) can drive malignancies, including lower-grade gliomas and secondary glioblastomas, chondrosarcomas, and acute myeloid leukemias. These mutations, which usually affect residue R132, ablate the normal activity of catalyzing the NADP+-dependent oxidation of isocitrate to α-ketoglutarate (αKG) while also acquiring a neomorphic activity of reducing αKG to d-2-hydroxyglutarate (D2HG). Mutant IDH1 can be selectively therapeutically targeted due to structural differences that occur in the wild type (WT) versus mutant form of the enzyme, though the full mechanisms of this selectivity are still under investigation. Here we probe the mechanistic features of the neomorphic activity and selective small molecule inhibition through a new lens, employing WaterMap and molecular dynamics simulations. These tools identified a high-energy path of water molecules connecting the inhibitor binding site with the αKG and NADP+ binding sites in mutant IDH1. This water path aligns spatially with the α10 helix from WT IDH1 crystal structures. Mutating residues at the termini of this water path specifically disrupted inhibitor binding and/or D2HG production, revealing additional key residues to consider in optimizing druglike molecules against mutant IDH1. Taken together, our findings from molecular simulations and mutant enzyme kinetic assays provide insight into how disrupting water paths through enzyme active sites can impact not only inhibitor potency but also substrate recognition and activity.
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Affiliation(s)
- Jennifer M Chambers
- Schrödinger , 120 West 45th Street , New York , New York 10036 , United States
| | - Wade Miller
- Schrödinger , 222 Third Street, Suite 2230 , Cambridge , Massachusetts 02142 , United States
| | - Giovanni Quichocho
- Department of Chemistry and Biochemistry , San Diego State University , San Diego , California 92182 , United States
| | - Viraj Upadhye
- Department of Chemistry and Biochemistry , San Diego State University , San Diego , California 92182 , United States
| | - Diego Avellaneda Matteo
- Department of Chemistry and Biochemistry , San Diego State University , San Diego , California 92182 , United States
| | - Andrey A Bobkov
- Sanford Burnham Prebys Medical Discovery Institute , La Jolla , California 92037 , United States
| | - Christal D Sohl
- Department of Chemistry and Biochemistry , San Diego State University , San Diego , California 92182 , United States
| | - Jamie M Schiffer
- Janssen Research and Development , 3210 Merryfield Row , San Diego , California 92121 , United States
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22
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Pettinger J, Carter M, Jones K, Cheeseman MD. Kinetic Optimization of Lysine-Targeting Covalent Inhibitors of HSP72. J Med Chem 2019; 62:11383-11398. [PMID: 31725295 PMCID: PMC6959841 DOI: 10.1021/acs.jmedchem.9b01709] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Indexed: 12/30/2022]
Abstract
The covalent inhibition mechanism of action, which overcomes competition with high-affinity, high-abundance substrates of challenging protein targets, can deliver effective chemical probes and drugs. The success of this strategy has centered on exposed cysteine residues as nucleophiles but the low abundance of cysteine in the proteome has limited its application. We have recently reported our discovery that lysine-56 in the difficult-to-drug target HSP72 could form a covalent bond with a small-molecule inhibitor. We now disclose the optimization of these targeted covalent inhibitors using rational design. Essential to our optimization was the development of a new covalent fluorescence polarization assay, which allows for the direct measurement of the key kinetic parameter in covalent inhibitor design, kinact/KI, extrapolation of the underlying parameters, kinact and Ki, and direct comparison to reversible analogues. Using our approach, we demonstrate a >100-fold enhancement in covalent efficiency and key learnings in lysine-selective electrophile optimization.
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Affiliation(s)
- Jonathan Pettinger
- Cancer Research UK Cancer
Therapeutics Unit, The Institute of Cancer
Research, London SW7 3RP, United Kingdom
| | - Michael Carter
- Cancer Research UK Cancer
Therapeutics Unit, The Institute of Cancer
Research, London SW7 3RP, United Kingdom
| | - Keith Jones
- Cancer Research UK Cancer
Therapeutics Unit, The Institute of Cancer
Research, London SW7 3RP, United Kingdom
| | - Matthew D. Cheeseman
- Cancer Research UK Cancer
Therapeutics Unit, The Institute of Cancer
Research, London SW7 3RP, United Kingdom
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Cuartas V, Crespo MDP, Priego EM, Persoons L, Daelemans D, Camarasa MJ, Insuasty B, Pérez-Pérez MJ. Design and Synthesis of New 6-Nitro and 6-Amino-3,3a,4,5-Tetrahydro-2 H-Benzo[ g]indazole Derivatives: Antiproliferative and Antibacterial Activity. Molecules 2019; 24:molecules24234236. [PMID: 31766444 PMCID: PMC6930490 DOI: 10.3390/molecules24234236] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 11/15/2019] [Accepted: 11/19/2019] [Indexed: 11/22/2022] Open
Abstract
New substituted benzo[g]indazoles functionalized with a 6-nitro and 6-amino groups have been synthesized by the reaction of benzylidene tetralones with hydrazine in acetic acid. The resulting conformationally-constrained compounds were evaluated for their antiproliferative activity against selected cancer cell lines. The nitro-based indazoles 11a, 11b, 12a and 12b have shown IC50 values between 5–15 μM against the lung carcinoma cell line NCI-H460. Moreover, the nitro compounds were tested for antibacterial activity where compounds 12a and 13b have shown MIC values of 250 and 62.5 μg/mL against N. gonorrhoeae with no hemolytic activity in human red blood cells (RBC).
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Affiliation(s)
- Viviana Cuartas
- Grupo de Investigación de Compuestos Heterocíclicos, Departamento de Química, Universidad del Valle, A. A. Cali 25360, Colombia;
- Centre for Bioinformatics and Photonics-CIBioFI, Calle 13 No. 100-00, Edificio E20, No. 1069, Cali 760032, Colombia
| | - María del Pilar Crespo
- Grupo de Biotecnología e Infecciones Bacterianas, Departamento de Microbiología, Universidad del Valle, Cali 760043, Colombia;
| | - Eva-María Priego
- Instituto de Química Médica (IQM, CSIC), Juan de la Cierva 3, 28006 Madrid, Spain; (E.-M.P.); (M.-J.C.)
| | - Leentje Persoons
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000 Leuven, Belgium; (L.P.); (D.D.)
| | - Dirk Daelemans
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000 Leuven, Belgium; (L.P.); (D.D.)
| | - María-José Camarasa
- Instituto de Química Médica (IQM, CSIC), Juan de la Cierva 3, 28006 Madrid, Spain; (E.-M.P.); (M.-J.C.)
| | - Braulio Insuasty
- Grupo de Investigación de Compuestos Heterocíclicos, Departamento de Química, Universidad del Valle, A. A. Cali 25360, Colombia;
- Centre for Bioinformatics and Photonics-CIBioFI, Calle 13 No. 100-00, Edificio E20, No. 1069, Cali 760032, Colombia
- Correspondence: (M.-J.P.-P.); (B.I.); Tel.: +34-91-258-7516 (M.-J.P.-P.); +57-315-484-6665 (B.I.); Fax: +34-91-5644853 (M.-J.P.-P.); +57-2339-3248 (B.I.)
| | - María-Jesús Pérez-Pérez
- Instituto de Química Médica (IQM, CSIC), Juan de la Cierva 3, 28006 Madrid, Spain; (E.-M.P.); (M.-J.C.)
- Correspondence: (M.-J.P.-P.); (B.I.); Tel.: +34-91-258-7516 (M.-J.P.-P.); +57-315-484-6665 (B.I.); Fax: +34-91-5644853 (M.-J.P.-P.); +57-2339-3248 (B.I.)
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Recent Advances in Selective and Irreversible Covalent Ligand Development and Validation. Cell Chem Biol 2019; 26:1486-1500. [PMID: 31631011 DOI: 10.1016/j.chembiol.2019.09.012] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 08/06/2019] [Accepted: 09/26/2019] [Indexed: 12/20/2022]
Abstract
Some of the most widely used drugs, such as aspirin and penicillin, are covalent drugs. Covalent binding can improve potency, selectivity, and duration of the effects, but the intrinsic reactivity represents a potential liability and may result in idiosyncratic toxicity. For decades, the cons were believed to outweigh the pros, and covalent targeting was deprioritized in drug discovery. Recently, several covalent inhibitors have been approved for cancer treatment, thus rebooting the field. In this review, we briefly reflect on the history of selective covalent targeting, and provide a comprehensive overview of emerging developments from a chemical biology stand-point. Our discussion will reflect on efforts to validate irreversible covalent ligands, expand the scope of targets, and discover new ligands and warheads. We conclude with a brief commentary of remaining limitations and emerging opportunities in selective covalent targeting.
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Ray S, Murkin AS. New Electrophiles and Strategies for Mechanism-Based and Targeted Covalent Inhibitor Design. Biochemistry 2019; 58:5234-5244. [PMID: 30990686 DOI: 10.1021/acs.biochem.9b00293] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Covalent inhibitors are experiencing a growing resurgence in drug design and are an increasingly useful tool in molecular biology. The ability to attach inhibitors to their targets by a covalent linkage offers pharmacodynamic and pharmacokinetic advantages, but this can also be a liability if undesired off-target reactions are not mitigated. The discovery of new electrophilic groups that react selectively with specific amino acid residues is therefore highly desirable in the design of targeted covalent inhibitors (TCIs). Additionally, the ability to control the reactivity through exploitation of the target enzyme's machinery, as in mechanism-based inhibitors (MBIs), greatly benefits from the discovery of new strategies. This Perspective showcases recent advances in electrophile development and their application in TCIs and MBIs, exhibiting high selectivity for their targets.
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Affiliation(s)
- Sneha Ray
- Department of Chemistry , University at Buffalo, The State University of New York , Buffalo , New York 14260-3000 , United States
| | - Andrew S Murkin
- Department of Chemistry , University at Buffalo, The State University of New York , Buffalo , New York 14260-3000 , United States
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Vasudevan A, Argiriadi MA, Baranczak A, Friedman MM, Gavrilyuk J, Hobson AD, Hulce JJ, Osman S, Wilson NS. Covalent binders in drug discovery. PROGRESS IN MEDICINAL CHEMISTRY 2019; 58:1-62. [PMID: 30879472 DOI: 10.1016/bs.pmch.2018.12.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covalent modulation of protein function can have multiple utilities including therapeutics, and probes to interrogate biology. While this field is still viewed with scepticism due to the potential for (idiosyncratic) toxicities, significant strides have been made in terms of understanding how to tune electrophilicity to selectively target specific residues. Progress has also been made in harnessing the potential of covalent binders to uncover novel biology and to provide an enhanced utility as payloads for Antibody Drug Conjugates. This perspective covers the tenets and applications of covalent binders.
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Affiliation(s)
| | | | | | | | - Julia Gavrilyuk
- AbbVie Stemcentrx, LLC, South San Francisco, CA, United States
| | | | | | - Sami Osman
- AbbVie Bioresearch Center, Worcester, MA, United States
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Gehringer M, Laufer SA. Emerging and Re-Emerging Warheads for Targeted Covalent Inhibitors: Applications in Medicinal Chemistry and Chemical Biology. J Med Chem 2019; 62:5673-5724. [PMID: 30565923 DOI: 10.1021/acs.jmedchem.8b01153] [Citation(s) in RCA: 370] [Impact Index Per Article: 74.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Targeted covalent inhibitors (TCIs) are designed to bind poorly conserved amino acids by means of reactive groups, the so-called warheads. Currently, targeting noncatalytic cysteine residues with acrylamides and other α,β-unsaturated carbonyl compounds is the predominant strategy in TCI development. The recent ascent of covalent drugs has stimulated considerable efforts to characterize alternative warheads for the covalent-reversible and irreversible engagement of noncatalytic cysteine residues as well as other amino acids. This Perspective article provides an overview of warheads-beyond α,β-unsaturated amides-recently used in the design of targeted covalent ligands. Promising reactive groups that have not yet demonstrated their utility in TCI development are also highlighted. Special emphasis is placed on the discussion of reactivity and of case studies illustrating applications in medicinal chemistry and chemical biology.
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Affiliation(s)
- Matthias Gehringer
- 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
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