1
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Tsuruno A, Kamoshita S, Hosoya S, Sakurai K. Dichlorotriazine-based multivalent probe for selective affinity labeling of carbohydrate-binding proteins. Org Biomol Chem 2024; 22:7659-7663. [PMID: 39193651 DOI: 10.1039/d4ob01285b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2024]
Abstract
A new series of multivalent gold nanoparticle probes bearing different electrophilic groups were synthesized and their affinity labeling reactivities were evaluated. The dichlorotriazine group was identified as a useful protein-reactive label, allowing selective capture of a target protein at nanomolar probe concentrations.
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Affiliation(s)
- Ayaka Tsuruno
- Tokyo University of Agriculture and Technology, Department of Biotechnology and Life Science, Koganei-shi, Tokyo 184-8588, Japan.
| | - Shione Kamoshita
- Tokyo University of Agriculture and Technology, Department of Biotechnology and Life Science, Koganei-shi, Tokyo 184-8588, Japan.
| | - Shoichi Hosoya
- Institute of Research, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Kaori Sakurai
- Tokyo University of Agriculture and Technology, Department of Biotechnology and Life Science, Koganei-shi, Tokyo 184-8588, Japan.
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2
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Pinto MF, Sirina J, Holliday ND, McWhirter CL. High-throughput kinetics in drug discovery. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100170. [PMID: 38964171 DOI: 10.1016/j.slasd.2024.100170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/21/2024] [Accepted: 06/17/2024] [Indexed: 07/06/2024]
Abstract
The importance of a drug's kinetic profile and interplay of structure-kinetic activity with PK/PD has long been appreciated in drug discovery. However, technical challenges have often limited detailed kinetic characterization of compounds to the latter stages of projects. This review highlights the advances that have been made in recent years in techniques, instrumentation, and data analysis to increase the throughput of detailed kinetic and mechanistic characterization, enabling its application earlier in the drug discovery process.
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Affiliation(s)
- Maria Filipa Pinto
- Artios Pharma Ltd, B940, Babraham Research Campus, Cambridge CB22 3FH, United Kingdom
| | - Julija Sirina
- Excellerate Bioscience Ltd, 21 The Triangle, NG2 Business Park, Nottingham, NG2 1AE, United Kingdom
| | - Nicholas D Holliday
- Excellerate Bioscience Ltd, 21 The Triangle, NG2 Business Park, Nottingham, NG2 1AE, United Kingdom; School of Life Sciences, The Medical School, University of Nottingham, Nottingham, NG7 2UH, United Kingdom
| | - Claire L McWhirter
- Artios Pharma Ltd, B940, Babraham Research Campus, Cambridge CB22 3FH, United Kingdom.
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3
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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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4
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Panina SB, Schweer JV, Zhang Q, Raina G, Hardtke HA, Kim S, Yang W, Siegel D, Zhang YJ. Targeting of REST with rationally-designed small molecule compounds exhibits synergetic therapeutic potential in human glioblastoma cells. BMC Biol 2024; 22:83. [PMID: 38609948 PMCID: PMC11015551 DOI: 10.1186/s12915-024-01879-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 04/04/2024] [Indexed: 04/14/2024] Open
Abstract
BACKGROUND Glioblastoma (GBM) is an aggressive brain cancer associated with poor prognosis, intrinsic heterogeneity, plasticity, and therapy resistance. In some GBMs, cell proliferation is fueled by a transcriptional regulator, repressor element-1 silencing transcription factor (REST). RESULTS Using CRISPR/Cas9, we identified GBM cell lines dependent on REST activity. We developed new small molecule inhibitory compounds targeting small C-terminal domain phosphatase 1 (SCP1) to reduce REST protein level and transcriptional activity in glioblastoma cells. Top leads of the series like GR-28 exhibit potent cytotoxicity, reduce REST protein level, and suppress its transcriptional activity. Upon the loss of REST protein, GBM cells can potentially compensate by rewiring fatty acid metabolism, enabling continued proliferation. Combining REST inhibition with the blockade of this compensatory adaptation using long-chain acyl-CoA synthetase inhibitor Triacsin C demonstrated substantial synergetic potential without inducing hepatotoxicity. CONCLUSIONS Our results highlight the efficacy and selectivity of targeting REST alone or in combination as a therapeutic strategy to combat high-REST GBM.
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Affiliation(s)
- Svetlana B Panina
- Department of Molecular Biosciences, The University of Texas at Austin, 2500 Speedway, Austin, TX, USA
| | - Joshua V Schweer
- Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California San Diego, 9500 Gilman Drive 0741, La Jolla, CA, USA
| | - Qian Zhang
- Department of Molecular Biosciences, The University of Texas at Austin, 2500 Speedway, Austin, TX, USA
| | - Gaurav Raina
- Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California San Diego, 9500 Gilman Drive 0741, La Jolla, CA, USA
| | - Haley A Hardtke
- Department of Molecular Biosciences, The University of Texas at Austin, 2500 Speedway, Austin, TX, USA
| | - Seungjin Kim
- Department of Molecular Biosciences, The University of Texas at Austin, 2500 Speedway, Austin, TX, USA
| | - Wanjie Yang
- Department of Molecular Biosciences, The University of Texas at Austin, 2500 Speedway, Austin, TX, USA
| | - Dionicio Siegel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California San Diego, 9500 Gilman Drive 0741, La Jolla, CA, USA
| | - Y Jessie Zhang
- Department of Molecular Biosciences, The University of Texas at Austin, 2500 Speedway, Austin, TX, USA.
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5
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Ambrose AJ, Zerio CJ, Sivinski J, Zhu X, Godek J, Sanchez JL, Khanna M, Khanna R, Lairson L, Zhang DD, Chapman E. Human Hsp70 Substrate-Binding Domains Recognize Distinct Client Proteins. Biochemistry 2024; 63:251-263. [PMID: 38243804 DOI: 10.1021/acs.biochem.3c00531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2024]
Abstract
The 13 Hsp70 proteins in humans act on unique sets of substrates with diversity often being attributed to J-domain-containing protein (Hsp40 or JDP) cofactors. We were therefore surprised to find drastically different binding affinities for Hsp70-peptide substrates, leading us to probe substrate specificity among the 8 canonical Hsp70s from humans. We used peptide arrays to characterize Hsp70 binding and then mined these data using machine learning to develop an algorithm for isoform-specific prediction of Hsp70 binding sequences. The results of this algorithm revealed recognition patterns not predicted based on local sequence alignments. We then showed that none of the human isoforms can complement heat-shocked DnaK knockout Escherichia coli cells. However, chimeric Hsp70s consisting of the human nucleotide-binding domain and the substrate-binding domain of DnaK complement during heat shock, providing further evidence in vivo of the divergent function of the Hsp70 substrate-binding domains. We also demonstrated that the differences in heat shock complementation among the chimeras are not due to loss of DnaJ binding. Although we do not exclude JDPs as additional specificity factors, our data demonstrate substrate specificity among the Hsp70s, which has important implications for inhibitor development in cancer and neurodegeneration.
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Affiliation(s)
- Andrew J Ambrose
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, United States
| | - Christopher J Zerio
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, United States
| | - Jared Sivinski
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, United States
| | - Xiaoyi Zhu
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, United States
| | - Jack Godek
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, United States
| | - Jonathan L Sanchez
- Department of Pharmacology, College of Medicine, The University of Arizona Health Sciences, Tucson, Arizona 85424, United States
| | - May Khanna
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, New York 10010, United States
| | - Rajesh Khanna
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, New York 10010, United States
| | - Luke Lairson
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Donna D Zhang
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, United States
| | - Eli Chapman
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721, United States
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6
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Liashuk OS, Andriashvili VA, Tolmachev AO, Grygorenko OO. Chemoselective Reactions of Functionalized Sulfonyl Halides. CHEM REC 2024; 24:e202300256. [PMID: 37823680 DOI: 10.1002/tcr.202300256] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/13/2023] [Indexed: 10/13/2023]
Abstract
Chemoselective transformations of functionalized sulfonyl fluorides and chlorides are surveyed comprehensively. It is shown that sulfonyl fluorides provide an excellent selectivity control in their reactions. Thus, numerous conditions are tolerated by the SO2 F group - from amide and ester formation to directed ortho-lithiation and transition-metal-catalyzed cross-couplings. Meanwhile, sulfur (VI) fluoride exchange (SuFEx) is also compatible with numerous functional groups, thus confirming its title of "another click reaction". On the contrary, with a few exceptions, most transformations of functionalized sulfonyl chlorides typically occur at the SO2 Cl moiety.
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Affiliation(s)
- Oleksandr S Liashuk
- Enamine Ltd. (www.enamine.net), Winston Churchill Street 78, Kyїv, 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyїv, 01601, Ukraine
| | - Vladyslav A Andriashvili
- Enamine Ltd. (www.enamine.net), Winston Churchill Street 78, Kyїv, 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyїv, 01601, Ukraine
| | - Andriy O Tolmachev
- Enamine Ltd. (www.enamine.net), Winston Churchill Street 78, Kyїv, 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyїv, 01601, Ukraine
| | - Oleksandr O Grygorenko
- Enamine Ltd. (www.enamine.net), Winston Churchill Street 78, Kyїv, 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyїv, 01601, Ukraine
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7
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Taylor KI, Ho JS, Trial HO, Carter AW, Kiessling LL. Assessing Squarates as Amine-Reactive Probes. J Am Chem Soc 2023; 145:25056-25060. [PMID: 37938802 PMCID: PMC10935565 DOI: 10.1021/jacs.2c05691] [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: 11/10/2023]
Abstract
Probes that covalently label protein targets facilitate the identification of ligand-binding sites. Lysine residues are prevalent in the proteome, making them attractive substrates for covalent probes. However, identifying electrophiles that undergo amine-specific, regioselective reactions with binding site lysine residues is challenging. Squarates can engage in two sequential conjugate addition-elimination reactions with amines. Nitrogen donation reduces the second reaction rate, making the mono squaramide a mild electrophile. We postulated that this mild electrophilicity would demand a longer residence time near the amine, affording higher selectivity for binding site lysines. Therefore, we compared the kinetics of squarate and monosquaramide amine substitution to alternative amine bioconjugation handles. The data revealed that N-hydroxy succinimidyl esters react 4 orders of magnitude faster, consistent with their labeling promiscuity. Squarate reactivity can be tuned by a substitution pattern. Electron-withdrawing groups on the vinylogous ester or amide increase reaction rates. Dithionosquarates react more rapidly than squarates, while vinylogous thioester analogs, dithiosquarates, react more slowly. We assessed squarate selectively using the UDP-sugar processing enzyme GlfT2 from Mycobacterium tuberculosis, which possesses 21 surface-exposed lysines. The reaction predominately modified one lysine proximal to a binding site to afford covalent inhibition. These findings demonstrate the selectivity of squaric esters and squaramides, which is a critical feature for affinity-based chemoproteomic probes.
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Affiliation(s)
- Katherine I. Taylor
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, United States
| | - Jordan S. Ho
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, United States
| | - Hallie O. Trial
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, United States
| | - Alan W. Carter
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, United States
| | - Laura L. Kiessling
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, United States
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8
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Ramachandran S, Makukhin N, Haubrich K, Nagala M, Forrester B, Lynch DM, Casement R, Testa A, Bruno E, Gitto R, Ciulli A. Structure-based design of a phosphotyrosine-masked covalent ligand targeting the E3 ligase SOCS2. Nat Commun 2023; 14:6345. [PMID: 37816714 PMCID: PMC10564737 DOI: 10.1038/s41467-023-41894-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 09/14/2023] [Indexed: 10/12/2023] Open
Abstract
The Src homology 2 (SH2) domain recognizes phosphotyrosine (pY) post translational modifications in partner proteins to trigger downstream signaling. Drug discovery efforts targeting the SH2 domains have long been stymied by the poor drug-like properties of phosphate and its mimetics. Here, we use structure-based design to target the SH2 domain of the E3 ligase suppressor of cytokine signaling 2 (SOCS2). Starting from the highly ligand-efficient pY amino acid, a fragment growing approach reveals covalent modification of Cys111 in a co-crystal structure, which we leverage to rationally design a cysteine-directed electrophilic covalent inhibitor MN551. We report the prodrug MN714 containing a pivaloyloxymethyl (POM) protecting group and evidence its cell permeability and capping group unmasking using cellular target engagement and in-cell 19F NMR spectroscopy. Covalent engagement at Cys111 competitively blocks recruitment of cellular SOCS2 protein to its native substrate. The qualified inhibitors of SOCS2 could find attractive applications as chemical probes to understand the biology of SOCS2 and its CRL5 complex, and as E3 ligase handles in proteolysis targeting chimera (PROTACs) to induce targeted protein degradation.
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Affiliation(s)
- Sarath Ramachandran
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee, DD1 5JJ, United Kingdom
| | - Nikolai Makukhin
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee, DD1 5JJ, United Kingdom
- Amphista Therapeutics Ltd, Cory Building, Granta Park, Great Abington, Cambridge, CB21 6GQ, United Kingdom
| | - Kevin Haubrich
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee, DD1 5JJ, United Kingdom
| | - Manjula Nagala
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee, DD1 5JJ, United Kingdom
| | - Beth Forrester
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee, DD1 5JJ, United Kingdom
| | - Dylan M Lynch
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee, DD1 5JJ, United Kingdom
| | - Ryan Casement
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee, DD1 5JJ, United Kingdom
| | - Andrea Testa
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee, DD1 5JJ, United Kingdom
- Amphista Therapeutics Ltd, Cory Building, Granta Park, Great Abington, Cambridge, CB21 6GQ, United Kingdom
| | - Elvira Bruno
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee, DD1 5JJ, United Kingdom
| | - Rosaria Gitto
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, Viale Stagno D'Alcontres 31, Pole Papardo, 98166, Messina, Italy
| | - Alessio Ciulli
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee, DD1 5JJ, United Kingdom.
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9
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Aatkar A, Vuorinen A, Longfield OE, Gilbert K, Peltier-Heap R, Wagner CD, Zappacosta F, Rittinger K, Chung CW, House D, Tomkinson NCO, Bush JT. Efficient Ligand Discovery Using Sulfur(VI) Fluoride Reactive Fragments. ACS Chem Biol 2023; 18:1926-1937. [PMID: 37084287 PMCID: PMC10510102 DOI: 10.1021/acschembio.3c00034] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 04/03/2023] [Indexed: 04/23/2023]
Abstract
Sulfur(VI) fluorides (SFs) have emerged as valuable electrophiles for the design of "beyond-cysteine" covalent inhibitors and offer potential for expansion of the liganded proteome. Since SFs target a broad range of nucleophilic amino acids, they deliver an approach for the covalent modification of proteins without requirement for a proximal cysteine residue. Further to this, libraries of reactive fragments present an innovative approach for the discovery of ligands and tools for proteins of interest by leveraging a breadth of mass spectrometry analytical approaches. Herein, we report a screening approach that exploits the unique properties of SFs for this purpose. Libraries of SF-containing reactive fragments were synthesized, and a direct-to-biology workflow was taken to efficiently identify hit compounds for CAII and BCL6. The most promising hits were further characterized to establish the site(s) of covalent modification, modification kinetics, and target engagement in cells. Crystallography was used to gain a detailed molecular understanding of how these reactive fragments bind to their target. It is anticipated that this screening protocol can be used for the accelerated discovery of "beyond-cysteine" covalent inhibitors.
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Affiliation(s)
- Arron Aatkar
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K.
- Department
of Pure and Applied Chemistry, University
of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, U.K.
| | - Aini Vuorinen
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K.
- The
Francis Crick Institute, London NW1 1AT, U.K.
| | - Oliver E. Longfield
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K.
- Department
of Pure and Applied Chemistry, University
of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, U.K.
| | - Katharine Gilbert
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K.
- Department
of Pure and Applied Chemistry, University
of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, U.K.
| | - Rachel Peltier-Heap
- GSK, South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Craig D. Wagner
- GSK, South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | | | | | - Chun-wa Chung
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K.
| | - David House
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K.
- The
Francis Crick Institute, London NW1 1AT, U.K.
| | - Nicholas C. O. Tomkinson
- Department
of Pure and Applied Chemistry, University
of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, U.K.
| | - Jacob T. Bush
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K.
- The
Francis Crick Institute, London NW1 1AT, U.K.
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10
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Zhu L, Chang X, Zhang S, Bai X, Finko AV, Xu X, Bian J, Liu X, Huang H. Enhancing the affinity of novel GLS1 allosteric inhibitors by targeting key residue Lys320. Future Med Chem 2023; 15:1393-1414. [PMID: 37610850 DOI: 10.4155/fmc-2023-0114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/25/2023] Open
Abstract
Aim: A series of novel GLS1 irreversible allosteric inhibitors targeting Lys320 might have robust enzyme inhibitory activity and potent antitumor activity. Materials & methods: Novel GLS1 allosteric inhibitors targeting Lys320 were synthesized and their anticancer activity was assessed. Moreover, GLS1 protein was used as a model system to analyze the reactivity of these electrophilic groups in GLS1 irreversible allosteric inhibitors with other amino acids, including tyrosine, histidine, serine and threonine, using biochemical and biophysical assays. Results: AC16 exhibited robust GLS1 inhibitory activity, antiproliferative effect in vitro, good plasma stability and potential covalent addition with GLS1 K320. Conclusion: This study opens a novel avenue for the design of robust irreversible GLS1 inhibitors targeting the allosteric site K320.
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Affiliation(s)
- Li Zhu
- Center of Drug Screening & Evaluation, Wannan Medical College, Wuhu, Anhui, 241000, PR China
| | - Xiujin Chang
- Center of Drug Screening & Evaluation, Wannan Medical College, Wuhu, Anhui, 241000, PR China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, PR China
| | - Shengpeng Zhang
- Center of Drug Screening & Evaluation, Wannan Medical College, Wuhu, Anhui, 241000, PR China
| | - Xiumei Bai
- Department of Chemistry, Lomonosov Moscow State University (MSU), Moscow, 119991, Russia
| | - Alexander V Finko
- Department of Chemistry, Lomonosov Moscow State University (MSU), Moscow, 119991, Russia
| | - Xi Xu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, PR China
| | - Jinlei Bian
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, PR China
| | - Xiaoping Liu
- Center of Drug Screening & Evaluation, Wannan Medical College, Wuhu, Anhui, 241000, PR China
| | - Huidan Huang
- Center of Drug Screening & Evaluation, Wannan Medical College, Wuhu, Anhui, 241000, PR China
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11
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Darabedian N, Ji W, Fan M, Lin S, Seo HS, Vinogradova EV, Yaron TM, Mills EL, Xiao H, Senkane K, Huntsman EM, Johnson JL, Che J, Cantley LC, Cravatt BF, Dhe-Paganon S, Stegmaier K, Zhang T, Gray NS, Chouchani ET. Depletion of creatine phosphagen energetics with a covalent creatine kinase inhibitor. Nat Chem Biol 2023; 19:815-824. [PMID: 36823351 PMCID: PMC10330000 DOI: 10.1038/s41589-023-01273-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 01/30/2023] [Indexed: 02/25/2023]
Abstract
Creatine kinases (CKs) provide local ATP production in periods of elevated energetic demand, such as during rapid anabolism and growth. Thus, creatine energetics has emerged as a major metabolic liability in many rapidly proliferating cancers. Whether CKs can be targeted therapeutically is unknown because no potent or selective CK inhibitors have been developed. Here we leverage an active site cysteine present in all CK isoforms to develop a selective covalent inhibitor of creatine phosphagen energetics, CKi. Using deep chemoproteomics, we discover that CKi selectively engages the active site cysteine of CKs in cells. A co-crystal structure of CKi with creatine kinase B indicates active site inhibition that prevents bidirectional phosphotransfer. In cells, CKi and its analogs rapidly and selectively deplete creatine phosphate, and drive toxicity selectively in CK-dependent acute myeloid leukemia. Finally, we use CKi to uncover an essential role for CKs in the regulation of proinflammatory cytokine production in macrophages.
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Affiliation(s)
- Narek Darabedian
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Wenzhi Ji
- Department of Chemical and Systems Biology, CHEM-H and SCI, Stanford Medical School, Stanford University, Stanford, CA, USA
| | - Mengyang Fan
- Department of Chemical and Systems Biology, CHEM-H and SCI, Stanford Medical School, Stanford University, Stanford, CA, USA
| | - Shan Lin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Hyuk-Soo Seo
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Ekaterina V Vinogradova
- Laboratory of Chemical Immunology and Proteomics, The Rockefeller University, New York, NY, USA
| | - Tomer M Yaron
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Evanna L Mills
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Immunology, Harvard Medical School, Boston, MA, USA
| | - Haopeng Xiao
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Kristine Senkane
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Emily M Huntsman
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Jared L Johnson
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Jianwei Che
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Lewis C Cantley
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Benjamin F Cravatt
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Sirano Dhe-Paganon
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Tinghu Zhang
- Department of Chemical and Systems Biology, CHEM-H and SCI, Stanford Medical School, Stanford University, Stanford, CA, USA
| | - Nathanael S Gray
- Department of Chemical and Systems Biology, CHEM-H and SCI, Stanford Medical School, Stanford University, Stanford, CA, USA.
| | - Edward T Chouchani
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
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12
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Huang H, Jones LH. Covalent drug discovery using sulfur(VI) fluoride exchange warheads. Expert Opin Drug Discov 2023:1-11. [PMID: 37243622 DOI: 10.1080/17460441.2023.2218642] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 05/23/2023] [Indexed: 05/29/2023]
Abstract
INTRODUCTION Covalent drug discovery has traditionally focused on targeting cysteine, but the amino acid is often absent in protein binding sites. This review makes the case to move beyond cysteine labeling using sulfur (VI) fluoride exchange (SuFEx) chemistry to expand the druggable proteome. AREAS COVERED Recent advances in SuFEx medicinal chemistry and chemical biology are described, which have enabled the development of covalent chemical probes that site-selectively engage amino acid residues (including tyrosine, lysine, histidine, serine, and threonine) in binding pockets. Areas covered include chemoproteomic mapping of the targetable proteome, structure-based design of covalent inhibitors and molecular glues, metabolic stability profiling, and synthetic methodologies that have expedited the delivery of SuFEx modulators. EXPERT OPINION Despite recent innovations in SuFEx medicinal chemistry, focused preclinical research is required to ensure the field moves from early chemical probe discovery to the delivery of transformational covalent drug candidates. The authors believe that covalent drug candidates designed to engage residues beyond cysteine using sulfonyl exchange warheads will likely enter clinical trials in the coming years.
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Affiliation(s)
- Huang Huang
- Center for Protein Degradation, Dana-Farber Cancer Institute, 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, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
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13
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Gilbert K, Vuorinen A, Aatkar A, Pogány P, Pettinger J, Grant EK, Kirkpatrick JM, Rittinger K, House D, Burley GA, Bush JT. Profiling Sulfur(VI) Fluorides as Reactive Functionalities for Chemical Biology Tools and Expansion of the Ligandable Proteome. ACS Chem Biol 2023; 18:285-295. [PMID: 36649130 PMCID: PMC9942091 DOI: 10.1021/acschembio.2c00633] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 01/05/2023] [Indexed: 01/18/2023]
Abstract
Here, we report a comprehensive profiling of sulfur(VI) fluorides (SVI-Fs) as reactive groups for chemical biology applications. SVI-Fs are reactive functionalities that modify lysine, tyrosine, histidine, and serine sidechains. A panel of SVI-Fs were studied with respect to hydrolytic stability and reactivity with nucleophilic amino acid sidechains. The use of SVI-Fs to covalently modify carbonic anhydrase II (CAII) and a range of kinases was then investigated. Finally, the SVI-F panel was used in live cell chemoproteomic workflows, identifying novel protein targets based on the type of SVI-F used. This work highlights how SVI-F reactivity can be used as a tool to expand the liganded proteome.
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Affiliation(s)
- Katharine
E. Gilbert
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, HertfordshireSG1 2NY, United Kingdom
- University
of Strathclyde, 295 Cathedral Street, GlasgowG11XL, United Kingdom
| | - Aini Vuorinen
- Crick-GSK
Biomedical LinkLabs, GlaxoSmithKline, Gunnels Wood Road, StevenageSG1 2NY, United Kingdom
| | - Arron Aatkar
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, HertfordshireSG1 2NY, United Kingdom
- University
of Strathclyde, 295 Cathedral Street, GlasgowG11XL, United Kingdom
| | - Peter Pogány
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, HertfordshireSG1 2NY, United Kingdom
| | - Jonathan Pettinger
- Crick-GSK
Biomedical LinkLabs, GlaxoSmithKline, Gunnels Wood Road, StevenageSG1 2NY, United Kingdom
| | - Emma K. Grant
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, HertfordshireSG1 2NY, United Kingdom
| | | | - Katrin Rittinger
- The
Francis Crick Institute, 1 Midland Road, LondonNW1 1AT, United Kingdom
| | - David House
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, HertfordshireSG1 2NY, United Kingdom
- Crick-GSK
Biomedical LinkLabs, GlaxoSmithKline, Gunnels Wood Road, StevenageSG1 2NY, United Kingdom
| | - Glenn A. Burley
- University
of Strathclyde, 295 Cathedral Street, GlasgowG11XL, United Kingdom
| | - Jacob T. Bush
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, HertfordshireSG1 2NY, United Kingdom
- Crick-GSK
Biomedical LinkLabs, GlaxoSmithKline, Gunnels Wood Road, StevenageSG1 2NY, United Kingdom
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14
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Rangaswamy AMM, Beh MHR, Soleimani E, Sequeira S, Cormier J, Robertson KN, Jakeman DL. Synthesis of 5'-Thymidine-Conjugated Formylphenylboronic Acids as Potential Lysine Targeting Iminoboronate Reversible Covalent Enzyme Probes. J Org Chem 2022; 87:13542-13555. [PMID: 36265169 DOI: 10.1021/acs.joc.2c01000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The design of reversible-covalent molecules to selectively target the ε-amino functionality of lysine residues in enzymes or proteins is a highly desirable goal. Herein, we describe synthetic methodology used to prepare a series of 5'-thymidine-linked formylphenylboronic acids as probes to interrogate sugar nucleotide processing enzymes that recognize thymidine. The first synthetic strategy mitigated the need for protecting group manipulations of thymidine by capitalizing upon the straightforward preparation, isolation, and reactivity of 5'-azidothymidine. An alkyne cycloaddition partner was installed through either a propargyl or ethynyl phenyl ketone derived boronic acid. The second strategy directly linked formylphenylboronic acids to 5-thymidine through an ether linkage installed using Mitsunobu conditions with 3'-O,3-dibenzoylthymidine. Iminoboronate formation was observed with a selected probe.
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Affiliation(s)
| | | | - Ebrahim Soleimani
- Department of Chemistry, Razi University, Kermanshah, 67149-67346, Iran
| | | | | | - Katherine N Robertson
- Department of Chemistry, Saint Mary's University, 923 Robie Street, Halifax, Nova Scotia B3H 3C3, Canada
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15
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Jia Y, Kim RQ, Kooij R, Ovaa H, Sapmaz A, Geurink PP. Chemical Toolkit for PARK7: Potent, Selective, and High-Throughput. J Med Chem 2022; 65:13288-13304. [PMID: 36149939 PMCID: PMC9574860 DOI: 10.1021/acs.jmedchem.2c01113] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The multifunctional human Parkinson's disease protein 7 (PARK7/DJ1) is an attractive therapeutic target due to its link with early-onset Parkinson's disease, upregulation in various cancers, and contribution to chemoresistance. However, only a few compounds have been identified to bind PARK7 due to the lack of a dedicated chemical toolbox. We report the creation of such a toolbox and showcase the application of each of its components. The selective PARK7 submicromolar inhibitor with a cyanimide reactive group covalently modifies the active site Cys106. Installment of different dyes onto the inhibitor delivered two PARK7 probes. The Rhodamine110 probe provides a high-throughput screening compatible FP assay, showcased by screening a compound library (8000 molecules). The SulfoCy5-equipped probe is a valuable tool to assess the effect of PARK7 inhibitors in a cell lysate. Our work creates new possibilities to explore PARK7 function in a physiologically relevant setting and develop new and improved PARK7 inhibitors.
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Affiliation(s)
- Yuqing Jia
- Oncode Institute & Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, The Netherlands
| | - Robbert Q Kim
- Oncode Institute & Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, The Netherlands
| | - Raymond Kooij
- Oncode Institute & Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, The Netherlands
| | - Huib Ovaa
- Oncode Institute & Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, The Netherlands
| | - Aysegul Sapmaz
- Oncode Institute & Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, The Netherlands
| | - Paul P Geurink
- Oncode Institute & Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, The Netherlands
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16
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Sun H, Xi M, Jin Q, Zhu Z, Zhang Y, Jia G, Zhu G, Sun M, Zhang H, Ren X, Zhang Y, Xu Z, Huang H, Shen J, Li B, Ge G, Chen K, Zhu W. Chemo- and Site-Selective Lysine Modification of Peptides and Proteins under Native Conditions Using the Water-Soluble Zolinium. J Med Chem 2022; 65:11840-11853. [DOI: 10.1021/acs.jmedchem.2c00937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Haiguo Sun
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Mengyu Xi
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Qiang Jin
- Shanghai Frontiers Science Center of TCM Chemical Biology; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Zhengdan Zhu
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Yani Zhang
- Shanghai Frontiers Science Center of TCM Chemical Biology; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Guihua Jia
- Shanghai Frontiers Science Center of TCM Chemical Biology; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Guanghao Zhu
- Shanghai Frontiers Science Center of TCM Chemical Biology; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Mengru Sun
- Shanghai Frontiers Science Center of TCM Chemical Biology; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Hongwei Zhang
- Shanghai Frontiers Science Center of TCM Chemical Biology; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Xuelian Ren
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Yong Zhang
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Zhijian Xu
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - He Huang
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Jingshan Shen
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Bo Li
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, No. 38 Xue Yuan Road, Haidian District, Beijing 100191, China
| | - Guangbo Ge
- Shanghai Frontiers Science Center of TCM Chemical Biology; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Kaixian Chen
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- Shanghai Frontiers Science Center of TCM Chemical Biology; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Weiliang Zhu
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- Shanghai Frontiers Science Center of TCM Chemical Biology; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
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17
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Zhu J, Qi G, Kuang Y, Zhao Y, Sun X, Zhu C, Hao X, Han Z. Identification of 9H-purin-6-amine derivatives as novel aldose reductase inhibitors for the treatment of diabetic complications. Arch Pharm (Weinheim) 2022; 355:e2200043. [PMID: 35466439 DOI: 10.1002/ardp.202200043] [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: 01/26/2022] [Revised: 03/29/2022] [Accepted: 03/31/2022] [Indexed: 11/09/2022]
Abstract
A series of 9H-purin-6-amine derivatives as aldose reductase (ALR) inhibitors were designed and synthesized. Most of these derivatives, having a C6-substituted benzylamine side chain and N9 carboxylic acid on the core structure, were found to be potent and selective ALR inhibitors, with submicromolar IC50 values against ALR2. Particularly, compound 4e was the most active with an IC50 value of 0.038 μM, and it was also proved to be endowed with excellent inhibitory selectivity. The structure-activity relationship and molecular docking studies highlighted the importance of the carboxylic acid head group along with different halogen substituents on the C6 benzylamine side chain of the 9H-purin-6-amine scaffold for the construction of strong and selective ALR inhibitors.
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Affiliation(s)
- Junkai Zhu
- Faculty of Chemistry and Chemical Engineering, Yancheng Institute of Technology, Yancheng, China
| | - Gang Qi
- Faculty of Chemistry and Chemical Engineering, Yancheng Institute of Technology, Yancheng, China
| | - Yan Kuang
- Faculty of Chemistry and Chemical Engineering, Yancheng Institute of Technology, Yancheng, China
| | - Yating Zhao
- Faculty of Chemistry and Chemical Engineering, Yancheng Institute of Technology, Yancheng, China
| | - Xinjie Sun
- Faculty of Chemistry and Chemical Engineering, Yancheng Institute of Technology, Yancheng, China
| | - Changjin Zhu
- Department of Applied Chemistry, Beijing Institute of Technology, Beijing, China
| | - Xin Hao
- Faculty of Chemistry and Chemical Engineering, Yancheng Institute of Technology, Yancheng, China
| | - Zhongfei Han
- Faculty of Chemistry and Chemical Engineering, Yancheng Institute of Technology, Yancheng, China.,Department of Applied Chemistry, Beijing Institute of Technology, Beijing, China
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18
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Liu L, Zhu R, Li J, Pei Y, Wang S, Xu P, Wang M, Wen Y, Zhang H, Du D, Ding H, Jiang H, Chen K, Zhou B, Yu L, Luo C. Computational and Structure-Based Development of High Potent Cell-Active Covalent Inhibitor Targeting the Peptidyl-Prolyl Isomerase NIMA-Interacting-1 (Pin1). J Med Chem 2022; 65:2174-2190. [PMID: 35089030 DOI: 10.1021/acs.jmedchem.1c01686] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The unique proline isomerase peptidyl-prolyl isomerase NIMA-interacting-1 (Pin1) is reported to activate numerous cancer-driving pathways simultaneously, and aberrant Pin1 activation is present in many human cancers. Here, we identified a novel hit compound, ZL-Pin01, that covalently modified Pin1 at Cys113 with an half-maximal inhibitory concentration (IC50) of 1.33 ± 0.07 μM through screening an in-house library. Crystallographic study drove the process of structure-guided optimization and led to the potent inhibitor ZL-Pin13 with an IC50 of 0.067 ± 0.03 μM. We obtained four co-crystal structures of Pin1 complexed with inhibitors that elucidated the detailed binding mode of the derivatives with Pin1. Interestingly, the co-crystal of Pin1 with ZL-Pin13 obtained by co-crystallization revealed the conformational change of Gln129 induced by the inhibitor. Furthermore, ZL-Pin13 effectively inhibited the proliferation and downregulated the Pin1 substrates in MDA-MB-231 cells. Collectively, we developed a potent covalent inhibitor of Pin1, ZL-Pin13, which could be an effective probe for studying the functional roles of Pin1.
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Affiliation(s)
- Liping Liu
- Drug Discovery and Design Center, The Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Rui Zhu
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China
| | - Jiacheng Li
- Drug Discovery and Design Center, The Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Yuan Pei
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China.,Department of Medicinal Chemistry, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Shuangshuang Wang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China
| | - Pan Xu
- Drug Discovery and Design Center, The Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Mingyu Wang
- Drug Discovery and Design Center, The Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Yu Wen
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China
| | - Hao Zhang
- Drug Discovery and Design Center, The Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Daohai Du
- Drug Discovery and Design Center, The Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Hong Ding
- Drug Discovery and Design Center, The Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Hualiang Jiang
- Drug Discovery and Design Center, The Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Kaixian Chen
- Drug Discovery and Design Center, The Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China.,Open Studio for Druggability Research of Marine Natural Products, Pilot National Laboratory for Marine Science and Technology (Qingdao), 1 Wenhai Road, Aoshanwei, Jimo, Qingdao 266237, China
| | - Bing Zhou
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China.,Department of Medicinal Chemistry, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Lifang Yu
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China
| | - Cheng Luo
- Drug Discovery and Design Center, The Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China.,School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China
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19
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O’Connor S, Le Bihan YV, Westwood IM, Liu M, Mak OW, Zazeri G, Povinelli APR, Jones AM, van Montfort R, Reynisson J, Collins I. Discovery and Characterization of a Cryptic Secondary Binding Site in the Molecular Chaperone HSP70. Molecules 2022; 27:817. [PMID: 35164081 PMCID: PMC8839746 DOI: 10.3390/molecules27030817] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/19/2022] [Accepted: 01/24/2022] [Indexed: 12/23/2022] Open
Abstract
Heat Shock Protein 70s (HSP70s) are key molecular chaperones that are overexpressed in many cancers and often associated with metastasis and poor prognosis. It has proven difficult to develop ATP-competitive, drug-like small molecule inhibitors of HSP70s due to the flexible and hydrophilic nature of the HSP70 ATP-binding site and its high affinity for endogenous nucleotides. The aim of this study was to explore the potential for the inhibition of HSP70 through alternative binding sites using fragment-based approaches. A surface plasmon resonance (SPR) fragment screen designed to detect secondary binding sites in HSP70 led to the identification by X-ray crystallography of a cryptic binding site in the nucleotide-binding domain (NBD) of HSP70 adjacent to the ATP-binding site. Fragment binding was confirmed and characterized as ATP-competitive using SPR and ligand-observed NMR methods. Molecular dynamics simulations were applied to understand the interactions with the protein upon ligand binding, and local secondary structure changes consistent with interconversion between the observed crystal structures with and without the cryptic pocket were detected. A virtual high-throughput screen (vHTS) against the cryptic pocket was conducted, and five compounds with diverse chemical scaffolds were confirmed to bind to HSP70 with micromolar affinity by SPR. These results identified and characterized a new targetable site on HSP70. While targeting HSP70 remains challenging, the new site may provide opportunities to develop allosteric ATP-competitive inhibitors with differentiated physicochemical properties from current series.
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Affiliation(s)
- Suzanne O’Connor
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SM2 5NG, UK; (S.O.); (Y.-V.L.B.); (I.M.W.); (M.L.); (R.v.M.)
| | - Yann-Vaï Le Bihan
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SM2 5NG, UK; (S.O.); (Y.-V.L.B.); (I.M.W.); (M.L.); (R.v.M.)
| | - Isaac M. Westwood
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SM2 5NG, UK; (S.O.); (Y.-V.L.B.); (I.M.W.); (M.L.); (R.v.M.)
| | - Manjuan Liu
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SM2 5NG, UK; (S.O.); (Y.-V.L.B.); (I.M.W.); (M.L.); (R.v.M.)
| | - Oi Wei Mak
- School of Pharmacy and Bioengineering, Keele University, Keele ST5 5BG, UK; (O.W.M.); (J.R.)
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Gabriel Zazeri
- School of Pharmacy, Institute of Clinical Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK; (G.Z.); (A.P.R.P.); (A.M.J.)
- Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas (IBILCE), UNESP, Rua Cristovão Colombo 2265, São José do Rio Preto 15054-000, Brazil
| | - Ana P. R. Povinelli
- School of Pharmacy, Institute of Clinical Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK; (G.Z.); (A.P.R.P.); (A.M.J.)
- Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas (IBILCE), UNESP, Rua Cristovão Colombo 2265, São José do Rio Preto 15054-000, Brazil
| | - Alan M. Jones
- School of Pharmacy, Institute of Clinical Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK; (G.Z.); (A.P.R.P.); (A.M.J.)
| | - Rob van Montfort
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SM2 5NG, UK; (S.O.); (Y.-V.L.B.); (I.M.W.); (M.L.); (R.v.M.)
| | - Jóhannes Reynisson
- School of Pharmacy and Bioengineering, Keele University, Keele ST5 5BG, UK; (O.W.M.); (J.R.)
| | - Ian Collins
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SM2 5NG, UK; (S.O.); (Y.-V.L.B.); (I.M.W.); (M.L.); (R.v.M.)
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20
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Kaiser A, Agostinelli E. Hypusinated EIF5A as a feasible drug target for Advanced Medicinal Therapies in the treatment of pathogenic parasites and therapy-resistant tumors. Amino Acids 2022; 54:501-511. [DOI: 10.1007/s00726-021-03120-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 12/21/2021] [Indexed: 11/30/2022]
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21
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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: 27] [Impact Index Per Article: 9.0] [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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22
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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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23
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Xu S, Cui S. SuFExable Isocyanides for Ugi Reaction: Synthesis of Sulfonyl Fluoro Peptides. Org Lett 2021; 23:5197-5202. [PMID: 34157840 DOI: 10.1021/acs.orglett.1c01734] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Herein, the sulfonyl fluoro isocyanides were first developed as a new type of SuFExable synthon, and they are used as building blocks in the Ugi reaction (U-4CR). The Ugi reaction was established and the substrate scope was investigated, and various sulfonyl fluoro α-amino amides and peptides could be reached in a one-step synthesis. Therefore, this protocol opens a new vision for SuFExable building blocks and click chemistry, and it also provides a distinct approach to sulfonyl fluoro peptides.
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Affiliation(s)
- Shuheng Xu
- Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Sunliang Cui
- Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
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24
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Cossar PJ, Wolter M, van Dijck L, Valenti D, Levy LM, Ottmann C, Brunsveld L. Reversible Covalent Imine-Tethering for Selective Stabilization of 14-3-3 Hub Protein Interactions. J Am Chem Soc 2021; 143:8454-8464. [PMID: 34047554 PMCID: PMC8193639 DOI: 10.1021/jacs.1c03035] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
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The stabilization
of protein complexes has emerged as a promising
modality, expanding the number of entry points for novel therapeutic
intervention. Targeting proteins that mediate protein–protein
interactions (PPIs), such as hub proteins, is equally challenging
and rewarding as they offer an intervention platform for a variety
of diseases, due to their large interactome. 14-3-3 hub proteins bind
phosphorylated motifs of their interaction partners in a conserved
binding channel. The 14-3-3 PPI interface is consequently only diversified
by its different interaction partners. Therefore, it is essential
to consider, additionally to the potency, also the selectivity of
stabilizer molecules. Targeting a lysine residue at the interface
of the composite 14-3-3 complex, which can be targeted explicitly
via aldimine-forming fragments, we studied the de novo design of PPI stabilizers under consideration of potential selectivity.
By applying cooperativity analysis of ternary complex formation, we
developed a reversible covalent molecular glue for the 14-3-3/Pin1
interaction. This small fragment led to a more than 250-fold stabilization
of the 14-3-3/Pin1 interaction by selective interfacing with a unique
tryptophan in Pin1. This study illustrates how cooperative complex
formation drives selective PPI stabilization. Further, it highlights
how specific interactions within a hub proteins interactome can be
stabilized over other interactions with a common binding motif.
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Affiliation(s)
- Peter J Cossar
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Madita Wolter
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Lars van Dijck
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Dario Valenti
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands.,Taros Chemicals GmbH & Co. KG, Emil-Figge-Straße 76a, 44227 Dortmund, Germany
| | - Laura M Levy
- Taros Chemicals GmbH & Co. KG, Emil-Figge-Straße 76a, 44227 Dortmund, Germany
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
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25
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Wolter M, Valenti D, Cossar PJ, Hristeva S, Levy LM, Genski T, Hoffmann T, Brunsveld L, Tzalis D, Ottmann C. An Exploration of Chemical Properties Required for Cooperative Stabilization of the 14-3-3 Interaction with NF-κB-Utilizing a Reversible Covalent Tethering Approach. J Med Chem 2021; 64:8423-8436. [PMID: 34076416 PMCID: PMC8237268 DOI: 10.1021/acs.jmedchem.1c00401] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
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Protein–protein
modulation has emerged as a proven approach
to drug discovery. While significant progress has been gained in developing
protein–protein interaction (PPI) inhibitors, the orthogonal
approach of PPI stabilization lacks established methodologies for
drug design. Here, we report the systematic ″bottom-up″
development of a reversible covalent PPI stabilizer. An imine bond
was employed to anchor the stabilizer at the interface of the 14-3-3/p65
complex, leading to a molecular glue that elicited an 81-fold increase
in complex stabilization. Utilizing protein crystallography and biophysical
assays, we deconvoluted how chemical properties of a stabilizer translate
to structural changes in the ternary 14-3-3/p65/molecular glue complex.
Furthermore, we explore how this leads to high cooperativity and increased
stability of the complex.
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Affiliation(s)
- Madita Wolter
- Department of Biomedical Engineering, Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Dario Valenti
- Department of Biomedical Engineering, Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands.,Medicinal Chemistry, Taros Chemicals GmbH & Co. KG, Emil-Figge-Straße 76a, 44227 Dortmund, Germany
| | - Peter J Cossar
- Department of Biomedical Engineering, Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Stanimira Hristeva
- Medicinal Chemistry, Taros Chemicals GmbH & Co. KG, Emil-Figge-Straße 76a, 44227 Dortmund, Germany
| | - Laura M Levy
- Medicinal Chemistry, Taros Chemicals GmbH & Co. KG, Emil-Figge-Straße 76a, 44227 Dortmund, Germany
| | - Thorsten Genski
- Medicinal Chemistry, Taros Chemicals GmbH & Co. KG, Emil-Figge-Straße 76a, 44227 Dortmund, Germany
| | - Torsten Hoffmann
- Medicinal Chemistry, Taros Chemicals GmbH & Co. KG, Emil-Figge-Straße 76a, 44227 Dortmund, Germany
| | - Luc Brunsveld
- Department of Biomedical Engineering, Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Dimitrios Tzalis
- Medicinal Chemistry, Taros Chemicals GmbH & Co. KG, Emil-Figge-Straße 76a, 44227 Dortmund, Germany
| | - Christian Ottmann
- Department of Biomedical Engineering, Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
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26
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Liu Y, Lv S, Peng L, Xie C, Gao L, Sun H, Lin L, Ding K, Li Z. Development and application of novel electrophilic warheads in target identification and drug discovery. Biochem Pharmacol 2021; 190:114636. [PMID: 34062128 DOI: 10.1016/j.bcp.2021.114636] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/24/2021] [Accepted: 05/27/2021] [Indexed: 10/21/2022]
Abstract
Nucleophilic amino acids play important roles in maintenance of protein structure and function, covalent modification of such amino acid residues by therapeutic agents is an efficient way to treat human diseases. Most of current clinical drugs are structurally limited to α,β-unsaturated amide as an electrophilic warhead. To alleviate this issue, many novel electrophiles have been developed in recent years that can covalently bind to different amino acid residues and provides a unique way to interrogate proteins, including "undruggable" targets. With an activity-based protein profiling (ABPP) approach, the activity and functionality of a protein and its binding sites can be assessed. This facilitates an understanding of protein function, and contributes to the discovery of new druggable targets and lead compounds. Meanwhile, many novel inhibitors bearing new reactive warhead were developed and displayed remarkable pharmaceutical properties. In this perspective, we have reviewed the recent remarkable progress of novel electrophiles and their applications in target identification and drug discovery.
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Affiliation(s)
- Yue Liu
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Shumin Lv
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Lijie Peng
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Chengliang Xie
- School of Pharmaceutical Science (Shenzhen), Sun Yat-sen University, Guangzhou 510000, China
| | - Liqian Gao
- School of Pharmaceutical Science (Shenzhen), Sun Yat-sen University, Guangzhou 510000, China
| | - Hongyan Sun
- Department of Chemistry, City University of Hong Kong, Hong Kong 999077, China
| | - Ligen Lin
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, Macau 999078, China
| | - Ke Ding
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China.
| | - Zhengqiu Li
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China; MOE Key Laboratory of Tumor Molecular Biology, Jinan University, Guangzhou, China.
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27
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Ambrose AJ, Chapman E. Function, Therapeutic Potential, and Inhibition of Hsp70 Chaperones. J Med Chem 2021; 64:7060-7082. [PMID: 34009983 DOI: 10.1021/acs.jmedchem.0c02091] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Hsp70s are among the most highly conserved proteins in all of biology. Through an iterative binding and release of exposed hydrophobic residues on client proteins, Hsp70s can prevent aggregation and promote folding to the native state of their client proteins. The human proteome contains eight canonical Hsp70s. Because Hsp70s are relatively promiscuous they play a role in folding a large proportion of the proteome. Hsp70s are implicated in disease through their ability to regulate protein homeostasis. In recent years, researchers have attempted to develop selective inhibitors of Hsp70 isoforms to better understand the role of individual isoforms in biology and as potential therapeutics. Selective inhibitors have come from rational design, forced localization, and serendipity, but the development of completely selective inhibitors remains elusive. In the present review, we discuss the Hsp70 structure and function, the known Hsp70 client proteins, the role of Hsp70s in disease, and current efforts to discover Hsp70 modulators.
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Affiliation(s)
- Andrew J Ambrose
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, 1703 East Mabel Street, Tucson, Arizona 85721, United States
| | - Eli Chapman
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, 1703 East Mabel Street, Tucson, Arizona 85721, United States
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28
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Zhou G, He L, Li KH, Pedroso CCS, Gochin M. A targeted covalent small molecule inhibitor of HIV-1 fusion. Chem Commun (Camb) 2021; 57:4528-4531. [PMID: 33956029 DOI: 10.1039/d1cc01013a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We describe a low molecular weight covalent inhibitor targeting a conserved lysine residue within the hydrophobic pocket of HIV-1 glycoprotein-41. The inhibitor bound selectively to the hydrophobic pocket and exhibited an order of magnitude enhancement of anti-fusion activity against HIV-1 compared to its non-covalent counterpart. The findings represent a significant advance in the quest to obtain non-peptide fusion inhibitors.
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Affiliation(s)
- Guangyan Zhou
- Department of Basic Sciences, Touro University California, 1310 Club Drive, Mare Island, Vallejo, CA 94592, USA.
| | - Li He
- Department of Basic Sciences, Touro University California, 1310 Club Drive, Mare Island, Vallejo, CA 94592, USA.
| | - Kathy H Li
- Department of Pharmaceutical Chemistry, UCSF School of Pharmacy, San Francisco, CA 94143, USA
| | - Cássio C S Pedroso
- Lawrence Berkeley National Laboratory, The Molecular Foundry, 1 Cyclotron Road, 67R5114, Berkeley, CA 94720, USA
| | - Miriam Gochin
- Department of Basic Sciences, Touro University California, 1310 Club Drive, Mare Island, Vallejo, CA 94592, USA. and Department of Pharmaceutical Chemistry, UCSF School of Pharmacy, San Francisco, CA 94143, USA
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29
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Gambini L, Udompholkul P, Baggio C, Muralidharan A, Kenjić N, Assar Z, Perry JJP, Pellecchia M. Design, Synthesis, and Structural Characterization of Lysine Covalent BH3 Peptides Targeting Mcl-1. J Med Chem 2021; 64:4903-4912. [PMID: 33797903 DOI: 10.1021/acs.jmedchem.1c00005] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Modulating disease-relevant protein-protein interactions (PPIs) using pharmacological tools is a critical step toward the design of novel therapeutic strategies. Over the years, however, targeting PPIs has proven a very challenging task owing to the large interfacial areas. Our recent efforts identified possible novel routes for the design of potent and selective inhibitors of PPIs using a structure-based design of covalent inhibitors targeting Lys residues. In this present study, we report on the design, synthesis, and characterizations of the first Lys-covalent BH3 peptide that has a remarkable affinity and selectivity for hMcl-1 over the closely related hBfl-1 protein. Our structural studies, aided by X-ray crystallography, provide atomic-level details of the inhibitor interactions that can be used to further translate these discoveries into novel generation, Lys-covalent pro-apoptotic agents.
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Affiliation(s)
- Luca Gambini
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Parima Udompholkul
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Carlo Baggio
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Aruljothi Muralidharan
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Nikola Kenjić
- Department of Biochemistry, College of Natural and Agricultural Sciences, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Zahra Assar
- Cayman Chemical, 1180 East Ellsworth Road, Ann Arbor, Michigan 48108, United States
| | - J Jefferson P Perry
- Department of Biochemistry, College of Natural and Agricultural Sciences, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Maurizio Pellecchia
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
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30
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Baillie TA. Approaches to mitigate the risk of serious adverse reactions in covalent drug design. Expert Opin Drug Discov 2020; 16:275-287. [PMID: 33006907 DOI: 10.1080/17460441.2021.1832079] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
INTRODUCTION Covalent inhibition of target proteins using high affinity ligands bearing weakly electrophilic warheads is being adopted increasingly as design strategy in the discovery of novel therapeutics, and several covalent drugs have now received regulatory approval for indications in oncology. Experience to date with targeted covalent inhibitors has led to a number of design principles that underlie the safety and efficacy of this increasingly important class of molecules. AREAS COVERED A review is provided of the current status of the covalent drug approach, emphasizing the unique benefits and attendant risks associated with reversible and irreversible binders. Areas of application beyond inhibition of tyrosine kinases are presented, and design considerations to de-risk covalent inhibitors with respect to undesirable off-target effects are discussed. EXPERT OPINION High selectivity for the intended protein target has emerged as a key consideration in mitigating safety risks associated with widespread proteome reactivity. Powerful chemical proteomics-based techniques are now available to assess selectivity in a drug discovery setting. Optimizing pharmacokinetics to capitalize on the intrinsically high potency of covalent drugs should lead to low daily doses and greater safety margins, while minimizing susceptibility to metabolic activation likewise will attenuate the risk of covalent drug toxicity.
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Affiliation(s)
- Thomas A Baillie
- Department of Medicinal Chemistry, School of Pharmacy, University of Washington Seattle, Seattle, WA, USA
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31
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Shao H, Gestwicki JE. Neutral analogs of the heat shock protein 70 (Hsp70) inhibitor, JG-98. Bioorg Med Chem Lett 2020; 30:126954. [PMID: 31952963 DOI: 10.1016/j.bmcl.2020.126954] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 01/01/2020] [Indexed: 12/19/2022]
Abstract
The heat shock protein 70 (Hsp70) family of molecular chaperones are highly expressed in tumors. Inhibitors containing a pyridinium-modified benzothiazole, such as JG-98, bind to a conserved, allosteric site in Hsp70, showing promising anti-proliferative activity in cancer cells. When bound to Hsp70, the charged pyridinium makes favorable contacts; however, this moiety also increases the inhibitor's fluorescence, giving rise to undesirable interference in biochemical and cell-based assays. Here, we explore whether the pyridinium can be replaced with a neutral pyridine. We report that pyridine-modified benzothiazoles, such as compound 17h (JG2-38), have reduced fluorescence, yet retain promising anti-proliferative activity (EC50 values ~0.1 to 0.07 µM) in breast and prostate cancer cell lines. These chemical probes are expected to be useful in exploring the roles of Hsp70s in tumorigenesis and cell survival.
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Affiliation(s)
- Hao Shao
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Jason E Gestwicki
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA.
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32
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Workman P. Reflections and Outlook on Targeting HSP90, HSP70 and HSF1 in Cancer: A Personal Perspective. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1243:163-179. [PMID: 32297218 DOI: 10.1007/978-3-030-40204-4_11] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This personal perspective focuses on small-molecule inhibitors of proteostasis networks in cancer-specifically the discovery and development of chemical probes and drugs acting on the molecular chaperones HSP90 and HSP70, and on the HSF1 stress pathway. Emphasis is on progress made and lessons learned and a future outlook is provided. Highly potent, selective HSP90 inhibitors have proved invaluable in exploring the role of this molecular chaperone family in biology and disease pathology. Clinical activity was observed, especially in non small cell lung cancer and HER2 positive breast cancer. Optimal use of HSP90 inhibitors in oncology will likely require development of creative combination strategies. HSP70 family members have proved technically harder to drug. However, recent progress has been made towards useful chemical tool compounds and these may signpost future clinical drug candidates. The HSF1 stress pathway is strongly validated as a target for cancer therapy. HSF1 itself is a ligandless transcription factor that is extremely challenging to drug directly. HSF1 pathway inhibitors have been identified mostly by phenotypic screening, including a series of bisamides from which a clinical candidate has been identified for treatment of ovarian cancer, multiple myeloma and potentially other cancers.
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Affiliation(s)
- Paul Workman
- CRUK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK.
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