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Petri L, Ábrányi-Balogh P, Csorba N, Keeley A, Simon J, Ranđelović I, Tóvári J, Schlosser G, Szabó D, Drahos L, Keserű GM. Activation-Free Sulfonyl Fluoride Probes for Fragment Screening. Molecules 2023; 28:molecules28073042. [PMID: 37049805 PMCID: PMC10096327 DOI: 10.3390/molecules28073042] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 04/14/2023] Open
Abstract
SuFEx chemistry is based on the unique reactivity of the sulfonyl fluoride group with a range of nucleophiles. Accordingly, sulfonyl fluorides label multiple nucleophilic amino acid residues, making these reagents popular in both chemical biology and medicinal chemistry applications. The reactivity of sulfonyl fluorides nominates this warhead chemotype as a candidate for an external, activation-free general labelling tag. Here, we report the synthesis and characterization of a small sulfonyl fluoride library that yielded the 3-carboxybenzenesulfonyl fluoride warhead for tagging tractable targets at nucleophilic residues. Based on these results, we propose that coupling diverse fragments to this warhead would result in a library of sulfonyl fluoride bits (SuFBits), available for screening against protein targets. SuFBits will label the target if it binds to the core fragment, which facilitates the identification of weak fragments by mass spectrometry.
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Affiliation(s)
- László Petri
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, 1117 Budapest, Hungary
- National Laboratory for Drug Research and Development, Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, 1117 Budapest, Hungary
| | - Péter Ábrányi-Balogh
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, 1117 Budapest, Hungary
- National Laboratory for Drug Research and Development, Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, 1117 Budapest, Hungary
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Szent Gellért tér 4, 1111 Budapest, Hungary
| | - Noémi Csorba
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, 1117 Budapest, Hungary
- National Laboratory for Drug Research and Development, Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, 1117 Budapest, Hungary
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Szent Gellért tér 4, 1111 Budapest, Hungary
| | - Aaron Keeley
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, 1117 Budapest, Hungary
| | - József Simon
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, 1117 Budapest, Hungary
- Research Centre for Natural Sciences, MS Metabolomics Research Group, Magyar Tudósok Krt. 2, 1117 Budapest, Hungary
| | | | - József Tóvári
- Department of Experimental Pharmacology and National Tumor Biology Laboratory POB 21, National Institute of Oncology, 1525 Budapest, Hungary
| | - Gitta Schlosser
- MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Institute of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter Sétány 1/A, 1117 Budapest, Hungary
| | - Dániel Szabó
- MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, 1117 Budapest, Hungary
| | - László Drahos
- MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, 1117 Budapest, Hungary
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, 1117 Budapest, Hungary
- National Laboratory for Drug Research and Development, Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, 1117 Budapest, Hungary
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Szent Gellért tér 4, 1111 Budapest, Hungary
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Giang HN, Chou FP, Chen CY, Chou SC, Huang SC, Wu T, Hue BT, Lin HC, Wu TK. Quinazolinone-Peptido-Nitrophenyl-Derivatives as Potential Inhibitors of SARS-CoV-2 Main Protease. Viruses 2023; 15. [PMID: 36851501 DOI: 10.3390/v15020287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/12/2023] [Accepted: 01/18/2023] [Indexed: 01/21/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 main protease (SARS-CoV-2-Mpro) plays an essential role in viral replication, transcription, maturation, and entry into host cells. Furthermore, its cleavage specificity for viruses, but not humans, makes it a promising drug target for the treatment of coronavirus disease 2019 (COVID-19). In this study, a fragment-based strategy including potential antiviral quinazolinone moiety and glutamine- or glutamate-derived peptidomimetic backbone and positioned nitro functional groups was used to synthesize putative Mpro inhibitors. Two compounds, G1 and G4, exhibited anti-Mpro enzymatic activity in a dose-dependent manner, with the calculated IC50 values of 22.47 ± 8.93 μM and 24.04 ± 0.67 μM, respectively. The bio-layer interferometer measured real-time binding. The dissociation kinetics of G1/Mpro and G4/Mpro also showed similar equilibrium dissociation constants (KD) of 2.60 × 10-5 M and 2.55 × 10-5 M, respectively, but exhibited distinct association/dissociation curves. Molecular docking of the two compounds revealed a similar binding cavity to the well-known Mpro inhibitor GC376, supporting a structure-function relationship. These findings may open a new avenue for developing new scaffolds for Mpro inhibition and advance anti-coronavirus drug research.
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Moumbock AFA, Tran HTT, Lamy E, Günther S. BC-11 is a covalent TMPRSS2 fragment inhibitor that impedes SARS-CoV-2 host cell entry. Arch Pharm (Weinheim) 2023; 356:e2200371. [PMID: 36316225 PMCID: PMC9874818 DOI: 10.1002/ardp.202200371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/04/2022] [Accepted: 10/07/2022] [Indexed: 11/07/2022]
Abstract
Host cell entry of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is facilitated via priming of its spike glycoprotein by the human transmembrane protease serine 2 (TMPRSS2). Although camostat and nafamostat are two highly potent covalent TMPRSS2 inhibitors, they nevertheless did not hold promise in COVID-19 clinical trials, presumably due to their short plasma half-lives. Herein, we report an integrative chemogenomics approach based on computational modeling and in vitro enzymatic assays, for repurposing serine-targeted covalent inhibitors. This led to the identification of BC-11 as a covalent TMPRSS2 inhibitor displaying a unique selectivity profile for serine proteases, ascribable to its boronic acid warhead. BC-11 showed modest inhibition of SARS-CoV-2 (omicron variant) spike pseudotyped particles in a cell-based entry assay, and a combination of BC-11 and AHN 1-055 (a spike glycoprotein inhibitor) demonstrated better viral entry inhibition than either compound alone. Given its low molecular weight and good activity against TMPRSS2, BC-11 qualifies as a good starting point for further structural optimizations.
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Affiliation(s)
- Aurélien F. A. Moumbock
- Faculty of Chemistry and Pharmacy, Institute of Pharmaceutical SciencesAlbert‐Ludwigs‐Universität FreiburgFreiburgGermany
| | - Hoai T. T. Tran
- Molecular Preventive Medicine, Faculty of MedicineUniversity Medical Center, Albert‐Ludwigs‐Universität FreiburgFreiburgGermany
| | - Evelyn Lamy
- Molecular Preventive Medicine, Faculty of MedicineUniversity Medical Center, Albert‐Ludwigs‐Universität FreiburgFreiburgGermany
| | - Stefan Günther
- Faculty of Chemistry and Pharmacy, Institute of Pharmaceutical SciencesAlbert‐Ludwigs‐Universität FreiburgFreiburgGermany
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Eden A, Zhao J, Xiao Y, Gibson J, Wang C. Covalent fragment inhibits intramembrane proteolysis. Front Mol Biosci 2022; 9:958399. [PMID: 36158579 PMCID: PMC9490316 DOI: 10.3389/fmolb.2022.958399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/01/2022] [Indexed: 01/09/2023] Open
Abstract
Alzheimer's disease (AD) is a serious public health crisis with only one current modifying treatment. The reduction of amyloid load by targeting γ-secretase (GS) has been a leading approach in AD drug discovery and development. Despite the focus on GS inhibition, multiple GS inhibitors (GSIs) have failed in clinical trials as a result of side effects including exacerbated cognitive decline. These side effects are largely attributable to inhibition of normal GS function. Standard enzyme inhibitors target catalytic or allosteric sites of the enzyme, including the active site presenilin, as previous GSIs did. To avoid issues observed from broad-spectrum GSIs we discovered that fragment 6H8 that covalently binds to the substrate of GS, the transmembrane domain of amyloid precursor protein (APPTM). Nuclear Magnetic Resonance (NMR) Spectroscopy combined with MALDI-TOF-MS established 6H8 covalently binds to APPTM. 6H8 acts as a Michael acceptor and covalently links to the side chain amines of lysine residues, specifically targeting a cluster of C-terminal lysines K53-K55. Through this modification, 6H8 can inhibit intramembrane proteolysis of an archaeal homolog of presenilin (the active subunit of GS) via substrate binding with a 2-4 μM IC50, determined by a gel-based cleavage assay. 6H8, while too small to be an effective drug candidate, can be combined with a specific non-covalent partner and function as an effective covalent warhead of a targeted covalent inhibitor (TCI). The future development of the 6H8 fragment into the covalent warhead of a TCI is, to our knowledge, a novel approach to AD drug discovery.
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Affiliation(s)
- Angela Eden
- Center for Biotechnology and Interdisciplinary Studies, Troy, NY, United States
- Department of Chemistry and Chemical Biology, Troy, NY, United States
- Department of Biological Sciences, Troy, NY, United States
| | - Jing Zhao
- Center for Biotechnology and Interdisciplinary Studies, Troy, NY, United States
| | - Yuanyuan Xiao
- Center for Biotechnology and Interdisciplinary Studies, Troy, NY, United States
| | - James Gibson
- Center for Biotechnology and Interdisciplinary Studies, Troy, NY, United States
| | - Chunyu Wang
- Center for Biotechnology and Interdisciplinary Studies, Troy, NY, United States
- Department of Chemistry and Chemical Biology, Troy, NY, United States
- Department of Biological Sciences, Troy, NY, United States
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Grams RJ, Hsu KL. Reactive chemistry for covalent probe and therapeutic development. Trends Pharmacol Sci 2022; 43:249-262. [PMID: 34998611 PMCID: PMC8840975 DOI: 10.1016/j.tips.2021.12.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 02/06/2023]
Abstract
Bioactive small molecules that form covalent bonds with a target protein are important tools for basic research and can be highly effective drugs. This review highlights reactive groups found in a collection of thiophilic and oxophilic drugs that mediate pharmacological activity through a covalent mechanism of action (MOA). We describe the application of advanced proteomic and bioanalytical methodologies for assessing selectivity of these covalent agents to guide and inspire the search for additional electrophiles suitable for covalent probe and therapeutic development. While the emphasis is on chemistry for modifying catalytic serine, threonine or cysteine residues, we devote a substantial fraction of the review to a collection of exploratory reactive groups of understudied residues on proteins.
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Affiliation(s)
- R. Justin Grams
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Ku-Lung Hsu
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA; Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA22908, USA; Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA; University of Virginia Cancer Center, University of Virginia, Charlottesville, VA 22903, USA.
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Yu Y, Nie Y, Feng Q, Qu J, Wang R, Bian L, Xia J. Targeted Covalent Inhibition of Grb2-Sos1 Interaction through Proximity-Induced Conjugation in Breast Cancer Cells. Mol Pharm 2017; 14:1548-1557. [PMID: 28060514 DOI: 10.1021/acs.molpharmaceut.6b00952] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Targeted covalent inhibitors of protein-protein interactions differ from reversible inhibitors in that the former bind and covalently bond the target protein at a specific site of the target. The site specificity is the result of the proximity of two reactive groups at the bound state, for example, one mild electrophile in the inhibitor and a natural cysteine in the target close to the ligand binding site. Only a few pharmaceutically relevant proteins have this structural feature. Grb2, a key adaptor protein in maintaining the ERK activity via binding Sos1 to activated RTKs, is one: the N-terminal SH3 domain of Grb2 (Grb2N-SH3) carries a unique solvent-accessible cysteine Cys32 close to its Sos1-binding site. Here we report the design of a peptide-based antagonist (a reactive peptide) that specifically binds to Grb2N-SH3 and subsequently undergoes a nucleophilic reaction with Cys32 to form a covalent bond thioether, to block Grb2-Sos1 interaction. Through rounds of optimization, we eventually obtained a dimeric reaction reactive peptide that can form a covalent adduct with endogenous Grb2 protein inside the cytosol of SK-BR-3 human breast cancer cells with pronounced inhibitory effect on cell mobility and viability. This work showcases a rational design of Grb2-targeted site-specific covalent inhibitor and its pronounced anticancer effect by targeting Grb2-Sos1 interaction.
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Affiliation(s)
- Yongsheng Yu
- Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine , Shanghai, China.,Department of Chemistry, The Chinese University of Hong Kong , Shatin, Hong Kong SAR, China
| | - Yunyu Nie
- Department of Chemistry, The Chinese University of Hong Kong , Shatin, Hong Kong SAR, China
| | - Qian Feng
- Department of Biomedical Engineering, The Chinese University of Hong Kong , Shatin, Hong Kong SAR, China
| | - Jiale Qu
- Department of Chemistry, The Chinese University of Hong Kong , Shatin, Hong Kong SAR, China
| | - Rui Wang
- Department of Chemistry, The Chinese University of Hong Kong , Shatin, Hong Kong SAR, China
| | - Liming Bian
- Department of Biomedical Engineering, The Chinese University of Hong Kong , Shatin, Hong Kong SAR, China
| | - Jiang Xia
- Department of Chemistry, The Chinese University of Hong Kong , Shatin, Hong Kong SAR, China
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