1
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Majou D. Endopeptidase activities of Clostridium botulinum toxins in the development of this bacterium. Res Microbiol 2024:104216. [PMID: 38897423 DOI: 10.1016/j.resmic.2024.104216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 05/30/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024]
Abstract
By-products like CO₂ and organic acids, produced during Clostridium botulinum growth, appear to inhibit its development and reduce ATP production. A decrease in ATP production creates an imbalance in the ATP/GTP ratio. GTP activates CodY, which regulates BoNT expression. This toxin is released into the extracellular medium. Its light chains act as a specific endopeptidase, targeting SNARE proteins. The specific amino acids released enter the cells and are metabolized by the Stickland reaction, resulting in the synthesis of ATP. This ATP might then be used by histidine kinases to activate Spo0A, the main regulator initiating sporulation, through phosphorylation.
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Affiliation(s)
- Didier Majou
- ACTIA, 149, Rue de Bercy, 75595 Paris Cedex 12, France.
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2
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Zmudzinski M, Rut W, Olech K, Granda J, Giurg M, Burda-Grabowska M, Kaleta R, Zgarbova M, Kasprzyk R, Zhang L, Sun X, Lv Z, Nayak D, Kesik-Brodacka M, Olsen SK, Weber J, Hilgenfeld R, Jemielity J, Drag M. Ebselen derivatives inhibit SARS-CoV-2 replication by inhibition of its essential proteins: PL pro and M pro proteases, and nsp14 guanine N7-methyltransferase. Sci Rep 2023; 13:9161. [PMID: 37280236 DOI: 10.1038/s41598-023-35907-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/25/2023] [Indexed: 06/08/2023] Open
Abstract
Proteases encoded by SARS-CoV-2 constitute a promising target for new therapies against COVID-19. SARS-CoV-2 main protease (Mpro, 3CLpro) and papain-like protease (PLpro) are responsible for viral polyprotein cleavage-a process crucial for viral survival and replication. Recently it was shown that 2-phenylbenzisoselenazol-3(2H)-one (ebselen), an organoselenium anti-inflammatory small-molecule drug, is a potent, covalent inhibitor of both the proteases and its potency was evaluated in enzymatic and antiviral assays. In this study, we screened a collection of 34 ebselen and ebselen diselenide derivatives for SARS-CoV-2 PLpro and Mpro inhibitors. Our studies revealed that ebselen derivatives are potent inhibitors of both the proteases. We identified three PLpro and four Mpro inhibitors superior to ebselen. Independently, ebselen was shown to inhibit the N7-methyltransferase activity of SARS-CoV-2 nsp14 protein involved in viral RNA cap modification. Hence, selected compounds were also evaluated as nsp14 inhibitors. In the second part of our work, we employed 11 ebselen analogues-bis(2-carbamoylaryl)phenyl diselenides-in biological assays to evaluate their anti-SARS-CoV-2 activity in Vero E6 cells. We present their antiviral and cytoprotective activity and also low cytotoxicity. Our work shows that ebselen, its derivatives, and diselenide analogues constitute a promising platform for development of new antivirals targeting the SARS-CoV-2 virus.
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Affiliation(s)
- Mikolaj Zmudzinski
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland.
| | - Wioletta Rut
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Kamila Olech
- Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Jarosław Granda
- Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Mirosław Giurg
- Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Małgorzata Burda-Grabowska
- Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Rafał Kaleta
- Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Michala Zgarbova
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Nám. 2, 16610, Prague, Czech Republic
| | - Renata Kasprzyk
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097, Warsaw, Poland
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Banacha 2C, 02-097, Warsaw, Poland
| | - Linlin Zhang
- Institute of Molecular Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Xinyuanyuan Sun
- Institute of Molecular Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Zongyang Lv
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Digant Nayak
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | | | - Shaun K Olsen
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Jan Weber
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Nám. 2, 16610, Prague, Czech Republic
| | - Rolf Hilgenfeld
- Institute of Molecular Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems Site, University of Lübeck, 23562, Lübeck, Germany
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097, Warsaw, Poland
| | - Marcin Drag
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland.
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3
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Fang Y, Chang AY, Verma D, Miyashita SI, Eszterhas S, Lee PG, Shen Y, Davis LR, Dong M, Bailey-Kellogg C, Griswold KE. Functional Deimmunization of Botulinum Neurotoxin Protease Domain via Computationally Driven Library Design and Ultrahigh-Throughput Screening. ACS Synth Biol 2023; 12:153-163. [PMID: 36623275 PMCID: PMC9872818 DOI: 10.1021/acssynbio.2c00426] [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: 08/05/2022] [Indexed: 01/11/2023]
Abstract
Botulinum neurotoxin serotype A (BoNT/A) is a widely used cosmetic agent that also has diverse therapeutic applications; however, adverse antidrug immune responses and associated loss of efficacy have been reported in clinical uses. Here, we describe computational design and ultrahigh-throughput screening of a massive BoNT/A light-chain (BoNT/A-LC) library optimized for reduced T cell epitope content and thereby dampened immunogenicity. We developed a functional assay based on bacterial co-expression of BoNT/A-LC library members with a Förster resonance energy transfer (FRET) sensor for BoNT/A-LC enzymatic activity, and we employed high-speed fluorescence-activated cell sorting (FACS) to identify numerous computationally designed variants having wild-type-like enzyme kinetics. Many of these variants exhibited decreased immunogenicity in humanized HLA transgenic mice and manifested in vivo paralytic activity when incorporated into full-length toxin. One variant achieved near-wild-type paralytic potency and a 300% reduction in antidrug antibody response in vivo. Thus, we have achieved a striking level of BoNT/A-LC functional deimmunization by combining computational library design and ultrahigh-throughput screening. This strategy holds promise for deimmunizing other biologics with complex superstructures and mechanisms of action.
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Affiliation(s)
- Yongliang Fang
- Thayer
School of Engineering, Dartmouth, Hanover, New Hampshire 03755, United States
- Department
of Urology, Boston Children’s Hospital, Boston, Massachusetts 02115, United States
- Department
of Microbiology and Department of Surgery, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Andrew Y. Chang
- Thayer
School of Engineering, Dartmouth, Hanover, New Hampshire 03755, United States
| | - Deeptak Verma
- Department
of Computer Science, Dartmouth, Hanover, New Hampshire 03755, United States
| | - Shin-Ichiro Miyashita
- Department
of Urology, Boston Children’s Hospital, Boston, Massachusetts 02115, United States
- Department
of Microbiology and Department of Surgery, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department
of Food, Aroma and Cosmetic Chemistry, Tokyo
University of Agriculture, 196 Yasaka, Abashiri 099-2493, Japan
| | - Susan Eszterhas
- Thayer
School of Engineering, Dartmouth, Hanover, New Hampshire 03755, United States
| | - Pyung-Gang Lee
- Department
of Urology, Boston Children’s Hospital, Boston, Massachusetts 02115, United States
- Department
of Microbiology and Department of Surgery, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Yi Shen
- Department
of Urology, Boston Children’s Hospital, Boston, Massachusetts 02115, United States
- Department
of Microbiology and Department of Surgery, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Lydia R. Davis
- Thayer
School of Engineering, Dartmouth, Hanover, New Hampshire 03755, United States
| | - Min Dong
- Department
of Urology, Boston Children’s Hospital, Boston, Massachusetts 02115, United States
- Department
of Microbiology and Department of Surgery, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Chris Bailey-Kellogg
- Department
of Computer Science, Dartmouth, Hanover, New Hampshire 03755, United States
| | - Karl E. Griswold
- Thayer
School of Engineering, Dartmouth, Hanover, New Hampshire 03755, United States
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4
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Alcala-Torano R, Islam M, Cika J, Ho Lam K, Jin R, Ichtchenko K, Shoemaker CB, Van Deventer JA. Yeast Display Enables Identification of Covalent Single-Domain Antibodies against Botulinum Neurotoxin Light Chain A. ACS Chem Biol 2022; 17:3435-3449. [PMID: 36459441 PMCID: PMC10065152 DOI: 10.1021/acschembio.2c00574] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
While covalent drug discovery is reemerging as an important route to small-molecule therapeutic leads, strategies for the discovery and engineering of protein-based irreversible binding agents remain limited. Here, we describe the use of yeast display in combination with noncanonical amino acids (ncAAs) to identify irreversible variants of single-domain antibodies (sdAbs), also called VHHs and nanobodies, targeting botulinum neurotoxin light chain A (LC/A). Starting from a series of previously described, structurally characterized sdAbs, we evaluated the properties of antibodies substituted with reactive ncAAs capable of forming covalent bonds with nearby groups after UV irradiation (when using 4-azido-l-phenylalanine) or spontaneously (when using O-(2-bromoethyl)-l-tyrosine). Systematic evaluations in yeast display format of more than 40 ncAA-substituted variants revealed numerous clones that retain binding function while gaining either UV-mediated or spontaneous crosslinking capabilities. Solution-based analyses indicate that ncAA-substituted clones exhibit site-dependent target specificity and crosslinking capabilities uniquely conferred by ncAAs. Interestingly, not all ncAA substitution sites resulted in crosslinking events, and our data showed no apparent correlation between detected crosslinking levels and distances between sdAbs and LC/A residues. Our findings highlight the power of yeast display in combination with genetic code expansion in the discovery of binding agents that covalently engage their targets. This platform streamlines the discovery and characterization of antibodies with therapeutically relevant properties that cannot be accessed in the conventional genetic code.
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Affiliation(s)
- Rafael Alcala-Torano
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States of America
| | - Mariha Islam
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States of America
| | - Jaclyn Cika
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York 10016, United States of America
| | - Kwok Ho Lam
- Department of Physiology and Biophysics, University of California, Irvine, California 92697, United States of America
| | - Rongsheng Jin
- Department of Physiology and Biophysics, University of California, Irvine, California 92697, United States of America
| | - Konstantin Ichtchenko
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York 10016, United States of America
| | - Charles B. Shoemaker
- Tufts Cummings School of Veterinary Medicine, North Grafton, Massachusetts 01536, United States of America
| | - James A. Van Deventer
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States of America
- Biomedical Engineering Department, Tufts University, Medford, Massachusetts 02155, United States of America
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5
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Liu J, Xu S, Huang C, Shen J, Yu S, Yu Y, Sun Q, Dai Q. Synthesis and activity evaluation of selenazole-coupled CPI-1 irreversible bifunctional inhibitors for botulinum toxin A light chain. Bioorg Med Chem Lett 2022; 73:128913. [PMID: 35914651 DOI: 10.1016/j.bmcl.2022.128913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 07/21/2022] [Accepted: 07/26/2022] [Indexed: 11/02/2022]
Abstract
A series of novel conjugates of benzoselenazole or selenazole and CPI-1 were designed, synthesized, and evaluated for inhibitory activities against the botulinum neurotoxin A (BoNT/A) light chain (LC) and BoNT/A in vivo. The results show that these compounds exhibit potent inhibitory activities to the LC with IC50 of 0.5-4.1 µM. The reaction kinetics and the mass spectra of the reaction products of LC with benzoselenazole- or selenazole- coupled CPI-1 demonstrate that the benzoselenazole group of most inhibitors is coupled to the LC of BoNT/A. These data indicate that the CPI-1 conjugates can inhibit both the active center of BoNT/A LC as well as Cys165, therefore functioning as irreversible bifunctional inhibitors. The detoxification activities in vivo show that one of the benzoselenazole-CPI-1 compounds prolongs the survival time of mice challenged by 2 × LD50 of BoNT/A. This work provides a new strategy to design potent antidotes of BoNT/A.
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6
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Pirazzini M, Montecucco C, Rossetto O. Toxicology and pharmacology of botulinum and tetanus neurotoxins: an update. Arch Toxicol 2022; 96:1521-1539. [PMID: 35333944 PMCID: PMC9095541 DOI: 10.1007/s00204-022-03271-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 02/28/2022] [Indexed: 12/27/2022]
Abstract
Tetanus and botulinum neurotoxins cause the neuroparalytic syndromes of tetanus and botulism, respectively, by delivering inside different types of neurons, metalloproteases specifically cleaving the SNARE proteins that are essential for the release of neurotransmitters. Research on their mechanism of action is intensively carried out in order to devise improved therapies based on antibodies and chemical drugs. Recently, major results have been obtained with human monoclonal antibodies and with single chain antibodies that have allowed one to neutralize the metalloprotease activity of botulinum neurotoxin type A1 inside neurons. In addition, a method has been devised to induce a rapid molecular evolution of the metalloprotease domain of botulinum neurotoxin followed by selection driven to re-target the metalloprotease activity versus novel targets with respect to the SNARE proteins. At the same time, an intense and wide spectrum clinical research on novel therapeutics based on botulinum neurotoxins is carried out, which are also reviewed here.
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Affiliation(s)
- Marco Pirazzini
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/B, 35131, Padova, Italy.,Centro Interdipartimentale di Ricerca di Miologia, CIR-Myo, University of Padova, Via U. Bassi 58/B, 35131, Padova, Italy
| | - Cesare Montecucco
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/B, 35131, Padova, Italy. .,Institute of Neuroscience, National Research Council, Via Ugo Bassi 58/B, 35131, Padova, Italy.
| | - Ornella Rossetto
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/B, 35131, Padova, Italy.,Centro Interdipartimentale di Ricerca di Miologia, CIR-Myo, University of Padova, Via U. Bassi 58/B, 35131, Padova, Italy.,Institute of Neuroscience, National Research Council, Via Ugo Bassi 58/B, 35131, Padova, Italy
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7
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Turner LD, Nielsen AL, Lin L, Pellett S, Sugane T, Olson ME, Johnson EA, Janda KD. Irreversible inhibition of BoNT/A protease: proximity-driven reactivity contingent upon a bifunctional approach. RSC Med Chem 2021; 12:960-969. [PMID: 34223161 PMCID: PMC8221255 DOI: 10.1039/d1md00089f] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/03/2021] [Indexed: 12/27/2022] Open
Abstract
Botulinum neurotoxin A (BoNT/A) is categorized as a Tier 1 bioterrorism agent and persists within muscle neurons for months, causing paralysis. A readily available treatment that abrogates BoNT/A's toxicity and longevity is a necessity in the event of a widespread BoNT/A attack and for clinical treatment of botulism, yet remains an unmet need. Herein, we describe a comprehensive warhead screening campaign of bifunctional hydroxamate-based inhibitors for the irreversible inhibition of the BoNT/A light chain (LC). Using the 2,4-dichlorocinnamic hydroxamic acid (DCHA) metal-binding pharmacophore modified with a pendent warhead, a total of 37 compounds, possessing 13 distinct warhead types, were synthesized and evaluated for time-dependent inhibition against the BoNT/A LC. Iodoacetamides, maleimides, and an epoxide were found to exhibit time-dependent inhibition and their k GSH measured as a description of reactivity. The epoxide exhibited superior time-dependent inhibition over the iodoacetamides, despite reacting with glutathione (GSH) 51-fold slower. The proximity-driven covalent bond achieved with the epoxide inhibitor was contingent upon the vital hydroxamate-Zn2+ anchor in placing the warhead in an optimal position for reaction with Cys165. Monofunctional control compounds exemplified the necessity of the bifunctional approach, and Cys165 modification was confirmed through high-resolution mass spectrometry (HRMS) and ablation of time-dependent inhibitory activity against a C165A variant. Compounds were also evaluated against BoNT/A-intoxicated motor neuron cells, and their cell toxicity, serum stability, and selectivity against matrix metalloproteinases (MMPs) were characterized. The bifunctional approach allows the use of less intrinsically reactive electrophiles to intercept Cys165, thus expanding the toolbox of potential warheads for selective irreversible BoNT/A LC inhibition. We envision that this dual-targeted strategy is amenable to other metalloproteases that also possess non-catalytic cysteines proximal to the active-site metal center.
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Affiliation(s)
- Lewis D Turner
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute of Research and Medicine (WIRM), Scripps Research 10550 N Torrey Pines Road La Jolla CA 92037 USA
| | - Alexander L Nielsen
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute of Research and Medicine (WIRM), Scripps Research 10550 N Torrey Pines Road La Jolla CA 92037 USA
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen Universitetsparken 2 DK-2100 Copenhagen Denmark
| | - Lucy Lin
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute of Research and Medicine (WIRM), Scripps Research 10550 N Torrey Pines Road La Jolla CA 92037 USA
| | - Sabine Pellett
- Department of Bacteriology, University of Wisconsin 1550 Linden Drive Madison WI 53706 USA
| | - Takashi Sugane
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute of Research and Medicine (WIRM), Scripps Research 10550 N Torrey Pines Road La Jolla CA 92037 USA
| | - Margaret E Olson
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute of Research and Medicine (WIRM), Scripps Research 10550 N Torrey Pines Road La Jolla CA 92037 USA
- College of Pharmacy, Roosevelt University Schaumburg IL 60173 USA
| | - Eric A Johnson
- Department of Bacteriology, University of Wisconsin 1550 Linden Drive Madison WI 53706 USA
| | - Kim D Janda
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute of Research and Medicine (WIRM), Scripps Research 10550 N Torrey Pines Road La Jolla CA 92037 USA
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8
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Zhang J, Yang L, Wang Y, Cao T, Sun Z, Xu J, Liu Y, Chen G. Ebselen-Agents for Sensing, Imaging and Labeling: Facile and Full-Featured Application in Biochemical Analysis. ACS APPLIED BIO MATERIALS 2021; 4:2217-2230. [PMID: 35014346 DOI: 10.1021/acsabm.0c01561] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Phenyl-1,2-benzoselenazol-3(2H)-one (ebselen) is a classical mimic of glutathione peroxidase (GPx). Thioredoxin interaction endows ebselen attractive biological functions, such as antioxidation and anti-infection, as well as versatile therapeutic usage. Accordingly, application of ebselen analogues in biosensing, chemical labeling, imaging analysis, disease pathology, drug development, clinical treatment, etc. have been widely developed, in which mercaptans, reactive oxygen species, reactive sulfur species, peptides, and proteins were involved. Herein, focusing on the application of ebselen-agents in biochemistry, we have made a systematic summary and comprehensive review. First, we summarized both the classical and the innovative methods for preparing ebselen-agents to present the synthetic strategies. Then we discussed the full functional applicability of ebselen analogues in three fields of biochemical analysis including the fluorescence sensing and bioimaging, derivatization for high throughput fluorescence analysis, and the labeling gents for proteomics. Finally, we discussed the current challenges and perspectives for ebselen-agents as analytical tools in biological research. By presenting the multifunctional applicability of ebselen, we hope this review could appeal researchers to design the ebselen-related biomaterials for biochemical analysis.
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Affiliation(s)
- Jiawei Zhang
- Key Laboratory of Life-Organic Analysis of Shandong Province, Qufu Normal University, Qufu 273165, China
| | - Lei Yang
- Key Laboratory of Life-Organic Analysis of Shandong Province, Qufu Normal University, Qufu 273165, China
| | - Yuxin Wang
- Key Laboratory of Life-Organic Analysis of Shandong Province, Qufu Normal University, Qufu 273165, China
| | - Tianyi Cao
- Key Laboratory of Life-Organic Analysis of Shandong Province, Qufu Normal University, Qufu 273165, China
| | - Zhiwei Sun
- Key Laboratory of Life-Organic Analysis of Shandong Province, Qufu Normal University, Qufu 273165, China
| | - Jie Xu
- Shaanxi Key Laboratory of Chemical Additives for Industry, College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Yuxia Liu
- Department of Chemical Engineering and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Guang Chen
- Key Laboratory of Life-Organic Analysis of Shandong Province, Qufu Normal University, Qufu 273165, China.,Shaanxi Key Laboratory of Chemical Additives for Industry, College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
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9
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Chan WC, Sharifzadeh S, Buhrlage SJ, Marto JA. Chemoproteomic methods for covalent drug discovery. Chem Soc Rev 2021; 50:8361-8381. [PMID: 34143170 DOI: 10.1039/d1cs00231g] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Covalent drugs constitute cornerstones of modern medicine. The past decade has witnessed growing enthusiasm for development of covalent inhibitors, fueled by clinical successes as well as advances in analytical techniques associated with the drug discovery pipeline. Among these, mass spectrometry-based chemoproteomic methods stand out due to their broad applicability from focused analysis of electrophile-containing compounds to surveying proteome-wide inhibitor targets. Here, we review applications of both foundational and cutting-edge chemoproteomic techniques across target identification, hit discovery, and lead characterization/optimization in covalent drug discovery. We focus on the practical aspects necessary for the general drug discovery scientist to design, interpret, and evaluate chemoproteomic experiments. We also present three case studies on clinical stage molecules to further showcase the real world significance and future opportunities of these methodologies.
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Affiliation(s)
- Wai Cheung Chan
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA. and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Shabnam Sharifzadeh
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA. and Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Sara J Buhrlage
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA. and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Jarrod A Marto
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA. and Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA, USA
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10
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Lin L, Olson ME, Sugane T, Turner LD, Tararina MA, Nielsen AL, Kurbanov EK, Pellett S, Johnson EA, Cohen SM, Allen KN, Janda KD. Catch and Anchor Approach To Combat Both Toxicity and Longevity of Botulinum Toxin A. J Med Chem 2020; 63:11100-11120. [PMID: 32886509 PMCID: PMC7581224 DOI: 10.1021/acs.jmedchem.0c01006] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Botulinum neurotoxins have remarkable persistence (∼weeks to months in cells), outlasting the small-molecule inhibitors designed to target them. To address this disconnect, inhibitors bearing two pharmacophores-a zinc binding group and a Cys-reactive warhead-were designed to leverage both affinity and reactivity. A series of first-generation bifunctional inhibitors was achieved through structure-based inhibitor design. Through X-ray crystallography, engagement of both the catalytic Zn2+ and Cys165 was confirmed. A second-generation series improved on affinity by incorporating known reversible inhibitor pharmacophores; the mechanism was confirmed by exhaustive dialysis, mass spectrometry, and in vitro evaluation against the C165S mutant. Finally, a third-generation inhibitor was shown to have good cellular activity and low toxicity. In addition to our findings, an alternative method of modeling time-dependent inhibition that simplifies assay setup and allows comparison of inhibition models is discussed.
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Affiliation(s)
- Lucy Lin
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute of Research and Medicine (WIRM), Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Margaret E. Olson
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute of Research and Medicine (WIRM), Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Takashi Sugane
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute of Research and Medicine (WIRM), Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Lewis D. Turner
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute of Research and Medicine (WIRM), Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Margarita A. Tararina
- Program in Biomolecular Pharmacology, Boston University School of Medicine, Boston, Massachusetts 02118, United States
| | - Alexander L. Nielsen
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute of Research and Medicine (WIRM), Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Elbek K. Kurbanov
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Sabine Pellett
- Department of Bacteriology, University of Wisconsin, 1550 Linden Drive, Madison, Wisconsin 53706, United States
| | - Eric A. Johnson
- Department of Bacteriology, University of Wisconsin, 1550 Linden Drive, Madison, Wisconsin 53706, United States
| | - Seth M. Cohen
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Karen N. Allen
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Kim D. Janda
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute of Research and Medicine (WIRM), Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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