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Zhang C, Zhao M, Wang G, Li Y. Recent Progress on Microtubule Degradation Agents. J Med Chem 2023; 66:13354-13368. [PMID: 37748178 DOI: 10.1021/acs.jmedchem.3c00517] [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: 09/27/2023]
Abstract
Targeted protein degradation (TPD) has emerged as the most promising approach for the specific knockdown of disease-associated proteins and is achieved by exploiting the cellular quality control machinery. TPD technologies are highly advantageous in overcoming drug resistance as they degrade the whole target protein. Microtubules play important roles in many cellular processes and are among the oldest and most well-established targets for tumor chemotherapy. However, the development of drug resistance, risk of hypersensitivity reactions, and intolerable toxicities severely restrict the clinical applications of microtubule-targeting agents (MTAs). Microtubule degradation agents (MDgAs) operate via completely different mechanisms compared with traditional MTAs and are capable of overcoming drug resistance. The emergence of MDgAs has expanded the scope of TPD and provided new avenues for the discovery of tubulin-targeted drugs. Herein, we summarized the development of MDgAs, and discussed their degradation mechanisms, mechanisms of action on the binding sites, potential opportunities, and challenges.
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Affiliation(s)
- Chufeng Zhang
- Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, Sichuan, China
| | - Min Zhao
- Laboratory of Metabolomics and Drug-Induced Liver Injury, Department of Gastroenterology & Hepatology, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Guan Wang
- Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, Sichuan, China
| | - Yong Li
- Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, Sichuan, China
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Johnson B, Li J, Adhikari J, Edwards MR, Zhang H, Schwarz T, Leung DW, Basler CF, Gross ML, Amarasinghe GK. Dimerization Controls Marburg Virus VP24-dependent Modulation of Host Antioxidative Stress Responses. J Mol Biol 2016; 428:3483-94. [PMID: 27497688 PMCID: PMC5010500 DOI: 10.1016/j.jmb.2016.07.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 07/27/2016] [Accepted: 07/27/2016] [Indexed: 12/13/2022]
Abstract
Marburg virus (MARV), a member of the Filoviridae family that also includes Ebola virus (EBOV), causes lethal hemorrhagic fever with case fatality rates that have exceeded 50% in some outbreaks. Within an infected cell, there are numerous host-viral interactions that contribute to the outcome of infection. Recent studies identified MARV protein 24 (mVP24) as a modulator of the host antioxidative responses, but the molecular mechanism remains unclear. Using a combination of biochemical and mass spectrometry studies, we show that mVP24 is a dimer in solution that directly binds to the Kelch domain of Kelch-like ECH-associated protein 1 (Keap1) to regulate nuclear factor (erythroid-derived 2)-like 2 (Nrf2). This interaction between Keap1 and mVP24 occurs through the Kelch interaction loop (K-Loop) of mVP24 leading to upregulation of antioxidant response element transcription, which is distinct from other Kelch binders that regulate Nrf2 activity. N-terminal truncations disrupt mVP24 dimerization, allowing monomeric mVP24 to bind Kelch with higher affinity and stimulate higher antioxidative stress response element (ARE) reporter activity. Mass spectrometry-based mapping of the interface revealed overlapping binding sites on Kelch for mVP24 and the Nrf2 proteins. Substitution of conserved cysteines, C209 and C210, to alanine in the mVP24 K-Loop abrogates Kelch binding and ARE activation. Our studies identify a shift in the monomer-dimer equilibrium of MARV VP24, driven by its interaction with Keap1 Kelch domain, as a critical determinant that modulates host responses to pathogenic Marburg viral infections.
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Affiliation(s)
- Britney Johnson
- Department of Pathology and Immunology, Washington University School of Medicine in St Louis, St Louis, MO 63110, USA
| | - Jing Li
- Department of Chemistry, Box 1134, Washington University, One Brookings Drive, St. Louis, Mo, 63130, USA
| | - Jagat Adhikari
- Department of Chemistry, Box 1134, Washington University, One Brookings Drive, St. Louis, Mo, 63130, USA
| | - Megan R Edwards
- Department of Pathology and Immunology, Washington University School of Medicine in St Louis, St Louis, MO 63110, USA; Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA
| | - Hao Zhang
- Department of Chemistry, Box 1134, Washington University, One Brookings Drive, St. Louis, Mo, 63130, USA
| | - Toni Schwarz
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Daisy W Leung
- Department of Pathology and Immunology, Washington University School of Medicine in St Louis, St Louis, MO 63110, USA
| | - Christopher F Basler
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michael L Gross
- Department of Chemistry, Box 1134, Washington University, One Brookings Drive, St. Louis, Mo, 63130, USA.
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine in St Louis, St Louis, MO 63110, USA.
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Chen YT, Collins TRL, Guan Z, Chen VB, Hsieh TS. Probing conformational changes in human DNA topoisomerase IIα by pulsed alkylation mass spectrometry. J Biol Chem 2012; 287:25660-8. [PMID: 22679013 DOI: 10.1074/jbc.m112.377606] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Type II topoisomerases are essential enzymes for solving DNA topological problems by passing one segment of DNA duplex through a transient double-strand break in a second segment. The reaction requires the enzyme to precisely control DNA cleavage and gate opening coupled with ATP hydrolysis. Using pulsed alkylation mass spectrometry, we were able to monitor the solvent accessibilities around 13 cysteines distributed throughout human topoisomerase IIα by measuring the thiol reactivities with monobromobimane. Most of the measured reactivities are in accordance with the predicted ones based on a homology structural model generated from available crystal structures. However, these results reveal new information for both the residues not covered in the structural model and potential differences between the modeled and solution holoenzyme structures. Furthermore, on the basis of the reactivity changes of several cysteines located at the N-gate and DNA gate, we could monitor the movement of topoisomerase II in the presence of cofactors and detect differences in the DNA gate between two closed clamp enzyme conformations locked by either 5'-adenylyl β,γ-imidodiphosphate or the anticancer drug ICRF-193.
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Affiliation(s)
- Yu-Tsung Chen
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
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Su D, Delaplane S, Luo M, Rempel DL, Vu B, Kelley MR, Gross ML, Georgiadis MM. Interactions of apurinic/apyrimidinic endonuclease with a redox inhibitor: evidence for an alternate conformation of the enzyme. Biochemistry 2010; 50:82-92. [PMID: 21117647 DOI: 10.1021/bi101248s] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Apurinic/apyrimidinic endonuclease (APE1) is an essential base excision repair protein that also functions as a reduction and oxidation (redox) factor in mammals. Through a thiol-based mechanism, APE1 reduces a number of important transcription factors, including AP-1, p53, NF-κB, and HIF-1α. What is known about the mechanism to date is that the buried residues Cys 65 and Cys 93 are critical for APE1's redox activity. To further detail the redox mechanism, we developed a chemical footprinting-mass spectrometric assay using N-ethylmaleimide (NEM), an irreversible Cys modifier, to characterize the interaction of the redox inhibitor, E3330, with APE1. When APE1 was incubated with E3330, two NEM-modified products were observed, one with two and a second with seven added NEMs; this latter product corresponds to a fully modified APE1. In a similar control reaction without E3330, only the +2NEM product was observed in which the two solvent-accessible Cys residues, C99 and C138, were modified by NEM. Through hydrogen-deuterium amide exchange with analysis by mass spectrometry, we found that the +7NEM-modified species incorporates approximately 40 more deuterium atoms than the native protein, which exchanges nearly identically as the +2NEM product, suggesting that APE1 can be trapped in a partially unfolded state. E3330 was also found to increase the extent of disulfide bond formation involving redox critical Cys residues in APE1 as assessed by liquid chromatography and tandem mass spectrometry, suggesting a basis for its inhibitory effects on APE1's redox activity. Collectively, our results suggest that APE1 adopts a partially unfolded state, which we propose is the redox active form of the enzyme.
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Affiliation(s)
- Dian Su
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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Ladner CL, Turner RJ, Edwards RA. Development of indole chemistry to label tryptophan residues in protein for determination of tryptophan surface accessibility. Protein Sci 2007; 16:1204-13. [PMID: 17525468 PMCID: PMC2206665 DOI: 10.1110/ps.062728407] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Solvent accessibility can be used to evaluate protein structural models, identify binding sites, and characterize protein conformational changes. The differential modification of amino acids at specific sites enables the accessible surface residues to be identified by mass spectrometry. Tryptophan residues within proteins can be differentially labeled with halocompounds by a photochemical reaction. In this study, tryptophan residues of carbonic anhydrase are reacted with chloroform, 2,2,2-trichloroethanol (TCE), 2,2,2-trichloroacetate (TCA), or 3-bromo-1-propanol (BP) under UV irradiation at 280 nm. The light-driven reactions with chloroform, TCE, TCA, and BP attach a formyl, hydroxyethanone, carboxylic acid, and propanol group, respectively, onto the indole ring of tryptophan. Trypsin and chymotrypsin digests of the modified carbonic anhydrase are used to map accessible tryptophan residues using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Tryptophan reactivity is determined by identifying peptides with tryptophan residues modified with the appropriate label. The reactivity is calculated from the frequency that the modification is identified and a semiquantitative measure of the amount of products formed. Both of these measures of tryptophan reactivity correlate significantly with the accessible surface area of tryptophan residues in carbonic anhydrase determined from the X-ray crystal structure. Therefore the photochemical reaction of halocompounds with tryptophan residues in carbonic anhydrase indicates the degree of solvent accessibility of these residues.
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Affiliation(s)
- Carol L Ladner
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
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Derakhshan B, Hao G, Gross SS. Balancing reactivity against selectivity: the evolution of protein S-nitrosylation as an effector of cell signaling by nitric oxide. Cardiovasc Res 2007; 75:210-9. [PMID: 17524376 PMCID: PMC1994943 DOI: 10.1016/j.cardiores.2007.04.023] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2007] [Revised: 04/20/2007] [Accepted: 04/24/2007] [Indexed: 01/22/2023] Open
Abstract
Produced by the action of lightning in the atmosphere of the pre-biotic earth, nitric oxide (NO) is a free radical molecule that provided the major nitrogen source for development of life. Remarkably, when atmospheric sources of NO became restrictive, organisms evolved the capacity for NO biosynthesis and NO took on bioregulatory roles. We now recognize NO as an ancestral regulator of diverse and important biological functions, acting throughout the phylogenetic tree. In mammals, NO has been implicated as a pivotal regulator of virtually every major physiological system. The bioactivities of NO, and reactive species derived from NO, arise predominantly from their covalent addition to proteins. Importantly, S-nitrosylation of protein cysteine (Cys) residues has emerged as a preeminent effector of NO bioactivity. How and why NO selectively adds to particular Cys residues in proteins is poorly understood, yet fundamental to how NO communicates its bioactivities. Also, evolutionary pressures that have shaped S-nitrosylation as a biosignaling modality are obscure. Considering recently recognized NO signaling paradigms, we speculate on the origin of NO signaling in biological systems and the molecular adaptations that have endowed NO with the ability to selectively target a subset of protein Cys residues that mediate biosignaling.
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Affiliation(s)
- Behrad Derakhshan
- Weill Medical College of Cornell University, Department of Pharmacology, 1300 York Avenue, New York, NY 10021, USA
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Hao G, Derakhshan B, Shi L, Campagne F, Gross SS. SNOSID, a proteomic method for identification of cysteine S-nitrosylation sites in complex protein mixtures. Proc Natl Acad Sci U S A 2006; 103:1012-7. [PMID: 16418269 PMCID: PMC1347989 DOI: 10.1073/pnas.0508412103] [Citation(s) in RCA: 286] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Reversible addition of NO to Cys-sulfur in proteins, a modification termed S-nitrosylation, has emerged as a ubiquitous signaling mechanism for regulating diverse cellular processes. A key first-step toward elucidating the mechanism by which S-nitrosylation modulates a protein's function is specification of the targeted Cys (SNO-Cys) residue. To date, S-nitrosylation site specification has been laboriously tackled on a protein-by-protein basis. Here we describe a high-throughput proteomic approach that enables simultaneous identification of SNO-Cys sites and their cognate proteins in complex biological mixtures. The approach, termed SNOSID (SNO Site Identification), is a modification of the biotin-swap technique [Jaffrey, S. R., Erdjument-Bromage, H., Ferris, C. D., Tempst, P. & Snyder, S. H. (2001) Nat. Cell. Biol. 3, 193-197], comprising biotinylation of protein SNO-Cys residues, trypsinolysis, affinity purification of biotinylated-peptides, and amino acid sequencing by liquid chromatography tandem MS. With this approach, 68 SNO-Cys sites were specified on 56 distinct proteins in S-nitrosoglutathione-treated (2-10 microM) rat cerebellum lysates. In addition to enumerating these S-nitrosylation sites, the method revealed endogenous SNO-Cys modification sites on cerebellum proteins, including alpha-tubulin, beta-tubulin, GAPDH, and dihydropyrimidinase-related protein-2. Whereas these endogenous SNO proteins were previously recognized, we extend prior knowledge by specifying the SNO-Cys modification sites. Considering all 68 SNO-Cys sites identified, a machine learning approach failed to reveal a linear Cys-flanking motif that predicts stable transnitrosation by S-nitrosoglutathione under test conditions, suggesting that undefined 3D structural features determine S-nitrosylation specificity. SNOSID provides the first effective tool for unbiased elucidation of the SNO proteome, identifying Cys residues that undergo reversible S-nitrosylation.
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Affiliation(s)
- Gang Hao
- Department of Pharmacology, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10021, USA
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Kim YJ, Sackett DL, Schapira M, Walsh DP, Min J, Pannell LK, Chang YT. Identification of 12Cysbeta on tubulin as the binding site of tubulyzine. Bioorg Med Chem 2005; 14:1169-75. [PMID: 16266809 PMCID: PMC1408322 DOI: 10.1016/j.bmc.2005.09.069] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2005] [Revised: 09/24/2005] [Accepted: 09/26/2005] [Indexed: 10/25/2022]
Abstract
We have undertaken quantitative binding site studies in order to identify the binding site of the known microtubule destabilizing agents, the tubulyzines, in the tubulin dimer. Two different approaches were employed that utilized the tubulyzines and their derivatives. The first approach was based on a chemical affinity labeling method using tubulyzine affinity derivatives, and the second approach employed the mass spectrometric measurement of the differential reactivity of cysteines using the tubulyzines and monobromobimane. Based on overlapping data from these two approaches, we propose that the tubulyzines bind at the guanosine-5'-triphosphate binding site of beta-tubulin. Interestingly, we also show that the tubulyzines' binding to tubulin induces a conformational change in tubulin that prevents further interaction of the 239Cysbeta with other reagents.
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Affiliation(s)
- Yeoun Jin Kim
- National Institute of Diabetes, Digestive, Kidney Diseases, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD 20892, USA
| | - Dan L. Sackett
- National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD 20892, USA
| | - Matthieu Schapira
- Department of Pharmacology, New York University Medical Center, New York, NY 10016, USA
| | - Daniel P. Walsh
- Department of Chemistry, New York University New York, NY 10003, USA
| | - Jaeki Min
- Department of Chemistry, New York University New York, NY 10003, USA
| | - Lewis K. Pannell
- National Institute of Diabetes, Digestive, Kidney Diseases, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD 20892, USA
| | - Young-Tae Chang
- Department of Chemistry, New York University New York, NY 10003, USA
- Corresponding author. Tel.: +1 212 998 8491; fax: +1 212 260 7905; e-mail:
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