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Taggart EL, Wolff EJ, Yanar P, Blobe JP, Shugrue CR. Development of an oxazole-based cleavable linker for peptides. Bioorg Med Chem 2024; 102:117663. [PMID: 38457910 DOI: 10.1016/j.bmc.2024.117663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 02/06/2024] [Accepted: 02/29/2024] [Indexed: 03/10/2024]
Abstract
We report the development of a new oxazole-based cleavable linker to release peptides from attached cargo. Oxazoles are stable to most reaction conditions, yet they can be rapidly cleaved in the presence of single-electron oxidants like cerium ammonium nitrate (CAN). An oxazole linker could be synthesized and attached to peptides through standard solid-phase peptide coupling reactions. Cleavage of these peptide-oxazole conjugates is demonstrated on a broad scope of peptides containing various natural and unnatural amino acids. These results represent the first example of a peptide-based linker that is cleaved through single-electron oxidation. The oxazole is also demonstrated to be a suitable linker for both the release of a peptide from a conjugated small molecule and the orthogonal release of cargo from a peptide containing multiple cleavable linkers. Oxazole linkers could serve as a promising tool for peptide screening platforms such as peptide-encoded libraries.
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Affiliation(s)
- Elizabeth L Taggart
- Department of Chemistry, University of Richmond, Gottwald Science Center B-100 138 UR Drive University of Richmond, VA 23173, United States
| | - Evan J Wolff
- Department of Chemistry, University of Richmond, Gottwald Science Center B-100 138 UR Drive University of Richmond, VA 23173, United States
| | - Pamira Yanar
- Department of Chemistry, University of Richmond, Gottwald Science Center B-100 138 UR Drive University of Richmond, VA 23173, United States
| | - John P Blobe
- Department of Chemistry, University of Richmond, Gottwald Science Center B-100 138 UR Drive University of Richmond, VA 23173, United States
| | - Christopher R Shugrue
- Department of Chemistry, University of Richmond, Gottwald Science Center B-100 138 UR Drive University of Richmond, VA 23173, United States.
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2
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Dinh Thanh N, Ngoc Toan V, Thi Kim Giang N, Thi Kim Van H, Son Hai D, Minh Tri N, Ngoc Toan D. Synthesis, biological and molecular modelling for 1,3,4-thiadiazole sulfonyl thioureas: bacterial and fungal activity. RSC Med Chem 2023; 14:2751-2767. [PMID: 38107183 PMCID: PMC10718584 DOI: 10.1039/d3md00508a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 10/24/2023] [Indexed: 12/19/2023] Open
Abstract
Some substituted thioureas (6a-i) containing a 1,3,4-thiadiazole ring were synthesized by the reaction of the corresponding substituted 2-amino-1,3,4-thiadiazoles 3a-i with p-toluenesulfonyl isocyanate in a one-pot procedure. The antibacterial and antifungal activities of these sulfonyl thioureas were estimated using a minimum inhibitory concentration protocol. Almost all the thioureas exhibited remarkable antimicrobial activity. Amongst the studied compounds, thioureas 6a, 6c, 6h, and 6i were better inhibitors against the bacterium S. aureus, with MIC values of 0.78-3.125 μg mL-1. These compounds were also tested for their inhibition against S. aureus enzymes, including enzymes of DNA gyrase, DNA topoisomerase IV (Topo IV), and dihydrofolate reductase. Amongst the compounds, 6h was a strong inhibitor, with IC50 values of 1.22, 53.78, and 0.23, respectively. Induced fit docking calculations were performed to observe the binding efficiency and steric interactions of these compounds. The obtained results showed that compound 6h was compatible with the active sites of S. aureus DNA gyrase 2XCS. This ligand interacted with residues ASP1083 (chain D), MET1121 (chain B), ARG1122 (chain D), and also with HOH2035, HOH2089, HOH2110, HOH2162. Molecular dynamics simulation in a water solvent system showed that the active interactions with residues ASP083 and MET1121 (chain B), along with ASP1083, MET1121, and ARG1122 (chain D), played an important role in stabilizing complex 6h/2XCS in the active pocket.
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Affiliation(s)
- Nguyen Dinh Thanh
- Faculty of Chemistry, University of Science (Vietnam National University, Hanoi) 19 Le Thanh Tong Ha Noi Viet Nam
| | - Vu Ngoc Toan
- Faculty of Chemistry, University of Science (Vietnam National University, Hanoi) 19 Le Thanh Tong Ha Noi Viet Nam
- Institute of New Technology, Military Institute of Science and Technology (Ministry of Military) 17 Hoang Sam, Cau Giay Ha Noi Viet Nam
| | - Nguyen Thi Kim Giang
- Faculty of Chemistry, University of Science (Vietnam National University, Hanoi) 19 Le Thanh Tong Ha Noi Viet Nam
- Institute of Science and Technology, Ministry of Public Security of Vietnam 47 Pham Van Dong, Cau Giay Ha Noi Vietnam
| | - Hoang Thi Kim Van
- Faculty of Chemistry, University of Science (Vietnam National University, Hanoi) 19 Le Thanh Tong Ha Noi Viet Nam
- Faculty of Chemical Technology, Viet Tri University of Industry Tien Kien, Lam Thao Phu Tho Viet Nam
| | - Do Son Hai
- Faculty of Chemistry, University of Science (Vietnam National University, Hanoi) 19 Le Thanh Tong Ha Noi Viet Nam
- Institute of Science and Technology, Ministry of Public Security of Vietnam 47 Pham Van Dong, Cau Giay Ha Noi Vietnam
| | - Nguyen Minh Tri
- Faculty of Chemistry, University of Science (Vietnam National University, Hanoi) 19 Le Thanh Tong Ha Noi Viet Nam
- Institute of Science and Technology, Ministry of Public Security of Vietnam 47 Pham Van Dong, Cau Giay Ha Noi Vietnam
| | - Duong Ngoc Toan
- Faculty of Chemistry, University of Science (Vietnam National University, Hanoi) 19 Le Thanh Tong Ha Noi Viet Nam
- Faculty of Chemistry, Thai Nguyen University of Education 20 Luong Ngoc Quyen Thai Nguyen Viet Nam
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3
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Thanh ND, Lan PH, Hai DS, Anh HH, Giang NTK, Van HTK, Toan VN, Tri NM, Toan DN. Thiourea derivatives containing 4-arylthiazoles and d-glucose moiety: design, synthesis, antimicrobial activity evaluation, and molecular docking/dynamics simulations. RSC Med Chem 2023; 14:1114-1130. [PMID: 37360390 PMCID: PMC10285754 DOI: 10.1039/d3md00010a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 04/15/2023] [Indexed: 06/28/2023] Open
Abstract
Some substituted glucose-conjugated thioureas containing 1,3-thiazole ring, 4a-h, were synthesized by the reaction of the corresponding substituted 2-amino-4-phenyl-1,3-thiazoles 2a-h with 2,3,4,6-tetra-O-acetyl-β-d-glucopyranosyl isocyanate. The antibacterial and antifungal activities of these thiazole-containing thioureas were estimated using a minimum inhibitory concentration protocol. Among these compounds, 4c, 4g, and 4h were better inhibitors with MIC = 0.78-3.125 μg mL-1. These three compounds were also tested for their ability to inhibit S. aureus enzymes, including DNA gyrase, DNA topoisomerase IV (Topo IV), and dihydrofolate reductase, and compound 4h was found to be a strong inhibitor with IC50 = 1.25 ± 0.12, 67.28 ± 1.21, and 0.13 ± 0.05 μM, respectively. Induced-fit docking and MM-GBSA calculations were performed to observe the binding efficiencies and steric interactions of these compounds. The obtained results showed that compound 4h is compatible with the active site of S. aureus DNA gyrase 2XCS with four H-bond interactions with residues Ala1118, Met1121, and F:DC11 and also three interactions with F:DG10 (two interactions) and F:DC11 (one interaction). Molecular dynamics simulation in a water solvent system showed that ligand 4h had active interactions with enzyme 2XCS through residues Ala1083, Glu1088, Ala1118, Gly1117, and Met1121.
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Affiliation(s)
- Nguyen Dinh Thanh
- Faculty of Chemistry, University of Science (Vietnam National University, Hanoi) 19 Le Thanh Tong Ha Noi Vietnam
| | - Pham Hong Lan
- Faculty of Chemistry, University of Science (Vietnam National University, Hanoi) 19 Le Thanh Tong Ha Noi Vietnam
- Institute of Science and Technology, Ministry of Public Security of Vietnam 47 Pham Van Dong Cau Giay Ha Noi Vietnam
| | - Do Son Hai
- Faculty of Chemistry, University of Science (Vietnam National University, Hanoi) 19 Le Thanh Tong Ha Noi Vietnam
- Institute of Science and Technology, Ministry of Public Security of Vietnam 47 Pham Van Dong Cau Giay Ha Noi Vietnam
| | - Hoang Huu Anh
- Faculty of Chemistry, University of Science (Vietnam National University, Hanoi) 19 Le Thanh Tong Ha Noi Vietnam
| | - Nguyen Thi Kim Giang
- Faculty of Chemistry, University of Science (Vietnam National University, Hanoi) 19 Le Thanh Tong Ha Noi Vietnam
- Institute of Science and Technology, Ministry of Public Security of Vietnam 47 Pham Van Dong Cau Giay Ha Noi Vietnam
| | - Hoang Thi Kim Van
- Faculty of Chemistry, University of Science (Vietnam National University, Hanoi) 19 Le Thanh Tong Ha Noi Vietnam
- Faculty of Chemical Technology, Viet Tri University of Industry Tien Kien Lam Thao Phu Tho Vietnam
| | - Vu Ngoc Toan
- Faculty of Chemistry, University of Science (Vietnam National University, Hanoi) 19 Le Thanh Tong Ha Noi Vietnam
- Institute of New Technology, Military Institute of Science and Technology (Ministry of Military) 17 Hoang Sam Cau Giay Ha Noi Vietnam
| | - Nguyen Minh Tri
- Faculty of Chemistry, University of Science (Vietnam National University, Hanoi) 19 Le Thanh Tong Ha Noi Vietnam
- Institute of New Technology, Military Institute of Science and Technology (Ministry of Military) 17 Hoang Sam Cau Giay Ha Noi Vietnam
| | - Duong Ngoc Toan
- Faculty of Chemistry, University of Science (Vietnam National University, Hanoi) 19 Le Thanh Tong Ha Noi Vietnam
- Faculty of Chemistry, Thai Nguyen University of Education 20 Luong Ngoc Quyen Thai Nguyen Vietnam
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4
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Toan VN, Thanh ND, Huyen LT, Hanh NT, Hai DS, Anh HH, Giang NTK, Van HTK. Design, Synthesis, α-Amylase/α-Glucosidase Inhibition Assay, Induced Fit Docking Study of New Hybrid Compounds Containing 4H-Pyrano[2,3-d]pyrimidine, 1H-1,2,3-Triazole and D-Glucose Components. Chem Biodivers 2022; 19:e202200680. [PMID: 36408921 DOI: 10.1002/cbdv.202200680] [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: 07/21/2022] [Accepted: 11/21/2022] [Indexed: 11/22/2022]
Abstract
In this study, the click chemistry between N-propargyl derivatives of substituted 4H-pyrano[2,3-d]pyrimidines and tetra-O-acetyl-α-d-glucopyranosyl azide carried out under catalytic conditions using catalyst CuI@Montmorillonite and additive N,N-diisopropylethylamine (DIPEA). The yields of obtained hybrid compounds having 4H-pyrano[2,3-d]pyrimidine connected to 1H-1,2,3-triazole rings were about 85-94 %. All these synthesized hybrid compounds were examined for in vitro α-amylase (with IC50 values in the range of 103.63±1.13 μM to 295.45±1.11 μM) and α-glucosidase (with IC50 values in the range of 45.63±1.14 μM to 184.52±1.15) inhibitory activity. Amongst this series, ethyl ester 8m showed the best inhibitory activity against α-amylase with IC50 of 103.63±1.13 μM, while ethyl ester 8t exhibited the highest activity against α-glucosidase with IC50 of 45.63±1.14 μM. The kinetics of the inhibition of compound 8t showed the competitive α-glucosidase inhibitor property of this compound. Furthermore, the most potent compounds had any cytotoxicity against human normal cells. Induced fit docking and molecular dynamics simulation calculations indicated that the inhibition potential compounds 8m and 8t had the active interactions with the residues in receptors of corresponding tested enzymes. The calculated binding free energy from MM-GBSA approach showed that the major energy components contributed to the active binding of these studied inhibitors, including Coulomb, lipophilic and van der Waals energy. Further, 300 ns MD simulation showed that studied ligand-protein complexes were stable and indicated the structural observations into mode of binding in these complexes.
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Affiliation(s)
- Vu Ngoc Toan
- Faculty of Chemistry, University of Science (Vietnam National University, Hanoi), 19 Le Thanh Tong, Hoan Kiem, Ha Noi, Viet Nam.,Institute of New Technology, Academy of Military Science and Technology, Ministry of Defence, 17 Hoang Sam, Cau Giay, Ha Noi, Viet Nam
| | - Nguyen Dinh Thanh
- Faculty of Chemistry, University of Science (Vietnam National University, Hanoi), 19 Le Thanh Tong, Hoan Kiem, Ha Noi, Viet Nam
| | - Le Thi Huyen
- Faculty of Chemistry, University of Science (Vietnam National University, Hanoi), 19 Le Thanh Tong, Hoan Kiem, Ha Noi, Viet Nam
| | - Nguyen Thi Hanh
- Faculty of Chemistry, University of Science (Vietnam National University, Hanoi), 19 Le Thanh Tong, Hoan Kiem, Ha Noi, Viet Nam
| | - Do Son Hai
- Faculty of Chemistry, University of Science (Vietnam National University, Hanoi), 19 Le Thanh Tong, Hoan Kiem, Ha Noi, Viet Nam.,Institute of Science and Technology, Ministry of Public Security of Vietnam, 47 Pham Van Dong, Cau Giay, Ha Noi, Viet Nam
| | - Hoang Huu Anh
- Faculty of Chemistry, University of Science (Vietnam National University, Hanoi), 19 Le Thanh Tong, Hoan Kiem, Ha Noi, Viet Nam
| | - Nguyen Thi Kim Giang
- Faculty of Chemistry, University of Science (Vietnam National University, Hanoi), 19 Le Thanh Tong, Hoan Kiem, Ha Noi, Viet Nam.,Institute of Science and Technology, Ministry of Public Security of Vietnam, 47 Pham Van Dong, Cau Giay, Ha Noi, Viet Nam
| | - Hoang Thi Kim Van
- Faculty of Chemistry, University of Science (Vietnam National University, Hanoi), 19 Le Thanh Tong, Hoan Kiem, Ha Noi, Viet Nam.,Faculty of Chemical Technology, Viet Tri University of Industry, Tien Kien, Lam Thao, Phu Tho, Viet Nam
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5
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Thanh ND, Hai DS, Thi Huyen L, Giang NTK, Thu Ha NT, Tung DT, Thi Le C, Van HTK, Toan VN. Synthesis and in vitro anticancer activity of 4H-pyrano[2,3-d]pyrimidine−1H-1,2,3-triazole hybrid compounds bearing D-glucose moiety with dual EGFR/HER2 inhibitory activity and induced fit docking study. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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6
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Son Hai D, Thi Thu Ha N, Tien Tung D, Thi Kim Giang N, Thi Thu Huong N, Huu Anh H, Thi Kim Van H, Ngoc Toan V, Toan DN, Thanh ND. Synthesis, biological evaluation and induced fit docking simulation study of d-glucose-conjugated 1 H-1,2,3-triazoles having 4 H-pyrano[2,3- d]pyrimidine ring as potential agents against bacteria and fungi. NEW J CHEM 2022. [DOI: 10.1039/d1nj05330b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Gluco-conjugated 1H-1,2,3-triazoles having 4H-pyrano[2,3-d]pyrimidines are synthesized via click chemistry of N-propargyl-4H-pyrano[2,3-d]pyrimidines and glucopyaranosyl azide using CuI@Montmorillonite. Their antibacterial, anti-MRSA, and antifungal activity is probed.
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Affiliation(s)
- Do Son Hai
- Faculty of Chemistry, VNU University of Science (Vietnam National University, Ha Noi), 19 Le Thanh Tong, Hoan Kiem, Ha Noi, Vietnam
- Institute of Science and Technology, Ministry of Public Security of Vietnam, 47 Pham Van Dong, Cau Giay, Ha Noi, Vietnam
| | - Nguyen Thi Thu Ha
- Faculty of Chemistry, VNU University of Science (Vietnam National University, Ha Noi), 19 Le Thanh Tong, Hoan Kiem, Ha Noi, Vietnam
| | - Do Tien Tung
- Faculty of Chemistry, VNU University of Science (Vietnam National University, Ha Noi), 19 Le Thanh Tong, Hoan Kiem, Ha Noi, Vietnam
| | - Nguyen Thi Kim Giang
- Faculty of Chemistry, VNU University of Science (Vietnam National University, Ha Noi), 19 Le Thanh Tong, Hoan Kiem, Ha Noi, Vietnam
- Institute of Science and Technology, Ministry of Public Security of Vietnam, 47 Pham Van Dong, Cau Giay, Ha Noi, Vietnam
| | - Nguyen Thi Thu Huong
- Faculty of Chemistry, VNU University of Science (Vietnam National University, Ha Noi), 19 Le Thanh Tong, Hoan Kiem, Ha Noi, Vietnam
| | - Hoang Huu Anh
- Faculty of Chemistry, VNU University of Science (Vietnam National University, Ha Noi), 19 Le Thanh Tong, Hoan Kiem, Ha Noi, Vietnam
| | - Hoang Thi Kim Van
- Faculty of Chemistry, VNU University of Science (Vietnam National University, Ha Noi), 19 Le Thanh Tong, Hoan Kiem, Ha Noi, Vietnam
- Faculty of Chemical Technology, Viet Tri University of Industry, Tien Kien, Lam Thao, Phu Tho, Vietnam
| | - Vu Ngoc Toan
- Faculty of Chemistry, VNU University of Science (Vietnam National University, Ha Noi), 19 Le Thanh Tong, Hoan Kiem, Ha Noi, Vietnam
- Institute for Chemistry and Materials, Military Institute of Science and Technology (Ministry of Military), Cau Giay, Ha Noi, Vietnam
| | - Duong Ngoc Toan
- Faculty of Chemistry, VNU University of Science (Vietnam National University, Ha Noi), 19 Le Thanh Tong, Hoan Kiem, Ha Noi, Vietnam
- Faculty of Chemistry, Thai Nguyen University of Education, 20 Luong Ngoc Quyen, Thai Nguyen, Vietnam
| | - Nguyen Dinh Thanh
- Faculty of Chemistry, VNU University of Science (Vietnam National University, Ha Noi), 19 Le Thanh Tong, Hoan Kiem, Ha Noi, Vietnam
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7
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Zartner L, Maffeis V, Schoenenberger CA, Dinu IA, Palivan CG. Membrane protein channels equipped with a cleavable linker for inducing catalysis inside nanocompartments. J Mater Chem B 2021; 9:9012-9022. [PMID: 34623367 PMCID: PMC8580015 DOI: 10.1039/d1tb01463c] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 10/01/2021] [Indexed: 11/25/2022]
Abstract
Precisely timed initiation of reactions and stability of the catalysts are fundamental in catalysis. We introduce here an efficient closing-opening method for nanocompartments that contain sensitive catalysts and so achieve a controlled and extended catalytic activity. We developed a chemistry-oriented approach for modifying a pore-forming membrane protein which allows for a stimuli-responsive pore opening within the membrane of polymeric nanocompartments. We synthesized a diol-containing linker that selectively binds to the pores, blocking them completely. In the presence of an external stimulus (periodate), the linker is cleaved allowing the diffusion of substrate through the pores to the nanocompartment interior where it sets off the in situ enzymatic reaction. Besides the precise initiation of catalytic activity by opening of the pores, oxidation by periodate guarantees the cleavage of the linker under mild conditions. Accordingly, this kind of responsive nanocompartment lends itself to harboring a large variety of sensitive catalysts such as proteins and enzymes.
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Affiliation(s)
- Luisa Zartner
- Department of Chemistry, University of Basel, BPR1096, Mattenstrasse 24a, 4058 Basel, Switzerland.
| | - Viviana Maffeis
- Department of Chemistry, University of Basel, BPR1096, Mattenstrasse 24a, 4058 Basel, Switzerland.
- NCCR-Molecular Systems Engineering, BPR1095, Mattenstrasse 24a, 4058 Basel, Switzerland
| | - Cora-Ann Schoenenberger
- Department of Chemistry, University of Basel, BPR1096, Mattenstrasse 24a, 4058 Basel, Switzerland.
- NCCR-Molecular Systems Engineering, BPR1095, Mattenstrasse 24a, 4058 Basel, Switzerland
| | - Ionel Adrian Dinu
- Department of Chemistry, University of Basel, BPR1096, Mattenstrasse 24a, 4058 Basel, Switzerland.
- NCCR-Molecular Systems Engineering, BPR1095, Mattenstrasse 24a, 4058 Basel, Switzerland
| | - Cornelia G Palivan
- Department of Chemistry, University of Basel, BPR1096, Mattenstrasse 24a, 4058 Basel, Switzerland.
- NCCR-Molecular Systems Engineering, BPR1095, Mattenstrasse 24a, 4058 Basel, Switzerland
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Shao Y, Bao H, Ma L, Yuan W, Zhang L, Yao J, Meng P, Peng Y, Zhang S, Cao T, Lu H. Enhancing Comprehensive Analysis of Newly Synthesized Proteins Based on Cleavable Bioorthogonal Tagging. Anal Chem 2021; 93:9408-9417. [PMID: 34197092 DOI: 10.1021/acs.analchem.1c00965] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Protein synthesis and degradation responding to environmental cues is critical for understanding the mechanisms involved. Chemical proteomics introducing bioorthogonal tagging into proteins and isolation by biotin affinity purification is applicable for enrichment of newly synthesized proteins (NSPs). Current enrichment methods based on biotin-streptavidin interaction lack efficiency to release enriched NSPs under mild conditions. Here we designed a novel method for enriching newly synthesized peptides by click chemistry followed by release of enriched peptides via tryptic digestion based on cleavable bioorthogonal tagging (CBOT). CBOT-modified peptides can further enhance identification in mass spectrometry analysis and provide a confirmation by small mass shift. Our method achieved an improvement in specificity (97.1%) and sensitivity for NSPs in cell lysate, corresponding to profiling at a depth of 4335 NSPs from 2 mg of starting materials in a single LC-MS/MS run. In addition, the CBOT strategy can quantify NSPs when coupling a pair of isotope-labeled azidohomoalanine (AHA/hAHA) with decent reproducibility. Furthermore, we applied it to analyze newly synthesized proteomes in the autophagy process after 6 h rapamycin stimulation in cells, 2910 NSPs were quantified, and 337 NSPs among them were significantly up- and down-regulated. We envision CBOT as an effective and alternative approach for bioorthogonal chemical proteomics to study stimuli-sensitive subsets.
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Affiliation(s)
- Yuyin Shao
- Shanghai Cancer Center and Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, Shanghai 200032, P. R. China
| | - Huimin Bao
- Shanghai Cancer Center and Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, Shanghai 200032, P. R. China
| | - Lixiang Ma
- Department of Anatomy, Histology & Embryology, School of Medical Sciences, Fudan University, Shanghai 200032, P. R. China
| | - Wenjuan Yuan
- Shanghai Cancer Center and Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, Shanghai 200032, P. R. China
| | - Lei Zhang
- Shanghai Cancer Center and Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, Shanghai 200032, P. R. China
| | - Jun Yao
- Shanghai Cancer Center and Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, Shanghai 200032, P. R. China
| | - Peiyi Meng
- Shanghai Cancer Center and Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, Shanghai 200032, P. R. China
| | - Ye Peng
- Shanghai Cancer Center and Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, Shanghai 200032, P. R. China
| | - Siwen Zhang
- Shanghai Cancer Center and Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, Shanghai 200032, P. R. China
| | - Ting Cao
- Shanghai Cancer Center and Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, Shanghai 200032, P. R. China
| | - Haojie Lu
- Shanghai Cancer Center and Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, Shanghai 200032, P. R. China
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9
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Shieh P, Hill MR, Zhang W, Kristufek SL, Johnson JA. Clip Chemistry: Diverse (Bio)(macro)molecular and Material Function through Breaking Covalent Bonds. Chem Rev 2021; 121:7059-7121. [PMID: 33823111 DOI: 10.1021/acs.chemrev.0c01282] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In the two decades since the introduction of the "click chemistry" concept, the toolbox of "click reactions" has continually expanded, enabling chemists, materials scientists, and biologists to rapidly and selectively build complexity for their applications of interest. Similarly, selective and efficient covalent bond breaking reactions have provided and will continue to provide transformative advances. Here, we review key examples and applications of efficient, selective covalent bond cleavage reactions, which we refer to herein as "clip reactions." The strategic application of clip reactions offers opportunities to tailor the compositions and structures of complex (bio)(macro)molecular systems with exquisite control. Working in concert, click chemistry and clip chemistry offer scientists and engineers powerful methods to address next-generation challenges across the chemical sciences.
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Affiliation(s)
- Peyton Shieh
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Megan R Hill
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Wenxu Zhang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Samantha L Kristufek
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jeremiah A Johnson
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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10
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Reimagining high-throughput profiling of reactive cysteines for cell-based screening of large electrophile libraries. Nat Biotechnol 2021; 39:630-641. [PMID: 33398154 PMCID: PMC8316984 DOI: 10.1038/s41587-020-00778-3] [Citation(s) in RCA: 129] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 11/17/2020] [Indexed: 01/28/2023]
Abstract
Current methods used for measuring amino acid side-chain reactivity lack the throughput needed to screen large chemical libraries for interactions across the proteome. Here we redesigned the workflow for activity-based protein profiling of reactive cysteine residues by using a smaller desthiobiotin-based probe, sample multiplexing, reduced protein starting amounts and software to boost data acquisition in real time on the mass spectrometer. Our method, streamlined cysteine activity-based protein profiling (SLC-ABPP), achieved a 42-fold improvement in sample throughput, corresponding to profiling library members at a depth of >8,000 reactive cysteine sites at 18 min per compound. We applied it to identify proteome-wide targets of covalent inhibitors to mutant Kirsten rat sarcoma (KRAS)G12C and Bruton's tyrosine kinase (BTK). In addition, we created a resource of cysteine reactivity to 285 electrophiles in three human cell lines, which includes >20,000 cysteines from >6,000 proteins per line. The goal of proteome-wide profiling of cysteine reactivity across thousand-member libraries under several cellular contexts is now within reach.
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11
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Beard HA, Korovesis D, Chen S, Verhelst SHL. Cleavable linkers and their application in MS-based target identification. Mol Omics 2021; 17:197-209. [PMID: 33507200 DOI: 10.1039/d0mo00181c] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covalent chemical probes are important tools in chemical biology. They range from post-translational modification (PTM)-derived metabolic probes, to activity-based probes and photoaffinity labels. Identification of the probe targets is often performed by tandem mass spectrometry-based proteomics methods. In the past fifteen years, cleavable linker technologies have been implemented in these workflows in order to identify probe targets with lower background and higher confidence. In addition, the linkers have enabled identification of modification sites. Overall, this has led to an increased knowledge of PTMs, enzyme function and drug action. This review gives an overview of the different types of cleavable linkers, and their benefits and limitations. Their applicability in target identification is also illustrated by several specific examples.
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Affiliation(s)
- Hester A Beard
- KU Leuven, Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology, Herestr. 49 box 802, 3000 Leuven, Belgium.
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12
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Lyu Z, Zhao Y, Buuh ZY, Gorman N, Goldman AR, Islam MS, Tang HY, Wang RE. Steric-Free Bioorthogonal Labeling of Acetylation Substrates Based on a Fluorine-Thiol Displacement Reaction. J Am Chem Soc 2021; 143:1341-1347. [PMID: 33433199 PMCID: PMC8300487 DOI: 10.1021/jacs.0c05605] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We have developed a novel bioorthogonal reaction that can selectively displace fluorine substitutions alpha to amide bonds. This fluorine-thiol displacement reaction (FTDR) allows for fluorinated cofactors or precursors to be utilized as chemical reporters, hijacking acetyltransferase-mediated acetylation both in vitro and in live cells, which cannot be achieved with azide- or alkyne-based chemical reporters. The fluoroacetamide labels can be further converted to biotin or fluorophore tags using FTDR, enabling the general detection and imaging of acetyl substrates. This strategy may lead to a steric-free labeling platform for substrate proteins, expanding our chemical toolbox for functional annotation of post-translational modifications in a systematic manner.
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Affiliation(s)
- Zhigang Lyu
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - Yue Zhao
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - Zakey Yusuf Buuh
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - Nicole Gorman
- Proteomics and Metabolomics Facility, The Wistar Institute, Philadelphia, Pennsylvania 19104, United States
| | - Aaron R Goldman
- Proteomics and Metabolomics Facility, The Wistar Institute, Philadelphia, Pennsylvania 19104, United States
| | - Md Shafiqul Islam
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - Hsin-Yao Tang
- Proteomics and Metabolomics Facility, The Wistar Institute, Philadelphia, Pennsylvania 19104, United States
| | - Rongsheng E Wang
- Department of Chemistry, Temple University, 1901 N. 13th Street, Philadelphia, Pennsylvania 19122, United States
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13
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Toan DN, Thanh ND, Truong MX, Van DT. Synthesis, Cytotoxicity, ADMET and Molecular Docking Studies of Some Quinoline-Pyrimidine Hybrid Compounds: 3-(2-Amino-6-arylpyrimidin-4- yl)-4-hydroxy-1-methylquinolin-2(1H)-ones. Med Chem 2020; 18:36-50. [PMID: 33380305 DOI: 10.2174/1573406417666201230092615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 09/01/2020] [Accepted: 10/12/2020] [Indexed: 11/22/2022]
Abstract
AIMS Synthesis of 3-(2-amino-6-arylpyrimidin-4-yl)-4-hydroxy-1-methylquinolin-2(1H)-ones and estimation their anticancer activities on HepG2 and KB cancer lines. BACKGROUND Many derivatives of quinoline-2-on have been consider to synthesize and evaluate their biological properties by organic chemists due to their various biological effects, including antibacterial, antioxidant, anti-inflammatory, anticancer activities. Quinolinepyrimidine hybrid compounds exhibited various biological activities, such as antituberculosis, antibacterial, anticancer, antifungal, etc. The connection of 4-hydroxyquinoline-2-one with 2-amino-pyrimidine could initiate the new activities. OBJECTIVE α,β-Unsaturated ketones of 3-acetyl-4-hydroxy-N-methylquinolin-2-one were prepared. Novel 2-amino-6-aryl-4-(4'-hydroxy-Nmethylquinolin- 2'-on-3'-yl)pyrimidines have been synthesized by reaction of these corresponding α,β-unsaturated ketones with guanidine hydrochloride. Human hepatocellular carcinoma HepG2 and squamous cell carcinoma KB cancer lines were used for screening their cytotoxicity. METHOD 3-Acetyl-4-hydroxy-N-methylquinolin-2-one was prepared from N-methylaniline and diethyl malonate. Reaction of (un)substituted benzaldehydes with this 4-hydroxyquinoline-2-one produced corresponding substituted α ,β-unsaturated ketones in the presence of piperidine as catalyst. 2-Amino-6-aryl-4-(4'-hydroxy-N-methylquinolin-2'-on-3'-yl)pyrimidines have been synthesized from these α,β-unsaturated ketones of 3-acetyl-4-hydroxy-N-methylquinolin-2-one by reaction of corresponding α ,β-unsaturated ketones with guanidine hydrochloride. All obtained pyrimidines were screened for anticancer activity using MTT bio-assay method. RESULT Seven substituted (E)-4-hydroxy-3-(3-(aryl)acryloyl)-1-methylquinolin-2(1H)-ones were prepared and converted to corresponding substituted 2-amino-6-aryl-4-(4'-hydroxy-N-methylquinolin-2'-on-3'-yl)pyrimidines with yields of 58-74%. All the synthesized pyrimidines were screened for their in vitro anticancer activity against human hepatocellular carcinoma HepG2 and squamous cell carcinoma KB cancer lines. Compounds 6b and 6e had the best activity in the series, with IC50 values equal to 1.32 and 1.33 μM, respectively. ADMET properties showed that compounds 6b, 6e, and 6f possessed the drug-likeness behavior. Cross-docking results indicated that residues GLN778(A), DT8(C), DT9(D), DA12(F), and DG13(F) in the binding pocket as potential ligand binding hot-spot residues for compounds 6b, 6e, and 6f. CONCLUSION New substituted 2-amino-6-aryl-4-(4'-hydroxy-N-methylquinolin-2'-on-3'-yl)pyrimidines were obtained and displayed significant inhibition against human hepatocellular carcinoma HepG2 and squamous cell carcinoma KB cancer lines.
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Affiliation(s)
- Duong Ngoc Toan
- Faculty of Chemistry, Thai Nguyen University of Education, 20 Luong Ngoc Quyen, Thai Nguyen. Vietnam
| | - Nguyen Dinh Thanh
- Faculty of Chemistry, VNU University of Science (Vietnam National University, Ha Noi), 19 Le Thanh Tong, Hoan Kiem, Ha Noi. Vietnam
| | - Mai Xuan Truong
- Faculty of Chemistry, Thai Nguyen University of Education, 20 Luong Ngoc Quyen, Thai Nguyen. Vietnam
| | - Dinh Thuy Van
- Faculty of Chemistry, Thai Nguyen University of Education, 20 Luong Ngoc Quyen, Thai Nguyen. Vietnam
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14
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Quinoline-pyrimidine hybrid compounds from 3-acetyl-4-hydroxy-1-methylquinolin-2(1H)-one: Study on synthesis, cytotoxicity, ADMET and molecular docking. ARAB J CHEM 2020. [DOI: 10.1016/j.arabjc.2020.09.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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15
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Pomplun S, Shugrue CR, Schmitt AM, Schissel CK, Farquhar CE, Pentelute BL. Secondary Amino Alcohols: Traceless Cleavable Linkers for Use in Affinity Capture and Release. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Sebastian Pomplun
- Massachusetts Institute of Technology Department of Chemistry 77 Massachusetts Ave. Cambridge MA 02139 USA
| | - Christopher R. Shugrue
- Massachusetts Institute of Technology Department of Chemistry 77 Massachusetts Ave. Cambridge MA 02139 USA
| | | | - Carly K. Schissel
- Massachusetts Institute of Technology Department of Chemistry 77 Massachusetts Ave. Cambridge MA 02139 USA
| | - Charlotte E. Farquhar
- Massachusetts Institute of Technology Department of Chemistry 77 Massachusetts Ave. Cambridge MA 02139 USA
| | - Bradley L. Pentelute
- Massachusetts Institute of Technology Department of Chemistry 77 Massachusetts Ave. Cambridge MA 02139 USA
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16
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Lopez Quezada L, Smith R, Lupoli TJ, Edoo Z, Li X, Gold B, Roberts J, Ling Y, Park SW, Nguyen Q, Schoenen FJ, Li K, Hugonnet JE, Arthur M, Sacchettini JC, Nathan C, Aubé J. Activity-Based Protein Profiling Reveals That Cephalosporins Selectively Active on Non-replicating Mycobacterium tuberculosis Bind Multiple Protein Families and Spare Peptidoglycan Transpeptidases. Front Microbiol 2020; 11:1248. [PMID: 32655524 PMCID: PMC7324553 DOI: 10.3389/fmicb.2020.01248] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 05/15/2020] [Indexed: 11/13/2022] Open
Abstract
As β-lactams are reconsidered for the treatment of tuberculosis (TB), their targets are assumed to be peptidoglycan transpeptidases, as verified by adduct formation and kinetic inhibition of Mycobacterium tuberculosis (Mtb) transpeptidases by carbapenems active against replicating Mtb. Here, we investigated the targets of recently described cephalosporins that are selectively active against non-replicating (NR) Mtb. NR-active cephalosporins failed to inhibit recombinant Mtb transpeptidases. Accordingly, we used alkyne analogs of NR-active cephalosporins to pull down potential targets through unbiased activity-based protein profiling and identified over 30 protein binders. None was a transpeptidase. Several of the target candidates are plausibly related to Mtb's survival in an NR state. However, biochemical tests and studies of loss of function mutants did not identify a unique target that accounts for the bactericidal activity of these beta-lactams against NR Mtb. Instead, NR-active cephalosporins appear to kill Mtb by collective action on multiple targets. These results highlight the ability of these β-lactams to target diverse classes of proteins.
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Affiliation(s)
- Landys Lopez Quezada
- Department of Microbiology & Immunology, Weill Cornell Medical College, New York, NY, United States
| | - Robert Smith
- Chemical Methodologies & Library Development Center, The University of Kansas, Lawrence, KS, United States
| | - Tania J Lupoli
- Department of Microbiology & Immunology, Weill Cornell Medical College, New York, NY, United States
| | - Zainab Edoo
- Sorbonne Université, Sorbonne Paris Cité, Université de Paris, INSERM, Centre de Recherche des Cordeliers, CRC, Paris, France
| | - Xiaojun Li
- Departments of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Ben Gold
- Department of Microbiology & Immunology, Weill Cornell Medical College, New York, NY, United States
| | - Julia Roberts
- Department of Microbiology & Immunology, Weill Cornell Medical College, New York, NY, United States
| | - Yan Ling
- Department of Microbiology & Immunology, Weill Cornell Medical College, New York, NY, United States
| | - Sae Woong Park
- Department of Microbiology & Immunology, Weill Cornell Medical College, New York, NY, United States
| | - Quyen Nguyen
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Frank J Schoenen
- Chemical Methodologies & Library Development Center, The University of Kansas, Lawrence, KS, United States
| | - Kelin Li
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jean-Emmanuel Hugonnet
- Sorbonne Université, Sorbonne Paris Cité, Université de Paris, INSERM, Centre de Recherche des Cordeliers, CRC, Paris, France
| | - Michel Arthur
- Sorbonne Université, Sorbonne Paris Cité, Université de Paris, INSERM, Centre de Recherche des Cordeliers, CRC, Paris, France
| | - James C Sacchettini
- Departments of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Carl Nathan
- Department of Microbiology & Immunology, Weill Cornell Medical College, New York, NY, United States
| | - Jeffrey Aubé
- Chemical Methodologies & Library Development Center, The University of Kansas, Lawrence, KS, United States.,Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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17
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Pomplun S, Shugrue CR, Schmitt AM, Schissel CK, Farquhar CE, Pentelute BL. Secondary Amino Alcohols: Traceless Cleavable Linkers for Use in Affinity Capture and Release. Angew Chem Int Ed Engl 2020; 59:11566-11572. [PMID: 32227406 DOI: 10.1002/anie.202003478] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 03/24/2020] [Indexed: 11/09/2022]
Abstract
Capture and release of peptides is often a critical operation in the pathway to discovering materials with novel functions. However, the best methods for efficient capture impede facile release. To overcome this challenge, we report linkers based on secondary amino alcohols for the release of peptides after capture. These amino alcohols are based on serine (seramox) or isoserine (isoseramox) and can be incorporated into peptides during solid-phase peptide synthesis through reductive amination. Both linkers are quantitatively cleaved within minutes under NaIO4 treatment. Cleavage of isoseramox produced a native peptide N-terminus. This linker also showed broad substrate compatibility; incorporation into a synthetic peptide library resulted in the identification of all sequences by nanoLC-MS/MS. The linkers are cell compatible; a cell-penetrating peptide that contained this linker was efficiently captured and identified after uptake into cells. These findings suggest that such secondary amino alcohol based linkers might be suitable tools for peptide-discovery platforms.
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Affiliation(s)
- Sebastian Pomplun
- Massachusetts Institute of Technology, Department of Chemistry, 77 Massachusetts Ave., Cambridge, MA, 02139, USA
| | - Christopher R Shugrue
- Massachusetts Institute of Technology, Department of Chemistry, 77 Massachusetts Ave., Cambridge, MA, 02139, USA
| | - Adeline M Schmitt
- Université de Strasbourg, 4 rue Blaise Pascal, 67000, Strasbourg, France
| | - Carly K Schissel
- Massachusetts Institute of Technology, Department of Chemistry, 77 Massachusetts Ave., Cambridge, MA, 02139, USA
| | - Charlotte E Farquhar
- Massachusetts Institute of Technology, Department of Chemistry, 77 Massachusetts Ave., Cambridge, MA, 02139, USA
| | - Bradley L Pentelute
- Massachusetts Institute of Technology, Department of Chemistry, 77 Massachusetts Ave., Cambridge, MA, 02139, USA
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18
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Rabalski AJ, Bogdan AR, Baranczak A. Evaluation of Chemically-Cleavable Linkers for Quantitative Mapping of Small Molecule-Cysteinome Reactivity. ACS Chem Biol 2019; 14:1940-1950. [PMID: 31430117 DOI: 10.1021/acschembio.9b00424] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Numerous reagents have been developed to enable chemical proteomic analysis of small molecule-protein interactomes. However, the performance of these reagents has not been systematically evaluated and compared. Herein, we report our efforts to conduct a parallel assessment of two widely used chemically cleavable linkers equipped with dialkoxydiphenylsilane (DADPS linker) and azobenzene (AZO linker) moieties. Profiling a cellular cysteinome using the iodoacetamide alkyne probe demonstrated a significant discrepancy between the experimental results obtained through the application of each of the reagents. To better understand the source of observed discrepancy, we evaluated the key sample preparation steps. We also performed a mass tolerant database search strategy using MSFragger software. This resulted in identifying a previously unreported artifactual modification on the residual mass of the azobenzene linker. Furthermore, we conducted a comparative analysis of enrichment modes using both cleavable linkers. This effort determined that enrichment of proteolytic digests yielded a far greater number of identified cysteine residues than the enrichment conducted prior to protein digest. Inspired by recent studies where multiplexed quantitative labeling strategies were applied to cleavable biotin linkers, we combined this further optimized protocol using the DADPS cleavable linker with tandem mass tag (TMT) labeling to profile the FDA-approved covalent EGFR kinase inhibitor dacomitinib against the cysteinome of an epidermoid cancer cell line. Our analysis resulted in the detection and quantification of over 10,000 unique cysteine residues, a nearly 3-fold increase over previous studies that used cleavable biotin linkers for enrichment. Critically, cysteine residues corresponding to proteins directly as well as indirectly modulated by dacomitinib treatment were identified. Overall, our study suggests that the dialkoxydiphenylsilane linker could be broadly applied wherever chemically cleavable linkers are required for chemical proteomic characterization of cellular proteomes.
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Affiliation(s)
- Adam J. Rabalski
- Drug Discovery Science & Technology, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064-6101, United States
| | - Andrew R. Bogdan
- Drug Discovery Science & Technology, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064-6101, United States
| | - Aleksandra Baranczak
- Drug Discovery Science & Technology, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064-6101, United States
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19
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Krömer M, Bártová K, Raindlová V, Hocek M. Synthesis of Dihydroxyalkynyl and Dihydroxyalkyl Nucleotides as Building Blocks or Precursors for Introduction of Diol or Aldehyde Groups to DNA for Bioconjugations. Chemistry 2018; 24:11890-11894. [PMID: 29790604 DOI: 10.1002/chem.201802282] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Indexed: 01/18/2023]
Abstract
(3,4-Dihydroxybut-1-ynyl)uracil, -cytosine and -7-deazaadenine 2'-deoxyribonucleoside triphosphates (dNTPs) were prepared by direct aqueous Sonogashira cross-coupling of halogenated dNTPs with dihydroxybut-1-yne and converted to 3,4-dihydroxybutyl dNTPs through catalytic hydrogenation. Sodium periodate oxidative cleavage of dihydroxybutyl-dUTP gave the desired aliphatic aldehyde-linked dUTP, whereas the oxidative cleavage of the corresponding deazaadenine dNTP gave a cyclic aminal. All dihydroxyalkyl or -alkynyl dNTPs and the formylethyl-dUTP were good substrates for DNA polymerases and were used for synthesis of diol- or aldehyde-linked DNA. The aldehyde linked DNA was used for the labelling or bioconjugations through hydrazone formation or reductive aminations.
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Affiliation(s)
- Matouš Krömer
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 12843, Prague 2, Czech Republic
| | - Kateřina Bártová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 12843, Prague 2, Czech Republic
| | - Veronika Raindlová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 12843, Prague 2, Czech Republic
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20
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Tian Y, Lin Q. Genetic encoding of 2-aryl-5-carboxytetrazole-based protein photo-cross-linkers. Chem Commun (Camb) 2018; 54:4449-4452. [PMID: 29652063 DOI: 10.1039/c8cc02431f] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Three γ-heteroatom-substituted N-methylpyrroletetrazole-lysines (mPyTXKs) were synthesized and subsequently incorporated into proteins site-specifically via genetic code expansion. The γ-seleno-substituted derivative, mPyTSeK, showed excellent incorporation efficiency in Escherichia coli and allowed site-selective photo-cross-linking of the GST dimer. Furthermore, the mPyTSeK-cross-linked GST dimer can be cleaved under mild oxidative conditions. The incorporation of mPyTXKs into proteins in mammalian cells was also demonstrated. Lastly, the recombinantly expressed mPyTSeK-encoded Grb2 was shown to covalently capture its interaction partner, EGFR, in mammalian cell lysate, which was subsequently released after treatment with H2O2.
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Affiliation(s)
- Yulin Tian
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260-3000, USA.
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21
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Hoch DG, Abegg D, Adibekian A. Cysteine-reactive probes and their use in chemical proteomics. Chem Commun (Camb) 2018; 54:4501-4512. [PMID: 29645055 DOI: 10.1039/c8cc01485j] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Proteomic profiling using bioorthogonal chemical probes that selectively react with certain amino acids is now a widely used method in life sciences to investigate enzymatic activities, study posttranslational modifications and discover novel covalent inhibitors. Over the past two decades, researchers have developed selective probes for several different amino acids, including lysine, serine, cysteine, threonine, tyrosine, aspartate and glutamate. Among these amino acids, cysteines are particularly interesting due to their highly diverse and complex biochemical role in our cells. In this feature article, we focus on the chemical probes and methods used to study cysteines in complex proteomes.
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Affiliation(s)
- Dominic G Hoch
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
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22
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Abstract
The detection, visualization, and identification of active proteases can be facilitated by activity-based probes, which covalently bind to a catalytic residue of the target protease. The synthesis of activity-based probes can be challenging. We here outline a simple protocol for probe synthesis based on standard solid phase peptide synthesis followed by capping of the N-terminus with a reactive electrophile as a warhead. The applicability of the probes is illustrated by labeling cysteine proteases in cell and tissue lysates with Western blotting or fluorescence scanning as a readout.
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23
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Abstract
The activity of proteases is tightly regulated, and dysregulation is linked to a variety of human diseases. For this reason, ABPP is a well-suited method to study protease biology and the design of protease probes has pushed the boundaries of ABPP. The development of highly selective protease probes is still a challenging task. After an introduction, the first section of this chapter discusses several strategies to enable detection of a single active protease species. These range from the usage of non-natural amino acids, combination of probes with antibodies, and engineering of the target proteases. A next section describes the different types of detection tags that facilitate the read-out possibilities including various types of imaging methods and mass spectrometry-based target identification. The power of protease ABPP is illustrated by examples for a selected number of proteases. It is expected that some protease probes that have been evaluated in animal models of human disease will find translation into clinical application in the near future.
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24
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Sharifzadeh S, Shirley JD, Carlson EE. Activity-Based Protein Profiling Methods to Study Bacteria: The Power of Small-Molecule Electrophiles. Curr Top Microbiol Immunol 2018; 420:23-48. [PMID: 30232601 DOI: 10.1007/82_2018_135] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
ABPP methods have been utilized for the last two decades as a means to investigate complex proteomes in all three domains of life. Extensive use in eukaryotes has provided a more fundamental understanding of the biological processes involved in numerous diseases and has driven drug discovery and treatment campaigns. However, the use of ABPP in prokaryotes has been less common, although it has gained more attention over the last decade. The urgent need for understanding bacteriophysiology and bacterial pathogenicity at a foundational level has never been more apparent, as the rise in antibiotic resistance has resulted in the inadequate and ineffective treatment of infections. This is not only a result of resistance to clinically used antibiotics, but also a lack of new drugs and equally as important, new drug targets. ABPP provides a means for which new, clinically relevant drug targets may be identified through gaining insight into biological processes. In this chapter, we place particular focus on the discussion of ABPP strategies that have been applied to study different classes of bacterial enzymes.
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Affiliation(s)
- Shabnam Sharifzadeh
- Department of Chemistry, University of Minnesota-Twin Cities, Minneapolis, MN, 55455, USA
| | - Joshua D Shirley
- Department of Medicinal Chemistry, University of Minnesota-Twin Cities, Minneapolis, MN, 55455, USA
| | - Erin E Carlson
- Department of Chemistry, University of Minnesota-Twin Cities, Minneapolis, MN, 55455, USA. .,Department of Medicinal Chemistry, University of Minnesota-Twin Cities, Minneapolis, MN, 55455, USA. .,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota-Twin Cities, Minneapolis, MN, 55455, USA.
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25
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Wawro AM, Aoki Y, Muraoka T, Tsumoto K, Kinbara K. Enzymatically cleavable traceless biotin tags for protein PEGylation and purification. Chem Commun (Camb) 2018; 54:1913-1916. [DOI: 10.1039/c7cc05814d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Immobilized lipase was successfully employed for the rapid removal of a biotin tag from a protein–PEG conjugate under mild conditions.
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Affiliation(s)
- Adam M. Wawro
- School of Life Science and Technology
- Tokyo Institute of Technology
- Yokohama 226-8501
- Japan
- Department of Bioengineering
| | - Yusuke Aoki
- School of Life Science and Technology
- Tokyo Institute of Technology
- Yokohama 226-8501
- Japan
| | - Takahiro Muraoka
- School of Life Science and Technology
- Tokyo Institute of Technology
- Yokohama 226-8501
- Japan
- PRESTO
| | - Kouhei Tsumoto
- Department of Bioengineering
- School of Engineering
- The University of Tokyo
- Tokyo 108-8656
- Japan
| | - Kazushi Kinbara
- School of Life Science and Technology
- Tokyo Institute of Technology
- Yokohama 226-8501
- Japan
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26
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Cowell J, Buck M, Essa AH, Clarke R, Vollmer W, Vollmer D, Hilkens CM, Isaacs JD, Hall MJ, Gray J. Traceless Cleavage of Protein-Biotin Conjugates under Biologically Compatible Conditions. Chembiochem 2017; 18:1688-1691. [PMID: 28581639 PMCID: PMC5708275 DOI: 10.1002/cbic.201700214] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Indexed: 12/14/2022]
Abstract
Biotinylation of amines is widely used to conjugate biomolecules, but either the resulting label is non-removable or its removal leaves a tag on the molecule of interest, thus affecting downstream processes. We present here a set of reagents (RevAmines) that allow traceless, reversible biotinylation under biologically compatible, mild conditions. Release following avidin-based capture is achieved through the cleavage of a (2-(alkylsulfonyl)ethyl) carbamate linker under mild conditions (200 mm ammonium bicarbonate, pH 8, 16-24 h, room temperature) that regenerates the unmodified amine. The capture and release of biotinylated proteins and peptides from neutravidin, fluorescent labelling through reversible biotinylation at the cell surface and the selective enrichment of proteins from bacterial periplasm are demonstrated. The tags are easily prepared, stable and offer the potential for future application in proteomics, activity-based protein profiling, affinity chromatography and bio-molecule tagging and purification.
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Affiliation(s)
- Joseph Cowell
- School of ChemistryNewcastle UniversityNewcastle upon TyneNE2 7RUUK
| | - Matthew Buck
- Musculoskeletal Research GroupInstitute of Cellular MedicineNewcastle UniversityNewcastle upon TyneNE2 4HHUK
| | - Ali H. Essa
- School of ChemistryNewcastle UniversityNewcastle upon TyneNE2 7RUUK
- Department of ChemistryCollege of ScienceUniversity of BasrahBasrahIraq
| | - Rebecca Clarke
- School of ChemistryNewcastle UniversityNewcastle upon TyneNE2 7RUUK
| | - Waldemar Vollmer
- Institute for Cell and Molecular BiosciencesNewcastle UniversityNewcastle upon TyneNE2 4HHUK
| | - Daniela Vollmer
- Institute for Cell and Molecular BiosciencesNewcastle UniversityNewcastle upon TyneNE2 4HHUK
| | - Catharien M. Hilkens
- Musculoskeletal Research GroupInstitute of Cellular MedicineNewcastle UniversityNewcastle upon TyneNE2 4HHUK
| | - John D. Isaacs
- Musculoskeletal Research GroupInstitute of Cellular MedicineNewcastle UniversityNewcastle upon TyneNE2 4HHUK
| | - Michael J. Hall
- School of ChemistryNewcastle UniversityNewcastle upon TyneNE2 7RUUK
| | - Joe Gray
- Institute for Cell and Molecular BiosciencesNewcastle UniversityNewcastle upon TyneNE2 4HHUK
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27
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Wright MH, Sieber SA. Chemical proteomics approaches for identifying the cellular targets of natural products. Nat Prod Rep 2017; 33:681-708. [PMID: 27098809 PMCID: PMC5063044 DOI: 10.1039/c6np00001k] [Citation(s) in RCA: 252] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
This review focuses on chemical probes to identify the protein binding partners of natural products in living systems.
Covering: 2010 up to 2016 Deconvoluting the mode of action of natural products and drugs remains one of the biggest challenges in chemistry and biology today. Chemical proteomics is a growing area of chemical biology that seeks to design small molecule probes to understand protein function. In the context of natural products, chemical proteomics can be used to identify the protein binding partners or targets of small molecules in live cells. Here, we highlight recent examples of chemical probes based on natural products and their application for target identification. The review focuses on probes that can be covalently linked to their target proteins (either via intrinsic chemical reactivity or via the introduction of photocrosslinkers), and can be applied “in situ” – in living systems rather than cell lysates. We also focus here on strategies that employ a click reaction, the copper-catalysed azide–alkyne cycloaddition reaction (CuAAC), to allow minimal functionalisation of natural product scaffolds with an alkyne or azide tag. We also discuss ‘competitive mode’ approaches that screen for natural products that compete with a well-characterised chemical probe for binding to a particular set of protein targets. Fuelled by advances in mass spectrometry instrumentation and bioinformatics, many modern strategies are now embracing quantitative proteomics to help define the true interacting partners of probes, and we highlight the opportunities this rapidly evolving technology provides in chemical proteomics. Finally, some of the limitations and challenges of chemical proteomics approaches are discussed.
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Affiliation(s)
- M H Wright
- Department of Chemistry, Technische Universität München, Lichtenbergstraße 4, 85748, Garching, Germany.
| | - S A Sieber
- Department of Chemistry, Technische Universität München, Lichtenbergstraße 4, 85748, Garching, Germany.
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28
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Zhuang C, Zhang W, Sheng C, Zhang W, Xing C, Miao Z. Chalcone: A Privileged Structure in Medicinal Chemistry. Chem Rev 2017; 117:7762-7810. [PMID: 28488435 PMCID: PMC6131713 DOI: 10.1021/acs.chemrev.7b00020] [Citation(s) in RCA: 753] [Impact Index Per Article: 107.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Privileged structures have been widely used as an effective template in medicinal chemistry for drug discovery. Chalcone is a common simple scaffold found in many naturally occurring compounds. Many chalcone derivatives have also been prepared due to their convenient synthesis. These natural products and synthetic compounds have shown numerous interesting biological activities with clinical potentials against various diseases. This review aims to highlight the recent evidence of chalcone as a privileged scaffold in medicinal chemistry. Multiple aspects of chalcone will be summarized herein, including the isolation of novel chalcone derivatives, the development of new synthetic methodologies, the evaluation of their biological properties, and the exploration of the mechanisms of action as well as target identification. This review is expected to be a comprehensive, authoritative, and critical review of the chalcone template to the chemistry community.
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Affiliation(s)
- Chunlin Zhuang
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China
| | - Wen Zhang
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China
| | - Chunquan Sheng
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China
| | - Wannian Zhang
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China
- School of Pharmacy, Ningxia Medical University, 1160 Shengli Street, Yinchuan 750004, China
| | - Chengguo Xing
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1345 Center Drive,
Gainesville, Florida 32610, United States
| | - Zhenyuan Miao
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China
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29
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Hewings DS, Flygare JA, Bogyo M, Wertz IE. Activity-based probes for the ubiquitin conjugation-deconjugation machinery: new chemistries, new tools, and new insights. FEBS J 2017; 284:1555-1576. [PMID: 28196299 PMCID: PMC7163952 DOI: 10.1111/febs.14039] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 01/21/2017] [Accepted: 02/10/2017] [Indexed: 12/17/2022]
Abstract
The reversible post‐translational modification of proteins by ubiquitin and ubiquitin‐like proteins regulates almost all cellular processes, by affecting protein degradation, localization, and complex formation. Deubiquitinases (DUBs) are proteases that remove ubiquitin modifications or cleave ubiquitin chains. Most DUBs are cysteine proteases, which makes them well suited for study by activity‐based probes. These DUB probes report on deubiquitinase activity by reacting covalently with the active site in an enzyme‐catalyzed manner. They have proven to be important tools to study DUB selectivity and proteolytic activity in different settings, to identify novel DUBs, and to characterize deubiquitinase inhibitors. Inspired by the efficacy of activity‐based probes for DUBs, several groups have recently reported probes for the ubiquitin conjugation machinery (E1, E2, and E3 enzymes). Many of these enzymes, while not proteases, also posses active site cysteine residues and can be targeted by covalent probes. In this review, we will discuss how features of the probe (cysteine‐reactive group, recognition element, and reporter tag) affect reactivity and suitability for certain experimental applications. We will also review the diverse applications of the current probes, and discuss the need for new probe types to study emerging aspects of ubiquitin biology.
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Affiliation(s)
- David S Hewings
- Discovery Chemistry, Genentech, South San Francisco, CA, USA.,Early Discovery Biochemistry, Genentech, South San Francisco, CA, USA.,Discovery Oncology, Genentech, South San Francisco, CA, USA.,Department of Pathology, Stanford University School of Medicine, CA, USA
| | - John A Flygare
- Discovery Chemistry, Genentech, South San Francisco, CA, USA
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, CA, USA
| | - Ingrid E Wertz
- Early Discovery Biochemistry, Genentech, South San Francisco, CA, USA.,Discovery Oncology, Genentech, South San Francisco, CA, USA
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30
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Gertsik N, Am Ende CW, Geoghegan KF, Nguyen C, Mukherjee P, Mente S, Seneviratne U, Johnson DS, Li YM. Mapping the Binding Site of BMS-708163 on γ-Secretase with Cleavable Photoprobes. Cell Chem Biol 2017; 24:3-8. [PMID: 28065657 DOI: 10.1016/j.chembiol.2016.12.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 11/11/2016] [Accepted: 12/13/2016] [Indexed: 01/21/2023]
Abstract
γ-Secretase, a four-subunit transmembrane aspartic proteinase, is a highly valued drug target in Alzheimer's disease and cancer. Despite significant progress in structural studies, the respective molecular mechanisms and binding modes of γ-secretase inhibitors (GSIs) and modulators (GSMs) remain uncertain. Here, we developed biotinylated cleavable-linker photoprobes based on the BMS-708163 GSI to study its interaction with γ-secretase. Comparison of four cleavable linkers indicated that the hydrazine-labile N-1-(4,4-dimethyl-2,6-dioxocyclohexylidene)ethyl (Dde) linker was cleaved most efficiently to release photolabeled and affinity-captured presenilin-1 (PS1), the catalytic subunit of γ-secretase. Peptide mapping showed that the BMS-708163-based probe photoinserted at L282 of PS1. This insertion site was consistent with the results of molecular dynamics simulations of the γ-secretase complex with inhibitor. Taken together, this work reveals the binding site of a GSI and offers insights into the mechanism of action of this class of inhibitors.
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Affiliation(s)
- Natalya Gertsik
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA; Biochemistry and Molecular Biology Program, Weill Graduate School of Medical Sciences of Cornell University, New York, NY 10021, USA
| | - Christopher W Am Ende
- Pfizer Worldwide Research and Development, Neuroscience Medicinal Chemistry, Groton, CT 06340, USA
| | - Kieran F Geoghegan
- Pfizer Worldwide Research and Development, Structural and Molecular Sciences, Groton, CT 06340, USA
| | - Chuong Nguyen
- Pfizer Worldwide Research and Development, Structural and Molecular Sciences, Groton, CT 06340, USA
| | - Paramita Mukherjee
- Pfizer Worldwide Research and Development, Neuroscience Medicinal Chemistry, Groton, CT 06340, USA
| | - Scot Mente
- Pfizer Worldwide Research and Development, Neuroscience Medicinal Chemistry and Chemical Biology, Cambridge, MA 02139, USA
| | - Uthpala Seneviratne
- Pfizer Worldwide Research and Development, Neuroscience Medicinal Chemistry and Chemical Biology, Cambridge, MA 02139, USA
| | - Douglas S Johnson
- Pfizer Worldwide Research and Development, Neuroscience Medicinal Chemistry and Chemical Biology, Cambridge, MA 02139, USA.
| | - Yue-Ming Li
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA; Xiangya International Academy of Translational Medicine, Central South University, Changsha, Hunan 410013, China.
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31
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Abstract
The discovery of the protein targets of small molecule probes is a crucial aspect of activity-based protein profiling and chemical biology. Mass spectrometry is the primary method for target identification, and in the last decade, cleavable linkers have become a popular strategy to facilitate protein enrichment and identification. In this chapter, we provide an overview of cleavable linkers used in chemical proteomics approaches, discuss their different chemistries, and describe how they aid in protein identification.
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Affiliation(s)
- Yinliang Yang
- Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany
| | - Marko Fonović
- Department of Biochemistry, Molecular and Structural Biology, Jožef Stefan Institute, Jamova cesta 39, Ljubljana, Slovenia
| | - Steven H L Verhelst
- Department of Cellular and Molecular Medicine, KU Leuven - University of Leuven, Herestr. 49 box 802, 3000 Leuven, Belgium, 3000, Leuven, Belgium.
- Leibniz Institute for AnalyticalSciences ISAS, Otto-Hahn-Str. 6b, 44227, Dortmund, Germany.
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32
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Gebert J, Schnölzer M, Warnken U, Kopitz J. Combining Click Chemistry-Based Proteomics With Dox-Inducible Gene Expression. Methods Enzymol 2016; 585:295-327. [PMID: 28109436 DOI: 10.1016/bs.mie.2016.09.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Inactivating mutations in single genes can trigger, prevent, promote, or alleviate diseases. Identifying such disease-related genes is a main pillar of medical research. Since proteins play a crucial role in mediating these effects, their impact on the diseased cells' proteome including posttranslational modifications has to be elucidated for a detailed understanding of the role of these genes in the disease process. In complex disorders, like cancer, several genes contribute to the disease process, thereby hampering the assignment of a proteomic change to the corresponding causative gene. To enable comprehensive screening for the impact of inactivation of a gene, e.g., loss of a tumor suppressor in cancer, on the cellular proteome, we present a strategy based on combination of three technologies that is recombinase-mediated cassette exchange, click chemistry, and mass spectrometry. The methodology is exemplified by the analysis of the proteomic changes induced by the loss of a tumor suppressor gene in colorectal cancer cells. To demonstrate the applicability to screen for posttranslational modification changes, we also describe the analysis of protein glycosylation changes caused by the tumor suppressor inactivation. In principle, this strategy can be applied to analyze the effects of any gene of interest on protein expression as well as posttranslational modification by glycosylation. Moreover adaptation of the strategy to an appropriate cell culture model has the potential for application on a broad range of diseases where the disease-promoting mutations have been identified.
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Affiliation(s)
- J Gebert
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany; Cancer Early Detection, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - M Schnölzer
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - U Warnken
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - J Kopitz
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany; Cancer Early Detection, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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33
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Strmiskova M, Desrochers GF, Shaw TA, Powdrill MH, Lafreniere MA, Pezacki JP. Chemical Methods for Probing Virus-Host Proteomic Interactions. ACS Infect Dis 2016; 2:773-786. [PMID: 27933785 DOI: 10.1021/acsinfecdis.6b00084] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Interactions between host and pathogen proteins constitute an important aspect of both infectivity and the host immune response. Different viruses have evolved complex mechanisms to hijack host-cell machinery and metabolic pathways to redirect resources and energy flow toward viral propagation. These interactions are often critical to the virus, and thus understanding these interactions at a molecular level gives rise to opportunities to develop novel antiviral strategies for therapeutic intervention. This review summarizes current advances in chemoproteomic methods for studying these molecular altercations between different viruses and their hosts.
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Affiliation(s)
- Miroslava Strmiskova
- Department of Chemistry and Biomolecular Sciences, Centre
for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, Ontario, Canada K1N 6N5
| | - Geneviève F. Desrochers
- Department of Chemistry and Biomolecular Sciences, Centre
for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, Ontario, Canada K1N 6N5
| | - Tyler A. Shaw
- Department of Chemistry and Biomolecular Sciences, Centre
for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, Ontario, Canada K1N 6N5
| | - Megan H. Powdrill
- Department of Chemistry and Biomolecular Sciences, Centre
for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, Ontario, Canada K1N 6N5
| | - Matthew A. Lafreniere
- Department of Chemistry and Biomolecular Sciences, Centre
for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, Ontario, Canada K1N 6N5
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular Sciences, Centre
for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, Ontario, Canada K1N 6N5
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34
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Lee S, Wang W, Lee Y, Sampson NS. Cyclic acetals as cleavable linkers for affinity capture. Org Biomol Chem 2016; 13:8445-52. [PMID: 26152933 DOI: 10.1039/c5ob01056j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Labeling proteins with biotin is a widely used method to identify target proteins due to biotin's strong binding affinity for streptavidin. Combined with alkyne-azide cycloaddition, which enables the coupling of probes to targeted proteins, biotin tags linked to an alkyne or azide have become a powerful tool for purification and analysis of proteins in proteomics. However, biotin requires harsh elution conditions to release the captured protein from the bead matrix. Use of these conditions reduces signal to noise and complicates the analysis. To improve affinity capture, cleavable linkers have been introduced. Here, we demonstrate the use of a cyclic acetal biotin probe that is prepared easily from commercially available starting materials, is stable to cell lysates, yet is cleaved under mildly acidic conditions, and which provides an aldehyde for further elaboration of the protein, if desired.
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Affiliation(s)
- Siyeon Lee
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, USA.
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35
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Detection of protease activity in cells and animals. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1864:130-42. [PMID: 25960278 DOI: 10.1016/j.bbapap.2015.04.029] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 04/21/2015] [Accepted: 04/28/2015] [Indexed: 01/05/2023]
Abstract
Proteases are involved in a wide variety of biologically and medically important events. They are entangled in a complex network of processes that regulate their activity, which makes their study intriguing, but challenging. For comprehensive understanding of protease biology and effective drug discovery, it is therefore essential to study proteases in models that are close to their complex native environments such as live cells or whole organisms. Protease activity can be detected by reporter substrates and activity-based probes, but not all of these reagents are suitable for intracellular or in vivo use. This review focuses on the detection of proteases in cells and in vivo. We summarize the use of probes and substrates as molecular tools, discuss strategies to deliver these tools inside cells, and describe sophisticated read-out techniques such as mass spectrometry and various imaging applications. This article is part of a Special Issue entitled: Physiological Enzymology and Protein Functions.
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36
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Tse J, Wang Y, Zengeya T, Rozners E, Tan-Wilson A. Peptide nucleic acid probe for protein affinity purification based on biotin-streptavidin interaction and peptide nucleic acid strand hybridization. Anal Biochem 2014; 470:34-40. [PMID: 25447466 DOI: 10.1016/j.ab.2014.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 10/06/2014] [Accepted: 10/09/2014] [Indexed: 01/25/2023]
Abstract
We describe a new method for protein affinity purification that capitalizes on the high affinity of streptavidin for biotin but does not require dissociation of the biotin-streptavidin complex for protein retrieval. Conventional reagents place both the selectively reacting group (the "warhead") and the biotin on the same molecule. We place the warhead and the biotin on separate molecules, each linked to a short strand of peptide nucleic acid (PNA), synthetic polymers that use the same bases as DNA but attached to a backbone that is resistant to attack by proteases and nucleases. As in DNA, PNA strands with complementary base sequences hybridize. In conditions that favor PNA duplex formation, the warhead strand (carrying the tagged protein) and the biotin strand form a complex that is held onto immobilized streptavidin. As in DNA, the PNA duplex dissociates at moderately elevated temperature; therefore, retrieval of the tagged protein is accomplished by a brief exposure to heat. Using iodoacetate as the warhead, 8-base PNA strands, biotin, and streptavidin-coated magnetic beads, we demonstrate retrieval of the cysteine protease papain. We were also able to use our iodoacetyl-PNA:PNA-biotin probe for retrieval and identification of a thiol reductase and a glutathione transferase from soybean seedling cotyledons.
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Affiliation(s)
- Jenny Tse
- Department of Chemistry, State University of New York at Binghamton, Binghamton, NY 13902, USA
| | - Yuanyuan Wang
- Department of Biological Sciences, State University of New York at Binghamton, Binghamton, NY 13902, USA
| | - Thomas Zengeya
- Department of Chemistry, State University of New York at Binghamton, Binghamton, NY 13902, USA
| | - Eriks Rozners
- Department of Chemistry, State University of New York at Binghamton, Binghamton, NY 13902, USA
| | - Anna Tan-Wilson
- Department of Biological Sciences, State University of New York at Binghamton, Binghamton, NY 13902, USA.
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37
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Lin JCY, Chou CC, Tu Z, Yeh LF, Wu SC, Khoo KH, Lin CH. Characterization of Protein Serotonylation via Bioorthogonal Labeling and Enrichment. J Proteome Res 2014; 13:3523-9. [DOI: 10.1021/pr5003438] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Jason Ching-Yao Lin
- Department
of Chemistry, National Tsing Hua University, 101 Kuang-Fu Road Section 2, Hsinchu 30013, Taiwan
| | | | | | | | - Shang-Chuen Wu
- Institute
of Biochemical Sciences, National Taiwan University, 1 Roosevelt
Road Section 4, Taipei 10617, Taiwan
| | - Kay-Hooi Khoo
- Institute
of Biochemical Sciences, National Taiwan University, 1 Roosevelt
Road Section 4, Taipei 10617, Taiwan
| | - Chun-Hung Lin
- Institute
of Biochemical Sciences, National Taiwan University, 1 Roosevelt
Road Section 4, Taipei 10617, Taiwan
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38
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Willems LI, Overkleeft HS, van Kasteren SI. Current developments in activity-based protein profiling. Bioconjug Chem 2014; 25:1181-91. [PMID: 24946272 DOI: 10.1021/bc500208y] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Activity-based protein profiling (ABPP) has emerged as a powerful strategy to study the activity of enzymes in complex proteomes. The aim of ABPP is to selectively visualize only the active forms of particular enzymes using chemical probes termed activity-based probes (ABPs). These probes are directed to the active site of a particular target protein (or protein family) where they react in a mechanism-based manner with an active site residue. This results in the selective labeling of only the catalytically active form of the enzyme, usually in a covalent manner. Besides the monitoring of a specific enzymatic activity, ABPP strategies have also been used to identify and characterize (unknown) protein functions, to study up- and down-regulation of enzymatic activity in various disease states, to discover and evaluate putative new enzyme inhibitors, and to identify the protein targets of covalently binding natural products. In this Topical Review we will provide a brief overview of some of the recent developments in the field of ABPP.
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Affiliation(s)
- Lianne I Willems
- Leiden University , Leiden Institute of Chemistry, Gorlaeus Laboratories, Einsteinweg 55, 2333 CC Leiden, The Netherlands
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39
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Yonezawa H, Nishiyama Y, Takeo K, Iwatsubo T, Tomita T, Yokoshima S, Fukuyama T. New photocleavable linker: α-Thioacetophenone-type linker. Bioorg Med Chem Lett 2014; 24:2831-3. [DOI: 10.1016/j.bmcl.2014.04.104] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 04/22/2014] [Accepted: 04/25/2014] [Indexed: 01/15/2023]
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40
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Yang Y, Yang X, Verhelst SHL. Comparative analysis of click chemistry mediated activity-based protein profiling in cell lysates. Molecules 2013; 18:12599-608. [PMID: 24126377 PMCID: PMC6270401 DOI: 10.3390/molecules181012599] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 08/07/2013] [Accepted: 09/26/2013] [Indexed: 12/14/2022] Open
Abstract
Activity-based protein profiling uses chemical probes that covalently attach to active enzyme targets. Probes with conventional tags have disadvantages, such as limited cell permeability or steric hindrance around the reactive group. A tandem labeling strategy with click chemistry is now widely used to study enzyme targets in situ and in vivo. Herein, the probes are reacted in live cells, whereas the ensuing detection by click chemistry takes place in cell lysates. We here make a comparison of the efficiency of the activity-based tandem labeling strategy by using Cu(I)-catalyzed and strain-promoted click chemistry, different ligands and different lysis conditions.
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Affiliation(s)
- Yinliang Yang
- Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany.
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41
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Černý M, Skalák J, Cerna H, Brzobohatý B. Advances in purification and separation of posttranslationally modified proteins. J Proteomics 2013; 92:2-27. [PMID: 23777897 DOI: 10.1016/j.jprot.2013.05.040] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 05/27/2013] [Accepted: 05/29/2013] [Indexed: 11/25/2022]
Abstract
Posttranslational modifications (PTMs) of proteins represent fascinating extensions of the dynamic complexity of living cells' proteomes. The results of enzymatically catalyzed or spontaneous chemical reactions, PTMs form a fourth tier in the gene - transcript - protein cascade, and contribute not only to proteins' biological functions, but also to challenges in their analysis. There have been tremendous advances in proteomics during the last decade. Identification and mapping of PTMs in proteins have improved dramatically, mainly due to constant increases in the sensitivity, speed, accuracy and resolution of mass spectrometry (MS). However, it is also becoming increasingly evident that simple gel-free shotgun MS profiling is unlikely to suffice for comprehensive detection and characterization of proteins and/or protein modifications present in low amounts. Here, we review current approaches for enriching and separating posttranslationally modified proteins, and their MS-independent detection. First, we discuss general approaches for proteome separation, fractionation and enrichment. We then consider the commonest forms of PTMs (phosphorylation, glycosylation and glycation, lipidation, methylation, acetylation, deamidation, ubiquitination and various redox modifications), and the best available methods for detecting and purifying proteins carrying these PTMs. This article is part of a Special Issue entitled: Posttranslational Protein modifications in biology and Medicine.
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Affiliation(s)
- Martin Černý
- Department of Molecular Biology and Radiobiology, Mendel University in Brno & CEITEC - Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, CZ-613 00 Brno, Czech Republic.
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42
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Nathani RI, Chudasama V, Ryan CP, Moody PR, Morgan RE, Fitzmaurice RJ, Smith MEB, Baker JR, Caddick S. Reversible protein affinity-labelling using bromomaleimide-based reagents. Org Biomol Chem 2013; 11:2408-11. [PMID: 23462873 PMCID: PMC3763775 DOI: 10.1039/c3ob40239h] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2013] [Accepted: 02/26/2013] [Indexed: 12/21/2022]
Abstract
Reversible protein biotinylation is readily affected via conjugation with a bromomaleimide-based reagent followed by reductive cleavage. The intermediate biotinylated protein constructs are stable at physiological temperature and pH 8.0. Quantitative reversibility is elegantly delivered under mild conditions of using a stoichiometric amount of a bis-thiol, thus providing an approach that will be of general interest in chemical biology and proteomics.
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Affiliation(s)
- Ramiz I. Nathani
- Department of Chemistry , University College London , 20 Gordon Street , London , WC1H OAJ , UK . ; Fax: +44 (0)20 7679 7463 ; Tel: +44(0)20 3108 5071
| | - Vijay Chudasama
- Department of Chemistry , University College London , 20 Gordon Street , London , WC1H OAJ , UK . ; Fax: +44 (0)20 7679 7463 ; Tel: +44(0)20 3108 5071
| | - Chris P. Ryan
- Department of Chemistry , University College London , 20 Gordon Street , London , WC1H OAJ , UK . ; Fax: +44 (0)20 7679 7463 ; Tel: +44(0)20 3108 5071
| | - Paul R. Moody
- Department of Chemistry , University College London , 20 Gordon Street , London , WC1H OAJ , UK . ; Fax: +44 (0)20 7679 7463 ; Tel: +44(0)20 3108 5071
| | - Rachel E. Morgan
- Department of Chemistry , University College London , 20 Gordon Street , London , WC1H OAJ , UK . ; Fax: +44 (0)20 7679 7463 ; Tel: +44(0)20 3108 5071
| | - Richard J. Fitzmaurice
- Department of Chemistry , University College London , 20 Gordon Street , London , WC1H OAJ , UK . ; Fax: +44 (0)20 7679 7463 ; Tel: +44(0)20 3108 5071
| | - Mark E. B. Smith
- Department of Chemistry , University College London , 20 Gordon Street , London , WC1H OAJ , UK . ; Fax: +44 (0)20 7679 7463 ; Tel: +44(0)20 3108 5071
| | - James R. Baker
- Department of Chemistry , University College London , 20 Gordon Street , London , WC1H OAJ , UK . ; Fax: +44 (0)20 7679 7463 ; Tel: +44(0)20 3108 5071
| | - Stephen Caddick
- Department of Chemistry , University College London , 20 Gordon Street , London , WC1H OAJ , UK . ; Fax: +44 (0)20 7679 7463 ; Tel: +44(0)20 3108 5071
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Yang Y, Verhelst SHL. Cleavable trifunctional biotin reagents for protein labelling, capture and release. Chem Commun (Camb) 2013; 49:5366-8. [DOI: 10.1039/c3cc42076k] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Maurer A, Zeyher C, Amin B, Kalbacher H. A Periodate-Cleavable Linker for Functional Proteomics under Slightly Acidic Conditions: Application for the Analysis of Intracellular Aspartic Proteases. J Proteome Res 2012; 12:199-207. [DOI: 10.1021/pr300758c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Andreas Maurer
- Interfaculty Institute of Biochemistry, University of Tuebingen, Ob dem Himmelreich 7, 72074
Tuebingen, Germany
| | - Claus Zeyher
- Interfaculty Institute of Biochemistry, University of Tuebingen, Ob dem Himmelreich 7, 72074
Tuebingen, Germany
| | - Bushra Amin
- Interfaculty Institute of Biochemistry, University of Tuebingen, Ob dem Himmelreich 7, 72074
Tuebingen, Germany
| | - Hubert Kalbacher
- Interfaculty Institute of Biochemistry, University of Tuebingen, Ob dem Himmelreich 7, 72074
Tuebingen, Germany
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