1
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Zhai Y, Zhang X, Chen Z, Yan D, Zhu L, Zhang Z, Wang X, Tian K, Huang Y, Yang X, Sun W, Wang D, Tsai YH, Luo T, Li G. Global profiling of functional histidines in live cells using small-molecule photosensitizer and chemical probe relay labelling. Nat Chem 2024:10.1038/s41557-024-01545-6. [PMID: 38834725 DOI: 10.1038/s41557-024-01545-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 04/26/2024] [Indexed: 06/06/2024]
Abstract
Recent advances in chemical proteomics have focused on developing chemical probes that react with nucleophilic amino acid residues. Although histidine is an attractive candidate due to its importance in enzymatic catalysis, metal binding and protein-protein interaction, its moderate nucleophilicity poses challenges. Its modification is frequently influenced by cysteine and lysine, which results in poor selectivity and narrow proteome coverage. Here we report a singlet oxygen and chemical probe relay labelling method that achieves high selectivity towards histidine. Libraries of small-molecule photosensitizers and chemical probes were screened to optimize histidine labelling, enabling histidine profiling in live cells with around 7,200 unique sites. Using NMR spectroscopy and X-ray crystallography, we characterized the reaction mechanism and the structures of the resulting products. We then applied this method to discover unannotated histidine sites key to enzymatic activity and metal binding in select metalloproteins. This method also revealed the accessibility change of histidine mediated by protein-protein interaction that influences select protein subcellular localization, underscoring its capability in discovering functional histidines.
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Affiliation(s)
- Yansheng Zhai
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Xinyu Zhang
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A & F University, Yangling, China
| | - Zijing Chen
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering, Ministry of Education and Beijing National Laboratory for Molecular Science, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | | | - Lin Zhu
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Zhe Zhang
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Xianghe Wang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Kailu Tian
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Yan Huang
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Xi Yang
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Wen Sun
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, Dalian, China
| | - Dong Wang
- Shenzhen University, Shenzhen, China
| | - Yu-Hsuan Tsai
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Tuoping Luo
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering, Ministry of Education and Beijing National Laboratory for Molecular Science, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Gang Li
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China.
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2
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Krieger IV, Yalamanchili S, Dickson P, Engelhart CA, Zimmerman MD, Wood J, Clary E, Nguyen J, Thornton N, Centrella PA, Chan B, Cuozzo JW, Gengenbacher M, Guié MA, Guilinger JP, Bienstock C, Hartl H, Hupp CD, Jetson R, Satoh T, Yeoman JTS, Zhang Y, Dartois V, Schnappinger D, Keefe AD, Sacchettini JC. Inhibitors of the Thioesterase Activity of Mycobacterium tuberculosis Pks13 Discovered Using DNA-Encoded Chemical Library Screening. ACS Infect Dis 2024; 10:1561-1575. [PMID: 38577994 PMCID: PMC11091879 DOI: 10.1021/acsinfecdis.3c00592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 04/06/2024]
Abstract
DNA-encoded chemical library (DEL) technology provides a time- and cost-efficient method to simultaneously screen billions of compounds for their affinity to a protein target of interest. Here we report its use to identify a novel chemical series of inhibitors of the thioesterase activity of polyketide synthase 13 (Pks13) from Mycobacterium tuberculosis (Mtb). We present three chemically distinct series of inhibitors along with their enzymatic and Mtb whole cell potency, the measure of on-target activity in cells, and the crystal structures of inhibitor-enzyme complexes illuminating their interactions with the active site of the enzyme. One of these inhibitors showed a favorable pharmacokinetic profile and demonstrated efficacy in an acute mouse model of tuberculosis (TB) infection. These findings and assay developments will aid in the advancement of TB drug discovery.
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Affiliation(s)
- Inna V. Krieger
- Department
of Biochemistry & Biophysics, Texas
A&M University, College
Station, Texas 77843, United States
| | | | - Paige Dickson
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Curtis A. Engelhart
- Department
of Microbiology and Immunology, Weill Cornell
Medicine, New York, New York 10021, United States
| | - Matthew D Zimmerman
- Center for
Discovery and Innovation, Hackensack Meridian
Health, Nutley, New Jersey 07110, United States
| | - Jeremy Wood
- Department
of Biochemistry & Biophysics, Texas
A&M University, College
Station, Texas 77843, United States
| | - Ethan Clary
- Department
of Biochemistry & Biophysics, Texas
A&M University, College
Station, Texas 77843, United States
| | - Jasmine Nguyen
- Department
of Biochemistry & Biophysics, Texas
A&M University, College
Station, Texas 77843, United States
| | - Natalie Thornton
- Department
of Microbiology and Immunology, Weill Cornell
Medicine, New York, New York 10021, United States
| | - Paolo A. Centrella
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Betty Chan
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- Auron
Therapeutics, 55 Chapel
Street, Newton, Massachusetts 02458, United States
| | - John W Cuozzo
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- Relay
Therapeutics, 399 Binney Street, Cambridge, Massachusetts 02141, United States
| | - Martin Gengenbacher
- Center for
Discovery and Innovation, Hackensack Meridian
Health, Nutley, New Jersey 07110, United States
| | - Marie-Aude Guié
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - John P Guilinger
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Corey Bienstock
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Hajnalka Hartl
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- Orogen
Therapeutics, 12 Gill
Street, Woburn, Massachusetts 01801, United States
| | - Christopher D. Hupp
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- Ipsen Bioscience
Inc., 1 Main Street, Cambridge, Massachusetts 02142, United States
| | - Rachael Jetson
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- Valo
Health, 75 Hayden Avenue, Lexington, Massachusetts 02141, United States
| | - Takashi Satoh
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- EXO
Therapeutics, 150 Cambridgepark
Drive, suite 300, Cambridge, Massachusetts 02140, United States
| | - John T. S. Yeoman
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- Recludix
Pharmaceuticals, 222
Third Street, Cambridge, Massachusetts 02142, United States
| | - Ying Zhang
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Veronique Dartois
- Center for
Discovery and Innovation, Hackensack Meridian
Health, Nutley, New Jersey 07110, United States
- Hackensack
Meridian School of Medicine, Hackensack
Meridian Health, Nutley, New Jersey 07110, United States
| | - Dirk Schnappinger
- Department
of Microbiology and Immunology, Weill Cornell
Medicine, New York, New York 10021, United States
| | - Anthony D. Keefe
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - James C. Sacchettini
- Department
of Biochemistry & Biophysics, Texas
A&M University, College
Station, Texas 77843, United States
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3
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Ali MY, Bar-Peled L. Chemical proteomics to study metabolism, a reductionist approach applied at the systems level. Cell Chem Biol 2024; 31:446-451. [PMID: 38518745 DOI: 10.1016/j.chembiol.2024.02.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 11/02/2023] [Accepted: 02/28/2024] [Indexed: 03/24/2024]
Abstract
Cellular metabolism encompasses a complex array of interconnected biochemical pathways that are required for cellular homeostasis. When dysregulated, metabolism underlies multiple human pathologies. At the heart of metabolic networks are enzymes that have been historically studied through a reductionist lens, and more recently, using high throughput approaches including genomics and proteomics. Merging these two divergent viewpoints are chemical proteomic technologies, including activity-based protein profiling, which combines chemical probes specific to distinct enzyme families or amino acid residues with proteomic analysis. This enables the study of metabolism at the network level with the precision of powerful biochemical approaches. Herein, we provide a primer on how chemical proteomic technologies custom-built for studying metabolism have unearthed fundamental principles in metabolic control. In parallel, these technologies have leap-frogged drug discovery through identification of novel targets and drug specificity. Collectively, chemical proteomics technologies appear to do the impossible: uniting systematic analysis with a reductionist approach.
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Affiliation(s)
- Md Yousuf Ali
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Liron Bar-Peled
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Medicine, Harvard Medical School, Boston, MA 02114, USA.
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4
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Bathla P, Mujawar A, De A, Sandanaraj BS. Development of Noninvasive Activity-Based Protein Profiling-Bioluminescence Resonance Energy Transfer Platform Technology Enables Target Engagement Studies with Absolute Specificity in Living Systems. ACS Pharmacol Transl Sci 2024; 7:375-383. [PMID: 38357276 PMCID: PMC10863430 DOI: 10.1021/acsptsci.3c00231] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 12/06/2023] [Accepted: 12/18/2023] [Indexed: 02/16/2024]
Abstract
Noninvasive, real-time, longitudinal imaging of protein functions in living systems with unprecedented specificity is one of the critical challenges of modern biomedical research. Toward that goal, here, we report a platform fusion technology called activity-based protein profiling-bioluminescence resonance energy transfer (ABPP-BRET). This method provides an opportunity to study the post-translational modification of a target protein in real time in living systems in a longitudinal manner. This semisynthetic BRET biosensor method is used for target engagement studies and further for inhibitor profiling in live cells. The simplicity of this method coupled with the critical physical distance-dependent BRET readout turned out to be a powerful method, thus pushing the activity-based protein profiling technology to the next level.
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Affiliation(s)
- Punita Bathla
- Department
of Biology, Department of Chemistry, Indian
Institute of Science Education and Research, Pune 411008, India
| | - Aaiyas Mujawar
- Molecular
Functional Imaging Lab, Advanced Centre
for Treatment Research Education in Cancer (ACTREC), Navi Mumbai 410210, India
- Homi
Bhabha National Institute, Mumbai 400094, India
| | - Abhijit De
- Molecular
Functional Imaging Lab, Advanced Centre
for Treatment Research Education in Cancer (ACTREC), Navi Mumbai 410210, India
- Homi
Bhabha National Institute, Mumbai 400094, India
| | - Britto S. Sandanaraj
- Department
of Biology, Department of Chemistry, Indian
Institute of Science Education and Research, Pune 411008, India
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5
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Gao Y, Ma M, Li W, Lei X. Chemoproteomics, A Broad Avenue to Target Deconvolution. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305608. [PMID: 38095542 PMCID: PMC10885659 DOI: 10.1002/advs.202305608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 11/29/2023] [Indexed: 12/22/2023]
Abstract
As a vital project of forward chemical genetic research, target deconvolution aims to identify the molecular targets of an active hit compound. Chemoproteomics, either with chemical probe-facilitated target enrichment or probe-free, provides a straightforward and effective approach to profile the target landscape and unravel the mechanisms of action. Canonical methods rely on chemical probes to enable target engagement, enrichment, and identification, whereas click chemistry and photoaffinity labeling techniques improve the efficiency, sensitivity, and spatial accuracy of target recognition. In comparison, recently developed probe-free methods detect protein-ligand interactions without the need to modify the ligand molecule. This review provides a comprehensive overview of different approaches and recent advancements for target identification and highlights the significance of chemoproteomics in investigating biological processes and advancing drug discovery processes.
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Affiliation(s)
- Yihui Gao
- Beijing National Laboratory for Molecular SciencesKey Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of EducationCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871China
| | - Mingzhe Ma
- Beijing National Laboratory for Molecular SciencesKey Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of EducationCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871China
- Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijing100871China
| | - Wenyang Li
- Beijing National Laboratory for Molecular SciencesKey Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of EducationCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871China
| | - Xiaoguang Lei
- Beijing National Laboratory for Molecular SciencesKey Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of EducationCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871China
- Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijing100871China
- Academy for Advanced Interdisciplinary StudiesPeking UniversityBeijing100871China
- Institute for Cancer ResearchShenzhen Bay LaboratoryShenzhenChina
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6
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Zhang Y, Liu Z, Hirschi M, Brodsky O, Johnson E, Won SJ, Nagata A, Petroski MD, Majmudar JD, Niessen S, VanArsdale T, Gilbert AM, Hayward MM, Stewart AE, Nager AR, Melillo B, Cravatt B. Expanding the ligandable proteome by paralog hopping with covalent probes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.18.576274. [PMID: 38293178 PMCID: PMC10827202 DOI: 10.1101/2024.01.18.576274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
More than half of the ~20,000 protein-encoding human genes have at least one paralog. Chemical proteomics has uncovered many electrophile-sensitive cysteines that are exclusive to a subset of paralogous proteins. Here, we explore whether such covalent compound-cysteine interactions can be used to discover ligandable pockets in paralogs that lack the cysteine. Leveraging the covalent ligandability of C109 in the cyclin CCNE2, we mutated the corresponding residue in paralog CCNE1 to cysteine (N112C) and found through activity-based protein profiling (ABPP) that this mutant reacts stereoselectively and site-specifically with tryptoline acrylamides. We then converted the tryptoline acrylamide-N112C-CCNE1 interaction into a NanoBRET-ABPP assay capable of identifying compounds that reversibly inhibit both N112C- and WT-CCNE1:CDK2 complexes. X-ray crystallography revealed a cryptic allosteric pocket at the CCNE1:CDK2 interface adjacent to N112 that binds the reversible inhibitors. Our findings thus provide a roadmap for leveraging electrophile-cysteine interactions to extend the ligandability of the proteome beyond covalent chemistry.
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Affiliation(s)
- Yuanjin Zhang
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Zhonglin Liu
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Marsha Hirschi
- Medicine Design, Pfizer Research and Development, Pfizer Inc., La Jolla, CA 92121, USA
| | - Oleg Brodsky
- Medicine Design, Pfizer Research and Development, Pfizer Inc., La Jolla, CA 92121, USA
| | - Eric Johnson
- Medicine Design, Pfizer Research and Development, Pfizer Inc., La Jolla, CA 92121, USA
| | - Sang Joon Won
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Asako Nagata
- Medicine Design, Pfizer Research and Development, Pfizer Inc., La Jolla, CA 92121, USA
| | | | - Jaimeen D Majmudar
- Discovery Sciences, Pfizer Research and Development, Pfizer Inc., Cambridge, MA 02139, USA
| | - Sherry Niessen
- Oncology Research and Development, Pfizer Inc., La Jolla, CA 92121, USA
- Current address: Belharra Therapeutics, 3985 Sorrento Valley Blvd suite c, San Diego, CA 92121
| | - Todd VanArsdale
- Oncology Research and Development, Pfizer Inc., La Jolla, CA 92121, USA
| | - Adam M Gilbert
- Discovery Sciences, Pfizer Research and Development, Pfizer Inc., Groton, CT 06340, USA
| | - Matthew M Hayward
- Discovery Sciences, Pfizer Research and Development, Pfizer Inc., Groton, CT 06340, USA
- Current address: Magnet Biomedicine, 321 Harrison Ave., Suite 600, Boston, MA 02118, USA
| | - Al E Stewart
- Medicine Design, Pfizer Research and Development, Pfizer Inc., La Jolla, CA 92121, USA
| | - Andrew R Nager
- Oncology Research and Development, Pfizer Inc., La Jolla, CA 92121, USA
| | - Bruno Melillo
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Benjamin Cravatt
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037 USA
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7
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Hocking B, Armstrong A, Mann DJ. Covalent fragment libraries in drug discovery-Design, synthesis, and screening methods. PROGRESS IN MEDICINAL CHEMISTRY 2023; 62:105-146. [PMID: 37981350 DOI: 10.1016/bs.pmch.2023.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2023]
Abstract
As the development of drugs with a covalent mode of action is becoming increasingly popular, well-validated covalent fragment-based drug discovery (FBDD) methods have been comparatively slow to keep up with the demand. In this chapter the principles of covalent fragment reactivity, library design, synthesis, and screening methods are explored in depth, focussing on literature examples with direct applications to practical covalent fragment library design and screening. Further, questions about the future of the field are explored and potential useful advances are proposed.
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Affiliation(s)
- Brad Hocking
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Alan Armstrong
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, United Kingdom
| | - David J Mann
- Department of Life Sciences, Imperial College London, London, United Kingdom.
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8
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Lv N, Huang C, Huang H, Dong Z, Chen X, Lu C, Zhang Y. Overexpression of Glutathione S-Transferases in Human Diseases: Drug Targets and Therapeutic Implications. Antioxidants (Basel) 2023; 12:1970. [PMID: 38001822 PMCID: PMC10668987 DOI: 10.3390/antiox12111970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/25/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
Glutathione S-transferases (GSTs) are a major class of phase II metabolic enzymes. Besides their essential role in detoxification, GSTs also exert diverse biological activities in the occurrence and development of various diseases. In the past few decades, much research interest has been paid to exploring the mechanisms of GST overexpression in tumor drug resistance. Correspondingly, many GST inhibitors have been developed and applied, solely or in combination with chemotherapeutic drugs, for the treatment of multi-drug resistant tumors. Moreover, novel roles of GSTs in other diseases, such as pulmonary fibrosis and neurodegenerative diseases, have been recognized in recent years, although the exact regulatory mechanisms remain to be elucidated. This review, firstly summarizes the roles of GSTs and their overexpression in the above-mentioned diseases with emphasis on the modulation of cell signaling pathways and protein functions. Secondly, specific GST inhibitors currently in pre-clinical development and in clinical stages are inventoried. Lastly, applications of GST inhibitors in targeting cell signaling pathways and intracellular biological processes are discussed, and the potential for disease treatment is prospected. Taken together, this review is expected to provide new insights into the interconnection between GST overexpression and human diseases, which may assist future drug discovery targeting GSTs.
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Affiliation(s)
- Ning Lv
- Clinical Pharmacology Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China; (N.L.); (H.H.)
| | - Chunyan Huang
- Clinical Pharmacology Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China; (N.L.); (H.H.)
| | - Haoyan Huang
- Clinical Pharmacology Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China; (N.L.); (H.H.)
| | - Zhiqiang Dong
- Department of Pharmacy, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing 211100, China;
| | - Xijing Chen
- Clinical Pharmacology Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China; (N.L.); (H.H.)
| | - Chengcan Lu
- Department of Pharmacy, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing 211100, China;
- Jiangning Clinical Medical College, Jiangsu University, Nanjing 211100, China
| | - Yongjie Zhang
- Clinical Pharmacology Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China; (N.L.); (H.H.)
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9
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Han JH, Lee EJ, Park W, Ha KT, Chung HS. Natural compounds as lactate dehydrogenase inhibitors: potential therapeutics for lactate dehydrogenase inhibitors-related diseases. Front Pharmacol 2023; 14:1275000. [PMID: 37915411 PMCID: PMC10616500 DOI: 10.3389/fphar.2023.1275000] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 09/27/2023] [Indexed: 11/03/2023] Open
Abstract
Lactate dehydrogenase (LDH) is a crucial enzyme involved in energy metabolism and present in various cells throughout the body. Its diverse physiological functions encompass glycolysis, and its abnormal activity is associated with numerous diseases. Targeting LDH has emerged as a vital approach in drug discovery, leading to the identification of LDH inhibitors among natural compounds, such as polyphenols, alkaloids, and terpenoids. These compounds demonstrate therapeutic potential against LDH-related diseases, including anti-cancer effects. However, challenges concerning limited bioavailability, poor solubility, and potential toxicity must be addressed. Combining natural compounds with LDH inhibitors has led to promising outcomes in preclinical studies. This review highlights the promise of natural compounds as LDH inhibitors for treating cancer, cardiovascular, and neurodegenerative diseases.
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Affiliation(s)
- Jung Ho Han
- Korean Medicine (KM)-Application Center, Korea Institute of Oriental Medicine (KIOM), Daegu, Republic of Korea
| | - Eun-Ji Lee
- Korean Medicine (KM)-Application Center, Korea Institute of Oriental Medicine (KIOM), Daegu, Republic of Korea
| | - Wonyoung Park
- Korean Convergence Medical Science Major, KIOM Campus, University of Science and Technology (UST), Daegu, Republic of Korea
| | - Ki-Tae Ha
- Korean Convergence Medical Science Major, KIOM Campus, University of Science and Technology (UST), Daegu, Republic of Korea
| | - Hwan-Suck Chung
- Korean Medicine (KM)-Application Center, Korea Institute of Oriental Medicine (KIOM), Daegu, Republic of Korea
- Department of Korean Medical Science, School of Korean Medicine, Pusan National University, Yangsan, Republic of Korea
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10
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Cravatt BF. Activity-based protein profiling - finding general solutions to specific problems. Isr J Chem 2023; 63:e202300029. [PMID: 37206575 PMCID: PMC10191372 DOI: 10.1002/ijch.202300029] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Indexed: 03/06/2023]
Abstract
In this retrospective/perspective, I will share thoughts on developing and applying the activity-based protein profiling (ABPP) technology, an endeavor that has consumed much of our lab's attention over our 25+ year existence. Before doing so, I first wish to thank the colleagues who so kindly contributed to this Special Issue. I am appreciative and humbled that they were willing to share their innovative and impactful science in this format.
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Affiliation(s)
- Benjamin F Cravatt
- The Department of Chemistry, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, CA 92037
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11
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Yang J, Korovesis D, Ji S, Kahler JP, Vanhoutte R, Verhelst SHL. Efficient Synthesis of an Alkyne Fluorophosphonate Activity‐Based Probe and Applications in Dual Colour Serine Hydrolase Labelling. Isr J Chem 2023. [DOI: 10.1002/ijch.202200094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Affiliation(s)
- Jian Yang
- Department of Cellular and Molecular Medicine KU Leuven – University of Leuven Herestraat 49, box 901b 3000 Leuven Belgium
| | - Dimitris Korovesis
- Department of Cellular and Molecular Medicine KU Leuven – University of Leuven Herestraat 49, box 901b 3000 Leuven Belgium
| | - Shanping Ji
- Department of Cellular and Molecular Medicine KU Leuven – University of Leuven Herestraat 49, box 901b 3000 Leuven Belgium
| | - Jan Pascal Kahler
- Department of Cellular and Molecular Medicine KU Leuven – University of Leuven Herestraat 49, box 901b 3000 Leuven Belgium
| | - Roeland Vanhoutte
- Department of Cellular and Molecular Medicine KU Leuven – University of Leuven Herestraat 49, box 901b 3000 Leuven Belgium
| | - Steven H. L. Verhelst
- Department of Cellular and Molecular Medicine KU Leuven – University of Leuven Herestraat 49, box 901b 3000 Leuven Belgium
- Leibniz Institut für Analytische Wissenschaften – ISAS – e.V. Otto-Hahn Strasse 6b 44227 Dortmund Germany
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12
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Racioppo B, Qiu N, Adibekian A. Serine Hydrolase Activity‐Based Probes for use in Chemical Proteomics. Isr J Chem 2023. [DOI: 10.1002/ijch.202300016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Affiliation(s)
- Brittney Racioppo
- Department of Chemistry University of Illinois Chicago Chicago Illinois 60607 United States
- Skaggs Doctoral Program in the Chemical and Biological Sciences, Scripps Research La Jolla California 92037 United States
| | - Nan Qiu
- Department of Chemistry University of Illinois Chicago Chicago Illinois 60607 United States
- Skaggs Doctoral Program in the Chemical and Biological Sciences, Scripps Research La Jolla California 92037 United States
| | - Alexander Adibekian
- Department of Chemistry University of Illinois Chicago Chicago Illinois 60607 United States
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13
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Brulet JW, Ciancone AM, Yuan K, Hsu K. Advances in Activity‐Based Protein Profiling of Functional Tyrosines in Proteomes. Isr J Chem 2023. [DOI: 10.1002/ijch.202300001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Affiliation(s)
- Jeffrey W. Brulet
- Department of Chemistry University of Virginia Charlottesville Virginia 22904 United States (K.-L.H
| | - Anthony M. Ciancone
- Department of Chemistry University of Virginia Charlottesville Virginia 22904 United States (K.-L.H
| | - Kun Yuan
- Department of Chemistry University of Virginia Charlottesville Virginia 22904 United States (K.-L.H
| | - Ku‐Lung Hsu
- Department of Chemistry University of Virginia Charlottesville Virginia 22904 United States (K.-L.H
- Department of Pharmacology University of Virginia School of Medicine Charlottesville Virginia 22908 United States
- Department of Molecular Physiology and Biological Physics University of Virginia Charlottesville Virginia 22908 United States
- University of Virginia Cancer Center University of Virginia Charlottesville VA 22903 USA
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14
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Sakamoto S, Hamachi I. Ligand‐Directed Chemistry for Protein Labeling for Affinity‐Based Protein Analysis. Isr J Chem 2023. [DOI: 10.1002/ijch.202200077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Affiliation(s)
- Seiji Sakamoto
- Department of Synthetic Chemistry and Biological Chemistry Graduate School of Engineering Kyoto University Katsura, Nishikyo-ku 615-8510 Kyoto Japan
- JST-ERATO Hamachi Innovative Molecular Technology for Neuroscience 615-8530 Kyoto Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry Graduate School of Engineering Kyoto University Katsura, Nishikyo-ku 615-8510 Kyoto Japan
- JST-ERATO Hamachi Innovative Molecular Technology for Neuroscience 615-8530 Kyoto Japan
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15
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Honeder SE, Tomin T, Schinagl M, Pfleger R, Hoehlschen J, Darnhofer B, Schittmayer M, Birner‐Gruenberger R. Research Advances Through Activity‐Based Lipid Hydrolase Profiling. Isr J Chem 2023. [DOI: 10.1002/ijch.202200078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Sophie Elisabeth Honeder
- Research and Diagnostic Institute of Pathology Medical University of Graz Stiftingtalstraße 6 8036 Graz Austria
| | - Tamara Tomin
- Institute of Chemical Technologies and Analytics University of Technology Vienna Getreidemarkt 9 1060 Wien Austria
| | - Maximilian Schinagl
- Institute of Chemical Technologies and Analytics University of Technology Vienna Getreidemarkt 9 1060 Wien Austria
| | - Raphael Pfleger
- Institute of Chemical Technologies and Analytics University of Technology Vienna Getreidemarkt 9 1060 Wien Austria
| | - Julia Hoehlschen
- Institute of Chemical Technologies and Analytics University of Technology Vienna Getreidemarkt 9 1060 Wien Austria
| | - Barbara Darnhofer
- Core Facility Mass Spectrometry Center for Medical Research Medical University of Graz Neue Stiftingtalstraße 24 8036 Graz Austria
| | - Matthias Schittmayer
- Institute of Chemical Technologies and Analytics University of Technology Vienna Getreidemarkt 9 1060 Wien Austria
| | - Ruth Birner‐Gruenberger
- Research and Diagnostic Institute of Pathology Medical University of Graz Stiftingtalstraße 6 8036 Graz Austria
- Institute of Chemical Technologies and Analytics University of Technology Vienna Getreidemarkt 9 1060 Wien Austria
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16
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Genome-wide siRNA screens identify RBBP9 function as a potential target in Fanconi anaemia-deficient head-and-neck squamous cell carcinoma. Commun Biol 2023; 6:37. [PMID: 36639418 PMCID: PMC9839743 DOI: 10.1038/s42003-022-04389-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 12/19/2022] [Indexed: 01/15/2023] Open
Abstract
Fanconi anaemia (FA) is a rare chromosomal-instability syndrome caused by mutations of any of the 22 known FA DNA-repair genes. FA individuals have an increased risk of head-and-neck squamous-cell-carcinomas (HNSCC), often fatal. Systemic intolerance to standard cisplatin-based protocols due to somatic-cell hypersensitivity underscores the urgent need to develop novel therapies. Here, we performed unbiased siRNA screens to unveil genetic interactions synthetic-lethal with FA-pathway deficiency in FA-patient HNSCC cell lines. We identified based on differential-lethality scores between FA-deficient and FA-proficient cells, next to common-essential genes such as PSMC1, PSMB2, and LAMTOR2, the otherwise non-essential RBBP9 gene. Accordingly, low dose of the FDA-approved RBBP9-targeting drug Emetine kills FA-HNSCC. Importantly both RBBP9-silencing as well as Emetine spared non-tumour FA cells. This study provides a minable genome-wide analyses of vulnerabilities to address treatment challenges in FA-HNSCC. Our investigation divulges a DNA-cross-link-repair independent lead, RBBP9, for targeted treatment of FA-HNSCCs without systemic toxicity.
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17
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He J, Li C, Hu W, Li C, Liu S, Sui J, Zhang T, Sun Q, Luo Y. Identification of selective mtbDHFR inhibitors by virtual screening and experimental approaches. Chem Biol Drug Des 2022; 100:1005-1016. [PMID: 34981654 DOI: 10.1111/cbdd.14018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/26/2021] [Accepted: 12/18/2021] [Indexed: 02/05/2023]
Abstract
mtbDHFR-targeting inhibition has become a promising approach for tuberculosis treatment. In the current research, a multi-step virtual screening effort toward ZINC and MCE databases was devoted to discover novel mtbDHFR inhibitors. Based on binding affinity of small molecules through molecular docking study in AutoDock Vina, the number of compounds was reduced to 952,688. Further, these compounds were employed by a step-by-step multiple docking programs of Schrödinger suite and filtered by pharmacokinetics and PAINS parameters. Finally, nine ZINC compounds and 400 MCE compounds were obtained. These compounds of binding ability were tested with mtbDHFR by FluoPol-ABPP approach established in this work. Finally, AF-353 compound was found to have strong binding effect to mtbDHFR. AF-353 was further tested for mtb and hDHFR enzymatic activities, and it was proved to possess 50-fold selectivity toward mtbDHFR over hDHFR. In silico MD simulation results supported this selectivity.
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Affiliation(s)
- Juan He
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Cong Li
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Wei Hu
- Chengdu FenDi pharmaceutical Co., Ltd., Chengdu, China
| | - Chungen Li
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Song Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Jing Sui
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, China
| | - Qingxiang Sun
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Youfu Luo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
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18
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Jia Y, Kim RQ, Kooij R, Ovaa H, Sapmaz A, Geurink PP. Chemical Toolkit for PARK7: Potent, Selective, and High-Throughput. J Med Chem 2022; 65:13288-13304. [PMID: 36149939 PMCID: PMC9574860 DOI: 10.1021/acs.jmedchem.2c01113] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The multifunctional human Parkinson's disease protein 7 (PARK7/DJ1) is an attractive therapeutic target due to its link with early-onset Parkinson's disease, upregulation in various cancers, and contribution to chemoresistance. However, only a few compounds have been identified to bind PARK7 due to the lack of a dedicated chemical toolbox. We report the creation of such a toolbox and showcase the application of each of its components. The selective PARK7 submicromolar inhibitor with a cyanimide reactive group covalently modifies the active site Cys106. Installment of different dyes onto the inhibitor delivered two PARK7 probes. The Rhodamine110 probe provides a high-throughput screening compatible FP assay, showcased by screening a compound library (8000 molecules). The SulfoCy5-equipped probe is a valuable tool to assess the effect of PARK7 inhibitors in a cell lysate. Our work creates new possibilities to explore PARK7 function in a physiologically relevant setting and develop new and improved PARK7 inhibitors.
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Affiliation(s)
- Yuqing Jia
- Oncode Institute & Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, The Netherlands
| | - Robbert Q Kim
- Oncode Institute & Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, The Netherlands
| | - Raymond Kooij
- Oncode Institute & Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, The Netherlands
| | - Huib Ovaa
- Oncode Institute & Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, The Netherlands
| | - Aysegul Sapmaz
- Oncode Institute & Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, The Netherlands
| | - Paul P Geurink
- Oncode Institute & Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, The Netherlands
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19
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Soleimany AP, Martin-Alonso C, Anahtar M, Wang CS, Bhatia SN. Protease Activity Analysis: A Toolkit for Analyzing Enzyme Activity Data. ACS OMEGA 2022; 7:24292-24301. [PMID: 35874224 PMCID: PMC9301967 DOI: 10.1021/acsomega.2c01559] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Analyzing the activity of proteases and their substrates is critical to defining the biological functions of these enzymes and to designing new diagnostics and therapeutics that target protease dysregulation in disease. While a wide range of databases and algorithms have been created to better predict protease cleavage sites, there is a dearth of computational tools to automate analysis of in vitro and in vivo protease assays. This necessitates individual researchers to develop their own analytical pipelines, resulting in a lack of standardization across the field. To facilitate protease research, here we present Protease Activity Analysis (PAA), a toolkit for the preprocessing, visualization, machine learning analysis, and querying of protease activity data sets. PAA leverages a Python-based object-oriented implementation that provides a modular framework for streamlined analysis across three major components. First, PAA provides a facile framework to query data sets of synthetic peptide substrates and their cleavage susceptibilities across a diverse set of proteases. To complement the database functionality, PAA also includes tools for the automated analysis and visualization of user-input enzyme-substrate activity measurements generated through in vitro screens against synthetic peptide substrates. Finally, PAA supports a set of modular machine learning functions to analyze in vivo protease activity signatures that are generated by activity-based sensors. Overall, PAA offers the protease community a breadth of computational tools to streamline research, taking a step toward standardizing data analysis across the field and in chemical biology and biochemistry at large.
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Affiliation(s)
- Ava P. Soleimany
- Harvard-MIT
Division of Health Sciences and Technology, MIT, Cambridge, Massachusetts 02139, United States
- Program
in Biophysics, Harvard University, Boston, Massachusetts 02115, United States
- Microsoft
Research New England, Cambridge, Massachusetts 02142, United States
| | - Carmen Martin-Alonso
- Harvard-MIT
Division of Health Sciences and Technology, MIT, Cambridge, Massachusetts 02139, United States
| | - Melodi Anahtar
- Harvard-MIT
Division of Health Sciences and Technology, MIT, Cambridge, Massachusetts 02139, United States
| | - Cathy S. Wang
- Department
of Biological Engineering, MIT, Cambridge, Massachusetts 02139, United States
| | - Sangeeta N. Bhatia
- Harvard-MIT
Division of Health Sciences and Technology, MIT, Cambridge, Massachusetts 02139, United States
- Department
of Electrical Engineering and Computer Science, MIT, Cambridge, Massachusetts 02139, United States
- Howard Hughes
Medical Institute, Cambridge, Massachusetts 02139, United States
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20
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McGregor NGS, Overkleeft HS, Davies GJ. Detecting and identifying glycoside hydrolases using cyclophellitol-derived activity-based probes. Methods Enzymol 2022; 664:103-134. [PMID: 35331370 DOI: 10.1016/bs.mie.2022.01.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The ability to detect active enzymes in a complex mixture of folded proteins (e.g., secretome, cell lysate) generally relies on observations of catalytic ability, necessitating the development of an activity assay that is compatible with the sample and selective for the enzyme(s) of interest. Deconvolution of the contributions of different enzymes to an observed catalytic ability further necessitates an often-challenging protein separation. The advent of broadly reactive activity-based probes (ABPs) for retaining glycoside hydrolases (GHs) has enabled an alternative, often complementary, assay for active GHs. Using activity-based protein profiling (ABPP) techniques, many retaining glycoside hydrolases can be separated, detected, and identified with high sensitivity and selectivity. This chapter outlines ABPP methods for the detection and identification of retaining glycoside hydrolases from microbial sources, including protein sample preparation from bacterial lysates and fungal secretomes, enzyme labeling and detection via fluorescence, and enzyme identification using affinity-based enrichment coupled to peptide sequencing following isobaric labeling.
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Affiliation(s)
- Nicholas G S McGregor
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York, United Kingdom
| | | | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York, United Kingdom.
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21
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Li G, Peng X, Guo Y, Gong S, Cao S, Qiu F. Currently Available Strategies for Target Identification of Bioactive Natural Products. Front Chem 2021; 9:761609. [PMID: 34660543 PMCID: PMC8515416 DOI: 10.3389/fchem.2021.761609] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 09/20/2021] [Indexed: 01/04/2023] Open
Abstract
In recent years, biologically active natural products have gradually become important agents in the field of drug research and development because of their wide availability and variety. However, the target sites of many natural products are yet to be identified, which is a setback in the pharmaceutical industry and has seriously hindered the translation of research findings of these natural products as viable candidates for new drug exploitation. This review systematically describes the commonly used strategies for target identification via the application of probe and non-probe approaches. The merits and demerits of each method were summarized using recent examples, with the goal of comparing currently available methods and selecting the optimum techniques for identifying the targets of bioactive natural products.
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Affiliation(s)
- Gen Li
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xuling Peng
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Yajing Guo
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Shaoxuan Gong
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Shijie Cao
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Feng Qiu
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
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22
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Chen D, Xiao Z, Guo H, Gogishvili D, Setroikromo R, van der Wouden PE, Dekker FJ. Identification of a Bromodomain-like Region in 15-Lipoxygenase-1 Explains Its Nuclear Localization. Angew Chem Int Ed Engl 2021; 60:21875-21883. [PMID: 34388301 PMCID: PMC8518382 DOI: 10.1002/anie.202106968] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Indexed: 01/17/2023]
Abstract
Lipoxygenase (LOX) activity provides oxidative lipid metabolites, which are involved in inflammatory disorders and tumorigenesis. Activity-based probes to detect the activity of LOX enzymes in their cellular context provide opportunities to explore LOX biology and LOX inhibition. Here, we developed Labelox B as a potent covalent LOX inhibitor for one-step activity-based labeling of proteins with LOX activity. Labelox B was used to establish an ELISA-based assay for affinity capture and antibody-based detection of specific LOX isoenzymes. Moreover, Labelox B enabled efficient activity-based labeling of endogenous LOXs in living cells. LOX proved to localize in the nucleus, which was rationalized by identification of a functional bromodomain-like consensus motif in 15-LOX-1. This indicates that 15-LOX-1 is not only involved in oxidative lipid metabolism, but also in chromatin binding, which suggests a potential role in chromatin modifications.
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Affiliation(s)
- Deng Chen
- Department Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy (GRIP)University of GroningenAntonius Deusinglaan 19713AVGroningenThe Netherlands
| | - Zhangping Xiao
- Department Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy (GRIP)University of GroningenAntonius Deusinglaan 19713AVGroningenThe Netherlands
| | - Hao Guo
- Department Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy (GRIP)University of GroningenAntonius Deusinglaan 19713AVGroningenThe Netherlands
| | - Dea Gogishvili
- Department Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy (GRIP)University of GroningenAntonius Deusinglaan 19713AVGroningenThe Netherlands
| | - Rita Setroikromo
- Department Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy (GRIP)University of GroningenAntonius Deusinglaan 19713AVGroningenThe Netherlands
| | - Petra E. van der Wouden
- Department Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy (GRIP)University of GroningenAntonius Deusinglaan 19713AVGroningenThe Netherlands
| | - Frank J. Dekker
- Department Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy (GRIP)University of GroningenAntonius Deusinglaan 19713AVGroningenThe Netherlands
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23
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Chen D, Xiao Z, Guo H, Gogishvili D, Setroikromo R, Wouden PE, Dekker FJ. Identification of a Bromodomain‐like Region in 15‐Lipoxygenase‐1 Explains Its Nuclear Localization. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106968] [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)
- Deng Chen
- Department Chemical and Pharmaceutical Biology Groningen Research Institute of Pharmacy (GRIP) University of Groningen Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Zhangping Xiao
- Department Chemical and Pharmaceutical Biology Groningen Research Institute of Pharmacy (GRIP) University of Groningen Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Hao Guo
- Department Chemical and Pharmaceutical Biology Groningen Research Institute of Pharmacy (GRIP) University of Groningen Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Dea Gogishvili
- Department Chemical and Pharmaceutical Biology Groningen Research Institute of Pharmacy (GRIP) University of Groningen Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Rita Setroikromo
- Department Chemical and Pharmaceutical Biology Groningen Research Institute of Pharmacy (GRIP) University of Groningen Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Petra E. Wouden
- Department Chemical and Pharmaceutical Biology Groningen Research Institute of Pharmacy (GRIP) University of Groningen Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Frank J. Dekker
- Department Chemical and Pharmaceutical Biology Groningen Research Institute of Pharmacy (GRIP) University of Groningen Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
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24
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Fang H, Peng B, Ong SY, Wu Q, Li L, Yao SQ. Recent advances in activity-based probes (ABPs) and affinity-based probes (A fBPs) for profiling of enzymes. Chem Sci 2021; 12:8288-8310. [PMID: 34221311 PMCID: PMC8221178 DOI: 10.1039/d1sc01359a] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/11/2021] [Indexed: 12/14/2022] Open
Abstract
Activity-based protein profiling (ABPP) is a technique that uses highly selective active-site targeted chemical probes to label and monitor the state of proteins. ABPP integrates the strengths of both chemical and biological disciplines. By utilizing chemically synthesized or modified bioactive molecules, ABPP is able to reveal complex physiological and pathological enzyme-substrate interactions at molecular and cellular levels. It is also able to provide critical information of the catalytic activity changes of enzymes, annotate new functions of enzymes, discover new substrates of enzymes, and allow real-time monitoring of the cellular location of enzymes. Based on the mechanism of probe-enzyme interaction, two types of probes that have been used in ABPP are activity-based probes (ABPs) and affinity-based probes (AfBPs). This review highlights the recent advances in the use of ABPs and AfBPs, and summarizes their design strategies (based on inhibitors and substrates) and detection approaches.
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Affiliation(s)
- Haixiao Fang
- Key Laboratory of Flexible Electronics (KLOFE), Institute of Advanced Materials (IAM), Nanjing Tech University (NanjingTech) 30 South Puzhu Road Nanjing 211816 P. R. China
| | - Bo Peng
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE), Xi'an Institute of Biomedical Materials & Engineering, Northwestern Polytechnical University 127 West Youyi Road Xi'an 710072 P. R. China
| | - Sing Yee Ong
- Department of Chemistry, National University of Singapore 4 Science Drive 2 117544 Singapore
| | - Qiong Wu
- Key Laboratory of Flexible Electronics (KLOFE), Institute of Advanced Materials (IAM), Nanjing Tech University (NanjingTech) 30 South Puzhu Road Nanjing 211816 P. R. China
| | - Lin Li
- Key Laboratory of Flexible Electronics (KLOFE), Institute of Advanced Materials (IAM), Nanjing Tech University (NanjingTech) 30 South Puzhu Road Nanjing 211816 P. R. China
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore 4 Science Drive 2 117544 Singapore
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25
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Glutathione S-Transferases in Cancer. Antioxidants (Basel) 2021; 10:antiox10050701. [PMID: 33946704 PMCID: PMC8146591 DOI: 10.3390/antiox10050701] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/23/2021] [Accepted: 04/27/2021] [Indexed: 02/06/2023] Open
Abstract
In humans, the glutathione S-transferases (GST) protein family is composed of seven members that present remarkable structural similarity and some degree of overlapping functionalities. GST proteins are crucial antioxidant enzymes that regulate stress-induced signaling pathways. Interestingly, overactive GST proteins are a frequent feature of many human cancers. Recent evidence has revealed that the biology of most GST proteins is complex and multifaceted and that these proteins actively participate in tumorigenic processes such as cell survival, cell proliferation, and drug resistance. Structural and pharmacological studies have identified various GST inhibitors, and these molecules have progressed to clinical trials for the treatment of cancer and other diseases. In this review, we discuss recent findings in GST protein biology and their roles in cancer development, their contribution in chemoresistance, and the development of GST inhibitors for cancer treatment.
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26
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Shaw TA, Powdrill MH, Sherratt AR, Garland K, Li BJ, Beauchemin AM, Pezacki JP. Reactivity of N-acyl hydrazone probes with the mammalian proteome. RSC Med Chem 2021; 12:797-803. [PMID: 34124678 DOI: 10.1039/d1md00027f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/16/2021] [Indexed: 11/21/2022] Open
Abstract
Small molecule probes with distinct reactivities are useful tools for the identification and characterization of protein modifications and function. Herein, we show that hydrazone probes with an N-carbamate structural motif react differently from N-carbamates within the human proteome. Mass spectrometry analysis of probe-treated mammalian cell lysates identified several proteins that were covalently modified by the hydrazone probes, including the cytidine deaminase APOBEC3A. We used this enzyme as a model to explore the reactivity of the probes with amino acid residues using LC-MS/MS. Both reactive serine and cysteine residues outside of the enzyme active site were covalently modified. A 1-napthol leaving group provided the most extensive reactivity. These results confirm a unique chemotype for hydrazone probes which can be further optimized to target distinct targets of the human proteome.
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Affiliation(s)
- Tyler A Shaw
- Department of Chemistry and Biomolecular Sciences, University of Ottawa 10 Marie Curie K1N 6N5 Ottawa Canada
| | - Megan H Powdrill
- Department of Chemistry and Biomolecular Sciences, University of Ottawa 10 Marie Curie K1N 6N5 Ottawa Canada
| | - Allison R Sherratt
- Department of Chemistry and Biomolecular Sciences, University of Ottawa 10 Marie Curie K1N 6N5 Ottawa Canada
| | - Keira Garland
- Department of Chemistry and Biomolecular Sciences, University of Ottawa 10 Marie Curie K1N 6N5 Ottawa Canada
| | - Bin-Jie Li
- Department of Chemistry and Biomolecular Sciences, University of Ottawa 10 Marie Curie K1N 6N5 Ottawa Canada
| | - André M Beauchemin
- Department of Chemistry and Biomolecular Sciences, University of Ottawa 10 Marie Curie K1N 6N5 Ottawa Canada
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular Sciences, University of Ottawa 10 Marie Curie K1N 6N5 Ottawa Canada
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27
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Borne AL, Brulet JW, Yuan K, Hsu KL. Development and biological applications of sulfur-triazole exchange (SuTEx) chemistry. RSC Chem Biol 2021; 2:322-337. [PMID: 34095850 PMCID: PMC8174820 DOI: 10.1039/d0cb00180e] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/05/2021] [Indexed: 12/27/2022] Open
Abstract
Sulfur electrophiles constitute an important class of covalent small molecules that have found widespread applications in synthetic chemistry and chemical biology. Various electrophilic scaffolds, including sulfonyl fluorides and arylfluorosulfates as recent examples, have been applied for protein bioconjugation to probe ligand sites amenable for chemical proteomics and drug discovery. In this review, we describe the development of sulfonyl-triazoles as a new class of electrophiles for sulfur-triazole exchange (SuTEx) chemistry. SuTEx achieves covalent reaction with protein sites through irreversible modification of a residue with an adduct group (AG) upon departure of a leaving group (LG). A principal differentiator of SuTEx from other chemotypes is the selection of a triazole heterocycle as the LG, which introduces additional capabilities for tuning the sulfur electrophile. We describe the opportunities afforded by modifications to the LG and AG alone or in tandem to facilitate nucleophilic substitution reactions at the SO2 center in cell lysates and live cells. As a result of these features, SuTEx serves as an efficient platform for developing chemical probes with tunable bioactivity to study novel nucleophilic sites on established and poorly annotated protein targets. Here, we highlight a suite of biological applications for the SuTEx electrophile and discuss future goals for this enabling covalent chemistry.
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Affiliation(s)
- Adam L. Borne
- Department of Pharmacology, University of Virginia School of MedicineCharlottesvilleVirginia 22908USA
| | - Jeffrey W. Brulet
- Department of Chemistry, University of VirginiaMcCormick Road, P.O. Box 400319CharlottesvilleVirginia 22904USA+1-434-297-4864
| | - Kun Yuan
- Department of Chemistry, University of VirginiaMcCormick Road, P.O. Box 400319CharlottesvilleVirginia 22904USA+1-434-297-4864
| | - Ku-Lung Hsu
- Department of Pharmacology, University of Virginia School of MedicineCharlottesvilleVirginia 22908USA
- Department of Chemistry, University of VirginiaMcCormick Road, P.O. Box 400319CharlottesvilleVirginia 22904USA+1-434-297-4864
- University of Virginia Cancer Center, University of VirginiaCharlottesvilleVA 22903USA
- Department of Molecular Physiology and Biological Physics, University of VirginiaCharlottesvilleVirginia 22908USA
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28
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Zhang Y, Qin W, Liu D, Liu Y, Wang C. Chemoproteomic profiling of itaconations in Salmonella. Chem Sci 2021; 12:6059-6063. [PMID: 33996001 PMCID: PMC8098682 DOI: 10.1039/d1sc00660f] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 03/05/2021] [Indexed: 12/28/2022] Open
Abstract
Itaconate is an immunoregulatory and anti-bacterial metabolite, and plays important roles in host-pathogen interactions. Chemoproteomic strategies have been used to explore the anti-inflammatory effects of itaconate on activated macrophages and it has been found that many key proteins in immune pathways were modified; however, how itaconate modulates pathogens was not fully understood. Here, we have designed and synthesized a series of itaconate-based bioorthogonal probes, which enable quantitative and site-specific profiling of itaconated proteins and sites in Salmonella. Among many proteins related to energy metabolism, we identified a key enzyme involved in the glyoxylate cycle, isocitrate lyase (ICL), as the most prominent target. Covalent modification of the active-site cysteine in ICL by itaconate abolishes the enzyme activity and suppresses bacterial growth. Our chemoproteomic study has uncovered the wide array of itaconation targets in Salmonella and provided a comprehensive resource for understanding the anti-bacterial function of this intriguing metabolite.
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Affiliation(s)
- Yanling Zhang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education China
- Peking-Tsinghua Center for Life Sciences, Peking University Beijing 100871 China
| | - Wei Qin
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education China
- Peking-Tsinghua Center for Life Sciences, Peking University Beijing 100871 China
| | - Dongyang Liu
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education China
- College of Chemistry and Molecular Engineering China
| | - Yuan Liu
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education China
- College of Chemistry and Molecular Engineering China
| | - Chu Wang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education China
- College of Chemistry and Molecular Engineering China
- Peking-Tsinghua Center for Life Sciences, Peking University Beijing 100871 China
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29
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Jing Y, Montano JL, Levy M, Lopez JE, Kung PP, Richardson P, Krajewski K, Florens L, Washburn MP, Meier JL. Harnessing Ionic Selectivity in Acetyltransferase Chemoproteomic Probes. ACS Chem Biol 2021; 16:27-34. [PMID: 33373188 PMCID: PMC9093059 DOI: 10.1021/acschembio.0c00766] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Chemical proteomics provides a powerful strategy for the high-throughput assignment of enzyme function or inhibitor selectivity. However, identifying optimized probes for an enzyme family member of interest and differentiating signal from the background remain persistent challenges in the field. To address this obstacle, here we report a physiochemical discernment strategy for optimizing chemical proteomics based on the coenzyme A (CoA) cofactor. First, we synthesize a pair of CoA-based sepharose pulldown resins differentiated by a single negatively charged residue and find this change alters their capture properties in gel-based profiling experiments. Next, we integrate these probes with quantitative proteomics and benchmark analysis of "probe selectivity" versus traditional "competitive chemical proteomics." This reveals that the former is well-suited for the identification of optimized pulldown probes for specific enzyme family members, while the latter may have advantages in discovery applications. Finally, we apply our anionic CoA pulldown probe to evaluate the selectivity of a recently reported small molecule N-terminal acetyltransferase inhibitor. These studies further validate the use of physical discriminant strategies in chemoproteomic hit identification and demonstrate how CoA-based chemoproteomic probes can be used to evaluate the selectivity of small molecule protein acetyltransferase inhibitors, an emerging class of preclinical therapeutic agents.
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Affiliation(s)
- Yihang Jing
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Jose L Montano
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Michaella Levy
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, United States
| | - Jeffrey E Lopez
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Pei-Pei Kung
- Worldwide Research and Development, Pfizer Inc., San Diego, California 92121, United States
| | - Paul Richardson
- Worldwide Research and Development, Pfizer Inc., San Diego, California 92121, United States
| | - Krzysztof Krajewski
- Department of Biochemistry and Biophysics, The University of North Carolina, Chapel Hill, North Carolina 27514, United States
| | - Laurence Florens
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, United States
| | - Michael P Washburn
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, United States
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
| | - Jordan L Meier
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
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30
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Ye Z, Wang Y, Wu H, Song T, Li X, Liu Q, Wang C. Chemoproteomic Profiling of an Ibrutinib Analogue Reveals its Unexpected Role in DNA Damage Repair. Chembiochem 2020; 22:129-133. [PMID: 32979005 DOI: 10.1002/cbic.202000527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/13/2020] [Indexed: 11/09/2022]
Abstract
Ibrutinib is an FDA-approved drug to treat B-lymphoid malignancies, which functions mechanistically as a covalent inhibitor for Bruton's tyrosine kinase (BTK). During the course of screening more potent and selective BTK inhibitors, we discovered that MM2-48, an ibrutinib analogue that contains the alkynyl amide functional group in place of the acrylamide warhead, exhibits a much stronger cytotoxicity. Comparative chemoproteomic profiling of the targets of ibrutinib and MM2-48 revealed that the alkynyl amide warhead exhibits much higher reactivity in proteomes. Unexpectedly, MM2-48 covalently targets a functional cysteine in a BRCA2 and CDKN1A-interacting protein, BCCIP, and significantly inhibits DNA damage repair. Our findings suggest that simultaneous inhibition of BTK activity and DNA damage repair might be a more effective therapeutic strategy for combating B-cell malignancies.
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Affiliation(s)
- Zi Ye
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Synthetic and Functional Biomolecules Center, Beijing National Laboratory of Molecular Science, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Peking, 100871, P. R. China
| | - Yankun Wang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Synthetic and Functional Biomolecules Center, Beijing National Laboratory of Molecular Science, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Peking, 100871, P. R. China
| | - Hong Wu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, P. R. China.,Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230036, Anhui, P. R. China
| | - Tong Song
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Synthetic and Functional Biomolecules Center, Beijing National Laboratory of Molecular Science, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Peking, 100871, P. R. China
| | - Xixiang Li
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, P. R. China.,Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230036, Anhui, P. R. China
| | - Qingsong Liu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, P. R. China.,Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230036, Anhui, P. R. China
| | - Chu Wang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Synthetic and Functional Biomolecules Center, Beijing National Laboratory of Molecular Science, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Peking, 100871, P. R. China
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31
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Cavalier JF, Spilling CD, Durand T, Camoin L, Canaan S. Lipolytic enzymes inhibitors: A new way for antibacterial drugs discovery. Eur J Med Chem 2020; 209:112908. [PMID: 33071055 DOI: 10.1016/j.ejmech.2020.112908] [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: 09/14/2020] [Revised: 09/29/2020] [Accepted: 10/03/2020] [Indexed: 10/23/2022]
Abstract
Tuberculosis (TB) caused by Mycobacterium tuberculosis (M. tb) still remains the deadliest infectious disease worldwide with 1.5 million deaths in 2018, of which about 15% are attributed to resistant strains. Another significant example is Mycobacterium abscessus (M. abscessus), a nontuberculous mycobacteria (NTM) responsible for cutaneous and pulmonary infections, representing up to 95% of NTM infections in cystic fibrosis (CF) patients. M. abscessus is a new clinically relevant pathogen and is considered one of the most drug-resistant mycobacteria for which standardized chemotherapeutic regimens are still lacking. Together the emergence of M. tb and M. abscessus multi-drug resistant strains with ineffective and expensive therapeutics, have paved the way to the development of new classes of anti-mycobacterial agents offering additional therapeutic options. In this context, specific inhibitors of mycobacterial lipolytic enzymes represent novel and promising antibacterial molecules to address this challenging issue. The results highlighted here include a complete overview of the antibacterial activities, either in broth medium or inside infected macrophages, of two families of promising and potent anti-mycobacterial multi-target agents, i.e. oxadiazolone-core compounds (OX) and Cyclophostin & Cyclipostins analogs (CyC); the identification and biochemical validation of their effective targets (e.g., the antigen 85 complex and TesA playing key roles in mycolic acid metabolism) together with their respective crystal structures. To our knowledge, these are the first families of compounds able to target and impair replicating as well as intracellular bacteria. We are still impelled in deciphering their mode of action and finding new potential therapeutic targets against mycobacterial-related diseases.
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Affiliation(s)
- Jean-François Cavalier
- Aix-Marseille Univ., CNRS, LISM, Institut de Microbiologie de La Méditerranée FR3479, Marseille, France.
| | - Christopher D Spilling
- Department of Chemistry and Biochemistry, University of Missouri-St. Louis, One University Boulevard, St. Louis, Missouri, 63121, United States
| | - Thierry Durand
- IBMM, Univ Montpellier, CNRS, ENSCM, Montpellier, France
| | - Luc Camoin
- Aix-Marseille Univ., INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Marseille Protéomique, Marseille, France
| | - Stéphane Canaan
- Aix-Marseille Univ., CNRS, LISM, Institut de Microbiologie de La Méditerranée FR3479, Marseille, France.
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32
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Dolui AK, Vijayaraj P. Functional Omics Identifies Serine Hydrolases That Mobilize Storage Lipids during Rice Seed Germination. PLANT PHYSIOLOGY 2020; 184:693-708. [PMID: 32817194 PMCID: PMC7536657 DOI: 10.1104/pp.20.00268] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 08/04/2020] [Indexed: 05/10/2023]
Abstract
Elucidating proteolipidome dynamics is crucial for understanding the roles of these molecules in plant physiology and disease. Sequence-based functional annotation of the protein is inadequate, since protein activities depend on posttranslational modification. In this study, we applied a gel-free activity-based protein profiling approach to unravel the active lipases, including other Serine hydrolases (SHs), expressed during seed germination in rice (Oryza sativa). We successfully mapped the active sites of 43 active SHs encompassing lipases/esterases, GDSL lipases, proteases, Ser carboxypeptidases, ABHD protein, pectin acetylesterase, and other SHs. The mRNA expression levels of those genes encoding the identified SHs were monitored using microarray analysis. The lipidome analysis revealed distinct patterns of molecular species distribution in individual lipid classes and displayed the metabolic connections between lipid mobilization and rice seedling growth. Changes in the mobilization of storage lipids and their molecular species remodeling were correlated with the expression of the identified lipases and their lipase activity in a time-dependent manner. The physiological significance of the identified SHs was explored during biotic stress with Fusarium verticillioides infection. The fungal infection significantly reduced lipase activity and lipid mobilization, thus impairing the rice seedling. Collectively, our data demonstrate application of the functional proteome strategy along with the shotgun lipidome approach for the identification of active SHs, and thus for deciphering the role of lipid homeostasis during rice seed germination.
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Affiliation(s)
- Achintya Kumar Dolui
- Lipid and Nutrition Laboratory, Department of Lipid Science, Council of Scientific and Industrial Research-Central Food Technological Research Institute, Mysore, Karnataka, 570020, India
- Academy of Scientific and Innovative Research, Ghaziabad, 201002, Uttar Pradesh, India
| | - Panneerselvam Vijayaraj
- Lipid and Nutrition Laboratory, Department of Lipid Science, Council of Scientific and Industrial Research-Central Food Technological Research Institute, Mysore, Karnataka, 570020, India
- Academy of Scientific and Innovative Research, Ghaziabad, 201002, Uttar Pradesh, India
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33
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Armstrong Z, Kuo CL, Lahav D, Liu B, Johnson R, Beenakker TJM, de Boer C, Wong CS, van Rijssel ER, Debets MF, Florea BI, Hissink C, Boot RG, Geurink PP, Ovaa H, van der Stelt M, van der Marel GM, Codée JDC, Aerts JMFG, Wu L, Overkleeft HS, Davies GJ. Manno-epi-cyclophellitols Enable Activity-Based Protein Profiling of Human α-Mannosidases and Discovery of New Golgi Mannosidase II Inhibitors. J Am Chem Soc 2020; 142:13021-13029. [DOI: 10.1021/jacs.0c03880] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zachary Armstrong
- Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, United Kingdom
| | - Chi-Lin Kuo
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Daniël Lahav
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Bing Liu
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Rachel Johnson
- Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, United Kingdom
| | - Thomas J. M. Beenakker
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Casper de Boer
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Chung-Sing Wong
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Erwin R. van Rijssel
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Marjoke F. Debets
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Bogdan I. Florea
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Colin Hissink
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Rolf G. Boot
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Paul P. Geurink
- Oncode Institute & Department of Cell and Chemical Biology, Leiden University Medical Centre, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Huib Ovaa
- Oncode Institute & Department of Cell and Chemical Biology, Leiden University Medical Centre, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Mario van der Stelt
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | | | - Jeroen D. C. Codée
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Johannes M. F. G. Aerts
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Liang Wu
- Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, United Kingdom
| | - Herman S. Overkleeft
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Gideon J. Davies
- Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, United Kingdom
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34
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Discovery of small-molecule enzyme activators by activity-based protein profiling. Nat Chem Biol 2020; 16:997-1005. [PMID: 32514184 PMCID: PMC7442688 DOI: 10.1038/s41589-020-0555-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 04/23/2020] [Indexed: 12/17/2022]
Abstract
Activity-based protein profiling (ABPP) has been used extensively to discover and optimize selective inhibitors of enzymes. Here, we show that ABPP can also be implemented to identify the converse – small-molecule enzyme activators. Using a kinetically controlled, fluorescence polarization-ABPP assay, we identify compounds that stimulate the activity of LYPLAL1 – a poorly characterized serine hydrolase with complex genetic links to human metabolic traits. We apply ABPP-guided medicinal chemistry to advance a lead into a selective LYPLAL1 activator suitable for use in vivo. Structural simulations coupled to mutational, biochemical, and biophysical analyses indicate that this compound increases LYPLAL1’s catalytic activity likely by enhancing the efficiency of the catalytic triad charge-relay system. Treatment with this LYPLAL1 activator confers beneficial effects in a mouse model of diet-induced obesity. These findings reveal a new mode of pharmacological regulation for this large enzyme family and suggest that ABPP may aid discovery of activators for additional enzyme classes.
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35
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Jorge P, Magalhães AP, Grainha T, Alves D, Sousa AM, Lopes SP, Pereira MO. Antimicrobial resistance three ways: healthcare crisis, major concepts and the relevance of biofilms. FEMS Microbiol Ecol 2020; 95:5532357. [PMID: 31305896 DOI: 10.1093/femsec/fiz115] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 07/12/2019] [Indexed: 12/13/2022] Open
Abstract
Worldwide, infections are resuming their role as highly effective killing diseases, as current treatments are failing to respond to the growing problem of antimicrobial resistance (AMR). The social and economic burden of AMR seems ever rising, with health- and research-related organizations rushing to collaborate on a worldwide scale to find effective solutions. Resistant bacteria are spreading even in first-world nations, being found not only in healthcare-related settings, but also in food and in the environment. In this minireview, the impact of AMR in healthcare systems and the major bacteria behind it are highlighted. Ecological aspects of AMR evolution and the complexity of its molecular mechanisms are explained. Major concepts, such as intrinsic, acquired and adaptive resistance, as well as tolerance and heteroresistance, are also clarified. More importantly, the problematic of biofilms and their role in AMR, namely their main resistance and tolerance mechanisms, are elucidated. Finally, some of the most promising anti-biofilm strategies being investigated are reviewed. Much is still to be done regarding the study of AMR and the discovery of new anti-biofilm strategies. Gladly, considerable research on this topic is generated every day and increasingly concerted actions are being engaged globally to try and tackle this problem.
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Affiliation(s)
- Paula Jorge
- Centre of Biological Engineering, Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Andreia Patrícia Magalhães
- Centre of Biological Engineering, Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Tânia Grainha
- Centre of Biological Engineering, Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Diana Alves
- Centre of Biological Engineering, Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Ana Margarida Sousa
- Centre of Biological Engineering, Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Susana Patrícia Lopes
- Centre of Biological Engineering, Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Maria Olívia Pereira
- Centre of Biological Engineering, Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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36
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Affiliation(s)
- Matthew D. Lloyd
- Drug & Target Development, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, U.K
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37
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Carvalho LAR, Almeida VT, Brito JA, Lum KM, Oliveira TF, Guedes RC, Gonçalves LM, Lucas SD, Cravatt BF, Archer M, Moreira R. 3-Oxo-β-sultam as a Sulfonylating Chemotype for Inhibition of Serine Hydrolases and Activity-Based Protein Profiling. ACS Chem Biol 2020; 15:878-883. [PMID: 32176480 DOI: 10.1021/acschembio.0c00090] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
3-Oxo-β-sultams are four-membered ring ambident electrophiles that can react with nucleophiles either at the carbonyl carbon or at the sulfonyl sulfur atoms, and that have been reported to inhibit serine hydrolases via acylation of the active-site serine residue. We have developed a panel of 3-oxo-β-sultam inhibitors and show, through crystallographic data, that they are regioselective sulfonylating electrophiles, covalently binding to the catalytic serine of human and porcine elastases through the sulfur atom. Application of 3-oxo-β-sultam-derived activity-based probes in a human proteome revealed their potential to label disease-related serine hydrolases and proteasome subunits. Activity-based protein profiling applications of 3-oxo-β-sultams should open up new opportunities to investigate these classes of enzymes in complex proteomes and expand the toolbox of available sulfur-based covalent protein modifiers in chemical biology.
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Affiliation(s)
- Luís A. R. Carvalho
- Department of Medicinal Chemistry, Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmacia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Vanessa T. Almeida
- Biological Chemistry Division, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, 2780-157 Oeiras, Portugal
| | - José A. Brito
- Biological Chemistry Division, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, 2780-157 Oeiras, Portugal
| | - Kenneth M. Lum
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Tânia F. Oliveira
- Biological Chemistry Division, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, 2780-157 Oeiras, Portugal
| | - Rita C. Guedes
- Department of Medicinal Chemistry, Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmacia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Lídia M. Gonçalves
- Department of Medicinal Chemistry, Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmacia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Susana D. Lucas
- Department of Medicinal Chemistry, Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmacia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Benjamin F. Cravatt
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Margarida Archer
- Biological Chemistry Division, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, 2780-157 Oeiras, Portugal
| | - Rui Moreira
- Department of Medicinal Chemistry, Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmacia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
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38
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Shenoy VM, Thompson BR, Shi J, Zhu HJ, Smith DE, Amidon GL. Chemoproteomic Identification of Serine Hydrolase RBBP9 as a Valacyclovir-Activating Enzyme. Mol Pharm 2020; 17:1706-1714. [DOI: 10.1021/acs.molpharmaceut.0c00131] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Vikram M. Shenoy
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
| | - Brian R. Thompson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
| | - Jian Shi
- Department of Clinical Pharmacy, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109-1065, United States
| | - Hao-Jie Zhu
- Department of Clinical Pharmacy, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109-1065, United States
| | - David E. Smith
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
| | - Gordon L. Amidon
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
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39
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Deng H, Lei Q, Wu Y, He Y, Li W. Activity-based protein profiling: Recent advances in medicinal chemistry. Eur J Med Chem 2020; 191:112151. [PMID: 32109778 DOI: 10.1016/j.ejmech.2020.112151] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 02/04/2020] [Accepted: 02/13/2020] [Indexed: 02/05/2023]
Abstract
Activity-based protein profiling (ABPP) has become an emerging chemical proteomic approach to illustrate the interaction mechanisms between compounds and proteins. This approach has combined organic synthesis, biochemistry, cell biology, biophysics and bioinformatics to accelerate the process of drug discovery in target identification and validation, as well as in the stage of lead discovery and optimization. This review will summarize new developments and applications of ABPP in medicinal chemistry. Here, we mainly described the design principles of activity-base probes (ABPs) and general workflows of ABPP approach. Moreover, we discussed various basic and advanced ABPP strategies and their applications in medicinal chemistry, including competitive and comparative ABPP, two-step ABPP, fluorescence polarization ABPP (FluoPol-ABPP) and ABPs for visualization. In conclusion, this review will give a general overview of the applications of ABPP as a powerful and efficient technique in medicinal chemistry.
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Affiliation(s)
- Hui Deng
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China; Targeted Tracer Research and Development Laboratory, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
| | - Qian Lei
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China; Targeted Tracer Research and Development Laboratory, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yangping Wu
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China; Targeted Tracer Research and Development Laboratory, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yang He
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China; Targeted Tracer Research and Development Laboratory, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Weimin Li
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China; Targeted Tracer Research and Development Laboratory, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
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40
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Dalton SE, Campos S. Covalent Small Molecules as Enabling Platforms for Drug Discovery. Chembiochem 2020; 21:1080-1100. [DOI: 10.1002/cbic.201900674] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Samuel E. Dalton
- Astex Pharmaceuticals 436 Cambridge Science Park Milton Road Cambridge CB4 0QA UK
| | - Sebastien Campos
- PharmaronDrug Discovery Services Europe Hertford Road Hoddesdon Hertfordshire EN11 9BU UK
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41
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Abstract
The mercapturic acid pathway is a major route for the biotransformation of xenobiotic and endobiotic electrophilic compounds and their metabolites. Mercapturic acids (N-acetyl-l-cysteine S-conjugates) are formed by the sequential action of the glutathione transferases, γ-glutamyltransferases, dipeptidases, and cysteine S-conjugate N-acetyltransferase to yield glutathione S-conjugates, l-cysteinylglycine S-conjugates, l-cysteine S-conjugates, and mercapturic acids; these metabolites constitute a "mercapturomic" profile. Aminoacylases catalyze the hydrolysis of mercapturic acids to form cysteine S-conjugates. Several renal transport systems facilitate the urinary elimination of mercapturic acids; urinary mercapturic acids may serve as biomarkers for exposure to chemicals. Although mercapturic acid formation and elimination is a detoxication reaction, l-cysteine S-conjugates may undergo bioactivation by cysteine S-conjugate β-lyase. Moreover, some l-cysteine S-conjugates, particularly l-cysteinyl-leukotrienes, exert significant pathophysiological effects. Finally, some enzymes of the mercapturic acid pathway are described as the so-called "moonlighting proteins," catalytic proteins that exert multiple biochemical or biophysical functions apart from catalysis.
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Affiliation(s)
- Patrick E Hanna
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - M W Anders
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY, USA
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42
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Hackler AL, FitzGerald FG, Dang VQ, Satz AL, Paegel BM. Off-DNA DNA-Encoded Library Affinity Screening. ACS COMBINATORIAL SCIENCE 2020; 22:25-34. [PMID: 31829554 DOI: 10.1021/acscombsci.9b00153] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
DNA-encoded library (DEL) technology is emerging as a key element of the small molecule discovery toolbox. Conventional DEL screens (i.e., on-DNA screening) interrogate large combinatorial libraries via affinity selection of DNA-tagged library members that are ligands of a purified and immobilized protein target. In these selections, the DNA tags can materially and undesirably influence target binding and, therefore, the experiment outcome. Here, we use a solid-phase DEL and droplet-based microfluidic screening to separate the DEL member from its DNA tag (i.e., off-DNA screening), for subsequent in-droplet laser-induced fluorescence polarization (FP) detection of target binding, obviating DNA tag interference. Using the receptor tyrosine kinase (RTK) discoidin domain receptor 1 (DDR1) as a proof-of-concept target in a droplet-scale competition-binding assay, we screened a 67 100-member solid-phase DEL of drug-like small molecules for competitive ligands of DDR1 and identified several known RTK inhibitor pharmacophores, including azaindole- and quinazolinone-containing monomers. Off-DNA DEL affinity screening with FP detection is potentially amenable to a wide array of target classes, including nucleic acid binding proteins, proteins that are difficult to overexpress and purify, or targets with no known activity assay.
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Affiliation(s)
| | | | | | - Alexander L. Satz
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel Hoffman-La Roche Ltd, Grenzacherstrasse 124, CH-4070 Basel, Switzerland
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43
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Homogeneous label-free protein binding assay using small-molecule-labeled DNA nanomachine with DNAzyme-Based chemiluminescence detection. Talanta 2020; 206:120175. [DOI: 10.1016/j.talanta.2019.120175] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 07/13/2019] [Accepted: 07/24/2019] [Indexed: 12/16/2022]
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44
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Historical, current and future developments of travelling wave ion mobility mass spectrometry: A personal perspective. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.115620] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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45
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Vinegoni C, Feruglio PF, Gryczynski I, Mazitschek R, Weissleder R. Fluorescence anisotropy imaging in drug discovery. Adv Drug Deliv Rev 2019; 151-152:262-288. [PMID: 29410158 PMCID: PMC6072632 DOI: 10.1016/j.addr.2018.01.019] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 01/29/2018] [Accepted: 01/30/2018] [Indexed: 12/15/2022]
Abstract
Non-invasive measurement of drug-target engagement can provide critical insights in the molecular pharmacology of small molecule drugs. Fluorescence polarization/fluorescence anisotropy measurements are commonly employed in protein/cell screening assays. However, the expansion of such measurements to the in vivo setting has proven difficult until recently. With the advent of high-resolution fluorescence anisotropy microscopy it is now possible to perform kinetic measurements of intracellular drug distribution and target engagement in commonly used mouse models. In this review we discuss the background, current advances and future perspectives in intravital fluorescence anisotropy measurements to derive pharmacokinetic and pharmacodynamic measurements in single cells and whole organs.
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Affiliation(s)
- Claudio Vinegoni
- Center for System Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
| | - Paolo Fumene Feruglio
- Center for System Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Department of Neurological, Biomedical and Movement Sciences, University of Verona, Verona, Italy
| | - Ignacy Gryczynski
- University of North Texas Health Science Center, Institute for Molecular Medicine, Fort Worth, TX, United States
| | - Ralph Mazitschek
- Center for System Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ralph Weissleder
- Center for System Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
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46
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Abstract
Ongoing advances in chemical proteomic methods have facilitated detection and quantification of enzymatic activity, a highly informative parameter that is not captured in protein abundance measurements. However, some biological questions remain unanswered, since current gel- or LC-MS/MS-based detection methods suffer from limitations stemming from sample homogenization, signal-averaging, and an inherent bias toward abundant proteins. To address these shortcomings, we recently developed an activity-based proximity ligation (ADPL) platform to capture and quantify enzyme activity on the level of single cells, with high intra- and intercellular spatial resolution. In this chapter, we briefly discuss the rationale behind the ADPL platform, the design transition from the initial "sandwich-complex" workflow to the optimized, "direct conjugate" ADPL method, and conclude with detailed protocols for each. We also describe our novel use of the homo-bifunctional linker, disuccinimidyl suberate (DSS), to conjugate proteins and oligonucleotides, thus generating the necessary antibody-oligonucleotide recognition reagents for ADPL. Finally, we demonstrate the utility of ADPL to characterize enzyme activity from cytosol to nucleus, and specifically detect enzyme activity using "direct conjugate" ADPL.
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47
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Natural product derivatization with β-lactones, β-lactams and epoxides toward ‘infinite’ binders. Tetrahedron 2019. [DOI: 10.1016/j.tet.2019.04.068] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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48
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Zhou Y, Liu Z, Zhang J, Dou T, Chen J, Ge G, Zhu S, Wang F. Prediction of ligand modulation patterns on membrane receptors via lysine reactivity profiling. Chem Commun (Camb) 2019; 55:4311-4314. [DOI: 10.1039/c9cc00520j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A mass spectrometry-based lysine reactivity profiling strategy for the prediction of the ligand modulation patterns on neuronal membrane receptors.
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Affiliation(s)
- Ye Zhou
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian
- China
| | - Zheyi Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian
- China
| | - Jinbao Zhang
- Institute of Neuroscience
- CAS Center for Excellence in Brain Science and Intelligence Technology
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
- Shanghai
| | - Tongyi Dou
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian
- China
| | - Jin Chen
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian
- China
| | - Guangbo Ge
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian
- China
| | - Shujia Zhu
- Institute of Neuroscience
- CAS Center for Excellence in Brain Science and Intelligence Technology
- Shanghai Institutes for Biological Sciences
- Chinese Academy of Sciences
- Shanghai
| | - Fangjun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian
- China
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49
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Tamura T, Hamachi I. Chemistry for Covalent Modification of Endogenous/Native Proteins: From Test Tubes to Complex Biological Systems. J Am Chem Soc 2018; 141:2782-2799. [DOI: 10.1021/jacs.8b11747] [Citation(s) in RCA: 156] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Tomonori Tamura
- Graduate School of Engineering, Department of Synthetic Chemistry and Biological Chemistry, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Itaru Hamachi
- Graduate School of Engineering, Department of Synthetic Chemistry and Biological Chemistry, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- ERATO, Japan Science and Technology Agency (JST), 5 Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
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50
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Glutathione Transferases: Potential Targets to Overcome Chemoresistance in Solid Tumors. Int J Mol Sci 2018; 19:ijms19123785. [PMID: 30487385 PMCID: PMC6321424 DOI: 10.3390/ijms19123785] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 11/23/2018] [Accepted: 11/24/2018] [Indexed: 12/14/2022] Open
Abstract
Multifunctional enzymes glutathione transferases (GSTs) are involved in the development of chemoresistance, thus representing a promising target for a novel approach in cancer treatment. This superfamily of polymorphic enzymes exhibits extraordinary substrate promiscuity responsible for detoxification of numerous conventional chemotherapeutics, at the same time regulating signaling pathways involved in cell proliferation and apoptosis. In addition to upregulated GST expression, different cancer cell types have a unique GST signature, enabling targeted selectivity for isoenzyme specific inhibitors and pro-drugs. As a result of extensive research, certain GST inhibitors are already tested in clinical trials. Catalytic properties of GST isoenzymes are also exploited in bio-activation of specific pro-drugs, enabling their targeted accumulation in cancer cells with upregulated expression of the appropriate GST isoenzyme. Moreover, the latest approach to increase specificity in treatment of solid tumors is development of GST pro-drugs that are derivatives of conventional anti-cancer drugs. A future perspective is based on the design of new drugs, which would selectively target GST overexpressing cancers more prone to developing chemoresistance, while decreasing side effects in off-target cells.
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