1
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Huang Q, Duan C, Ma H, Nong C, Zheng Q, Zhou J, Zhao N, Mou X, Liu T, Zou S, Yang N, Tong A, Qin W, Bao R. Structural and functional characterization of itaconyl-CoA hydratase and citramalyl-CoA lyase involved in itaconate metabolism of Pseudomonas aeruginosa. Structure 2024; 32:941-952.e3. [PMID: 38677288 DOI: 10.1016/j.str.2024.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 02/23/2024] [Accepted: 04/02/2024] [Indexed: 04/29/2024]
Abstract
Itaconate is a key anti-inflammatory/antibacterial metabolite in pathogen-macrophage interactions that induces adaptive changes in Pseudomonas aeruginosa-exposed airways. However, the impact and mechanisms underlying itaconate metabolism remain unclear. Our study reveals that itaconate significantly upregulates the expression of pyoverdine in P. aeruginosa and enhances its tolerance to tobramycin. Notably, the enzymes responsible for efficient itaconate metabolism, PaIch and PaCcl, play crucial roles in both utilizing itaconate and clearing its toxic metabolic intermediates. By using protein crystallography and molecular dynamics simulations analyses, we have elucidated the unique catalytic center and substrate-binding pocket of PaIch, which contribute to its highly efficient catalysis. Meanwhile, analysis of PaCcl has revealed how interactions between domains regulate the conformational changes of the active sites and binding pockets, influencing the catalytic process. Overall, our research uncovers the significance and mechanisms of PaIch and PaCcl in the efficient metabolism of itaconate by P. aeruginosa.
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Affiliation(s)
- Qin Huang
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Chenxi Duan
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Haichuan Ma
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Cheng Nong
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Qianqian Zheng
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Jun Zhou
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Ninglin Zhao
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xingyu Mou
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Tonggen Liu
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Shuang Zou
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Ningchuan Yang
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Aiping Tong
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Wenming Qin
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, CAS, Shanghai, China.
| | - Rui Bao
- Center of Infectious Diseases, Division of Infectious Diseases in State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China.
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2
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Chang H, Ji R, Zhu Z, Wang Y, Yan S, He D, Jia Q, Huang P, Cheng T, Wang R, Zhou Y. Target identification, and optimization of dioxygenated amide derivatives as potent antibacterial agents with FabH inhibitory activity. Eur J Med Chem 2024; 265:116064. [PMID: 38159483 DOI: 10.1016/j.ejmech.2023.116064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 01/03/2024]
Abstract
The enzyme FabH plays a critical role in the initial step of fatty acid biosynthesis, which is vital for the survival of bacteria. As a result, FabH has emerged as an appealing target for the development of novel antibacterial agents. In this study, employing the chemical proteomics method, we validated the previously identified skeleton amide derivatives bearing dioxygenated rings, potentially formed through metabolic processes. Building upon the proteomics findings, we then synthesized and evaluated 32 compounds containing N-heterocyclic amides for their antimicrobial activity for future optimizing the deoxygenated amides. Several compounds demonstrated potent antimicrobial properties with low toxicity, particularly compound 25, which exhibited remarkable potential as an agent with an MIC range of 1.25-3.13 μg/mL against the tested bacterial strains and an IC50 of 2.0 μM against E. coli-derived FabH. Furthermore, we evaluated nine analogues with relatively low MIC values through cytotoxicity and hemolytic activity assessments, Lipinski's rule-of-five criteria, and in silico ADMET predictions to ascertain their druggability potential. Notably, a detailed docking simulation was performed to investigate the binding interactions of compound 25 within the binding pocket of E. coli FabH, which encouragingly revealed strong binding interactions. Based on our findings, compound 25 emerges as the optimal candidate for in vivo therapy aimed at treating infected skin defects. Remarkably, the application of compound 25 demonstrated a significant reduction in the duration of wound infection and notably accelerated the healing process of infected wounds, achieving an impressive 94 % healing rate by day 10.
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Affiliation(s)
- Haoyun Chang
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China; Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, 315300, China
| | - Ruiying Ji
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, 315300, China
| | - Zhiyu Zhu
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, 315300, China
| | - Yapin Wang
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, 315300, China
| | - Shaopeng Yan
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, 315300, China
| | - Dan He
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, 315300, China
| | - Qike Jia
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, 315300, China
| | - Peng Huang
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China.
| | - Tao Cheng
- Pharmaron (Ningbo) Technology Development Co. Ltd., Ningbo, 315336, China
| | - Rui Wang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518118, China.
| | - Yang Zhou
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, 315300, China.
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3
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Tian Y, Wan N, Zhang H, Shao C, Ding M, Bao Q, Hu H, Sun H, Liu C, Zhou K, Chen S, Wang G, Ye H, Hao H. Chemoproteomic mapping of the glycolytic targetome in cancer cells. Nat Chem Biol 2023; 19:1480-1491. [PMID: 37322158 DOI: 10.1038/s41589-023-01355-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 05/04/2023] [Indexed: 06/17/2023]
Abstract
Hyperactivated glycolysis is a metabolic hallmark of most cancer cells. Although sporadic information has revealed that glycolytic metabolites possess nonmetabolic functions as signaling molecules, how these metabolites interact with and functionally regulate their binding targets remains largely elusive. Here, we introduce a target-responsive accessibility profiling (TRAP) approach that measures changes in ligand binding-induced accessibility for target identification by globally labeling reactive proteinaceous lysines. With TRAP, we mapped 913 responsive target candidates and 2,487 interactions for 10 major glycolytic metabolites in a model cancer cell line. The wide targetome depicted by TRAP unveils diverse regulatory modalities of glycolytic metabolites, and these modalities involve direct perturbation of enzymes in carbohydrate metabolism, intervention of an orphan transcriptional protein's activity and modulation of targetome-level acetylation. These results further our knowledge of how glycolysis orchestrates signaling pathways in cancer cells to support their survival, and inspire exploitation of the glycolytic targetome for cancer therapy.
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Affiliation(s)
- Yang Tian
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Ning Wan
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Hanqing Zhang
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Chang Shao
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Ming Ding
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Qiuyu Bao
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Haiyang Hu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Huiyong Sun
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Chenguang Liu
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Kun Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Cardiology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Shuai Chen
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Cardiology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Guangji Wang
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Hui Ye
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China.
| | - Haiping Hao
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China.
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4
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Loi VV, Busche T, Kuropka B, Müller S, Methling K, Lalk M, Kalinowski J, Antelmann H. Staphylococcus aureus adapts to the immunometabolite itaconic acid by inducing acid and oxidative stress responses including S-bacillithiolations and S-itaconations. Free Radic Biol Med 2023; 208:859-876. [PMID: 37793500 DOI: 10.1016/j.freeradbiomed.2023.09.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/21/2023] [Accepted: 09/26/2023] [Indexed: 10/06/2023]
Abstract
Staphylococcus aureus is a major pathogen, which has to defend against reactive oxygen and electrophilic species encountered during infections. Activated macrophages produce the immunometabolite itaconate as potent electrophile and antimicrobial upon pathogen infection. In this work, we used transcriptomics, metabolomics and shotgun redox proteomics to investigate the specific stress responses, metabolic changes and redox modifications caused by sublethal concentrations of itaconic acid in S. aureus. In the RNA-seq transcriptome, itaconic acid caused the induction of the GlnR, KdpDE, CidR, SigB, GraRS, PerR, CtsR and HrcA regulons and the urease-encoding operon, revealing an acid and oxidative stress response and impaired proteostasis. Neutralization using external urea as ammonium source improved the growth and decreased the expression of the glutamine synthetase-controlling GlnR regulon, indicating that S. aureus experienced ammonium starvation upon itaconic acid stress. In the extracellular metabolome, the amounts of acetate and formate were decreased, while secretion of pyruvate and the neutral product acetoin were strongly enhanced to avoid intracellular acidification. Exposure to itaconic acid affected the amino acid uptake and metabolism as revealed by the strong intracellular accumulation of lysine, threonine, histidine, aspartate, alanine, valine, leucine, isoleucine, cysteine and methionine. In the proteome, itaconic acid caused widespread S-bacillithiolation and S-itaconation of redox-sensitive antioxidant and metabolic enzymes, ribosomal proteins and translation factors in S. aureus, supporting its oxidative and electrophilic mode of action in S. aureus. In phenotype analyses, the catalase KatA, the low molecular weight thiol bacillithiol and the urease provided protection against itaconic acid-induced oxidative and acid stress in S. aureus. Altogether, our results revealed that under physiological infection conditions, such as in the acidic phagolysome, itaconic acid is a highly effective antimicrobial against multi-resistant S. aureus isolates, which acts as weak acid causing an acid, oxidative and electrophilic stress response, leading to S-bacillithiolation and itaconation.
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Affiliation(s)
- Vu Van Loi
- Freie Universität Berlin, Institute of Biology-Microbiology, D-14195, Berlin, Germany
| | - Tobias Busche
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, D-33615, Bielefeld, Germany
| | - Benno Kuropka
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, D-14195, Berlin, Germany
| | - Susanne Müller
- Freie Universität Berlin, Institute of Biology-Microbiology, D-14195, Berlin, Germany
| | - Karen Methling
- Department of Cellular Biochemistry and Metabolomics, University of Greifswald, 17487, Greifswald, Germany
| | - Michael Lalk
- Department of Cellular Biochemistry and Metabolomics, University of Greifswald, 17487, Greifswald, Germany
| | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, D-33615, Bielefeld, Germany
| | - Haike Antelmann
- Freie Universität Berlin, Institute of Biology-Microbiology, D-14195, Berlin, Germany.
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5
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Han L, Chang PV. Activity-based protein profiling in microbes and the gut microbiome. Curr Opin Chem Biol 2023; 76:102351. [PMID: 37429085 PMCID: PMC10527501 DOI: 10.1016/j.cbpa.2023.102351] [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: 12/15/2022] [Revised: 05/21/2023] [Accepted: 05/24/2023] [Indexed: 07/12/2023]
Abstract
Activity-based protein profiling (ABPP) is a powerful chemical approach for probing protein function and enzymatic activity in complex biological systems. This strategy typically utilizes activity-based probes that are designed to bind a specific protein, amino acid residue, or protein family and form a covalent bond through a reactivity-based warhead. Subsequent analysis by mass spectrometry-based proteomic platforms that involve either click chemistry or affinity-based labeling to enrich for the tagged proteins enables identification of protein function and enzymatic activity. ABPP has facilitated elucidation of biological processes in bacteria, discovery of new antibiotics, and characterization of host-microbe interactions within physiological contexts. This review will focus on recent advances and applications of ABPP in bacteria and complex microbial communities.
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Affiliation(s)
- Lin Han
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Pamela V Chang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA; Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA; Cornell Center for Immunology, Cornell University, Ithaca, NY 14853, USA; Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, NY 14853, USA.
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6
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Prince A, Wong Fok Lung T. Immunometabolic control by Klebsiella pneumoniae. IMMUNOMETABOLISM (COBHAM, SURREY) 2023; 5:e00028. [PMID: 37492184 PMCID: PMC10364963 DOI: 10.1097/in9.0000000000000028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 06/27/2023] [Indexed: 07/27/2023]
Abstract
Klebsiella pneumoniae is a common Gram-negative pathogen associated with community-acquired and healthcare-associated infections. Its ability to acquire genetic elements resulted in its rapid development of resistance to virtually all antimicrobial agents. Once infection is established, K. pneumoniae is able to evade the host immune response and perhaps more importantly, undergo metabolic rewiring to optimize its ability to maintain infection. K. pneumoniae lipopolysaccharide and capsular polysaccharide are central factors in the induction and evasion of immune clearance. Less well understood is the importance of immunometabolism, the intersection between cellular metabolism and immune function, in the host response to K. pneumoniae infection. Bacterial metabolism itself is perceived as a metabolic stress to the host, altering the microenvironment at the site of infection. In this review, we will discuss the metabolic responses induced by K. pneumoniae, particularly in response to stimulation with the metabolically active bacteria versus pathogen-associated molecular patterns alone, and their implications in shaping the nature of the immune response and the infection outcome. A better understanding of the immunometabolic response to K. pneumoniae may help identify new targets for therapeutic intervention in the treatment of multidrug-resistant bacterial infections.
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Affiliation(s)
- Alice Prince
- Department of Pediatrics, Columbia University, New York, NY, USA
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7
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Sahadevan R, Binoy A, Vechalapu SK, Nanjan P, Sadhukhan S. In situ global proteomics profiling of EGCG targets using a cell-permeable and Click-able bioorthogonal probe. Int J Biol Macromol 2023; 237:123991. [PMID: 36907293 DOI: 10.1016/j.ijbiomac.2023.123991] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 03/01/2023] [Accepted: 03/05/2023] [Indexed: 03/12/2023]
Abstract
Despite possessing a wide spectrum of biological activities, molecular targets of EGCG remain elusive and as a result, its precise mode of action is still unknown. Herein, we have developed a novel cell-permeable and Click-able bioorthogonal probe for EGCG, YnEGCG for in situ detection and identification of its interacting proteins. The strategic structural modification on YnEGCG allowed it to retain innate biological activities of EGCG (IC50 59.52 ± 1.14 μM and 9.07 ± 0.01 μM for cell viability and radical scavenging activity, respectively). Chemoproteomics profiling identified 160 direct EGCG targets, with H:L ratio ≥ 1.10 from the list of 207 proteins, including multiple new proteins that were previously unknown. The targets were broadly distributed in various subcellular compartments suggesting a polypharmacological mode of action of EGCG. GO analysis revealed that the primary targets belonged to the enzymes that regulate key metabolic processes including glycolysis and energy homeostasis, also the cytoplasm (36 %) and mitochondria (15.6 %) contain the majority of EGCG targets. Further, we validated that EGCG interactome was closely associated with apoptosis indicating its role in inducing toxicity in cancer cells. For the first time, this in situ chemoproteomics approach could identify a direct and specific EGCG interactome under physiological conditions in an unbiased manner.
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Affiliation(s)
- Revathy Sahadevan
- Department of Chemistry, Indian Institute of Technology Palakkad, Kerala, India
| | - Anupama Binoy
- Department of Chemistry, Indian Institute of Technology Palakkad, Kerala, India
| | - Sai K Vechalapu
- Department of Chemistry, Indian Institute of Technology Kanpur, Uttar Pradesh, India
| | - Pandurangan Nanjan
- Department of Chemistry, Indian Institute of Technology Palakkad, Kerala, India
| | - Sushabhan Sadhukhan
- Department of Chemistry, Indian Institute of Technology Palakkad, Kerala, India; Physical & Chemical Biology Laboratory, Indian Institute of Technology Palakkad, Kerala, India; Department of Biological Sciences & Engineering, Indian Institute of Technology Palakkad, Kerala, India.
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8
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Malarney KP, Chang PV. Chemoproteomic Approaches for Unraveling Prokaryotic Biology. Isr J Chem 2023; 63:e202200076. [PMID: 37842282 PMCID: PMC10575470 DOI: 10.1002/ijch.202200076] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Indexed: 03/07/2023]
Abstract
Bacteria are ubiquitous lifeforms with important roles in the environment, biotechnology, and human health. Many of the functions that bacteria perform are mediated by proteins and enzymes, which catalyze metabolic transformations of small molecules and modifications of proteins. To better understand these biological processes, chemical proteomic approaches, including activity-based protein profiling, have been developed to interrogate protein function and enzymatic activity in physiologically relevant contexts. Here, chemoproteomic strategies and technological advances for studying bacterial physiology, pathogenesis, and metabolism are discussed. The development of chemoproteomic approaches for characterizing protein function and enzymatic activity within bacteria remains an active area of research, and continued innovations are expected to provide breakthroughs in understanding bacterial biology.
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Affiliation(s)
- Kien P Malarney
- Department of Microbiology, Cornell University, Ithaca, NY 14853 (USA)
| | - Pamela V Chang
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853 (USA)
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853 (USA)
- Cornell Center for Immunology, Cornell University, Ithaca, NY 14853 (USA)
- Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, NY 14853 (USA)
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9
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Xiao W, Chen Y, Wang C. Quantitative Chemoproteomic Methods for Reactive Cysteinome Profiling. Isr J Chem 2023. [DOI: 10.1002/ijch.202200100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Weidi Xiao
- 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 100871 Peking China
- Peking-Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary Studies Peking University Beijing 100871 China
| | - Ying Chen
- 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 100871 Peking China
- Peking-Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary Studies Peking University Beijing 100871 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 College of Chemistry and Molecular Engineering Peking University 100871 Peking China
- Peking-Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary Studies Peking University Beijing 100871 China
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10
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Meng Y, Zhang L, Zhang L, Wang Z, Wang X, Li C, Chen Y, Shang S, Li L. CysModDB: a comprehensive platform with the integration of manually curated resources and analysis tools for cysteine posttranslational modifications. Brief Bioinform 2022; 23:6775608. [PMID: 36305460 PMCID: PMC9677505 DOI: 10.1093/bib/bbac460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 08/27/2022] [Accepted: 09/26/2022] [Indexed: 12/14/2022] Open
Abstract
The unique chemical reactivity of cysteine residues results in various posttranslational modifications (PTMs), which are implicated in regulating a range of fundamental biological processes. With the advent of chemical proteomics technology, thousands of cysteine PTM (CysPTM) sites have been identified from multiple species. A few CysPTM-based databases have been developed, but they mainly focus on data collection rather than various annotations and analytical integration. Here, we present a platform-dubbed CysModDB, integrated with the comprehensive CysPTM resources and analysis tools. CysModDB contains five parts: (1) 70 536 experimentally verified CysPTM sites with annotations of sample origin and enrichment techniques, (2) 21 654 modified proteins annotated with functional regions and structure information, (3) cross-references to external databases such as the protein-protein interactions database, (4) online computational tools for predicting CysPTM sites and (5) integrated analysis tools such as gene enrichment and investigation of sequence features. These parts are integrated using a customized graphic browser and a Basket. The browser uses graphs to represent the distribution of modified sites with different CysPTM types on protein sequences and mapping these sites to the protein structures and functional regions, which assists in exploring cross-talks between the modified sites and their potential effect on protein functions. The Basket connects proteins and CysPTM sites to the analysis tools. In summary, CysModDB is an integrated platform to facilitate the CysPTM research, freely accessible via https://cysmoddb.bioinfogo.org/.
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Affiliation(s)
| | | | - Laizhi Zhang
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Ziyu Wang
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Xuanwen Wang
- College of Computer Science and Technology, Qingdao University, Qingdao, China
| | - Chan Li
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Yu Chen
- College of Computer Science and Technology, Qingdao University, Qingdao, China
| | - Shipeng Shang
- Corresponding authors: Lei Li, Faculty of Biomedical and Rehabilitation Engineering, University of Health and Rehabilitation Sciences, Qingdao 266071, China. Tel/Fax: +86 532 8581 2983; E-mail: ; Shipeng Shang, School of Basic Medicine, Qingdao University, Qingdao 266071, China. Tel.: +86 532 8595 1111; Fax: +86 532 8581 2983; E-mail:
| | - Lei Li
- Corresponding authors: Lei Li, Faculty of Biomedical and Rehabilitation Engineering, University of Health and Rehabilitation Sciences, Qingdao 266071, China. Tel/Fax: +86 532 8581 2983; E-mail: ; Shipeng Shang, School of Basic Medicine, Qingdao University, Qingdao 266071, China. Tel.: +86 532 8595 1111; Fax: +86 532 8581 2983; E-mail:
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11
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Guo H, Yang Y, Zhang Q, Deng JR, Yang Y, Li S, So PK, Lam TC, Wong MK, Zhao Q. Integrated Mass Spectrometry Reveals Celastrol As a Novel Catechol-O-methyltransferase Inhibitor. ACS Chem Biol 2022; 17:2003-2009. [PMID: 35302751 DOI: 10.1021/acschembio.2c00011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Natural product celastrol is known to have various biological activities, yet its molecular targets that correspond to many activities remain unclear. Here, we used multiple mass-spectrometry-based approaches to identify catechol-O-methyltransferase (COMT) as a major binding target of celastrol and characterized their interaction comprehensively. Celastrol was found to inhibit the enzymatic activity of COMT and increased the dopamine level in neuroendocrine chromaffin cells significantly. Our study not only revealed a novel binding target of celastrol but also provided a new scaffold and cysteine hot spot for developing new generation COMT inhibitors in combating neurological disorders.
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Affiliation(s)
- Haijun Guo
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, SAR 999077, China
| | - Yang Yang
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, SAR 999077, China
| | - Qi Zhang
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, SAR 999077, China
- Centre for Eye and Vision Research, 17W Hong Kong Science Park, Hong Kong, SAR 999077, China
| | - Jie-Ren Deng
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, SAR 999077, China
| | - Ying Yang
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, SAR 999077, China
| | - Shuqi Li
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, SAR 999077, China
| | - Pui-Kin So
- University Research Facility in Life Sciences, The Hong Kong Polytechnic University, Hong Kong, SAR 999077, China
| | - Thomas C. Lam
- Centre for Eye and Vision Research, 17W Hong Kong Science Park, Hong Kong, SAR 999077, China
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Hong Kong, SAR 999077, China
- Research Centre for SHARP Vision, The Hong Kong Polytechnic University, Hong Kong, SAR 999077, China
| | - Man-kin Wong
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, SAR 999077, China
| | - Qian Zhao
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, SAR 999077, China
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12
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Itaconate and itaconate derivatives target JAK1 to suppress alternative activation of macrophages. Cell Metab 2022; 34:487-501.e8. [PMID: 35235776 DOI: 10.1016/j.cmet.2022.02.002] [Citation(s) in RCA: 107] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 11/24/2021] [Accepted: 02/02/2022] [Indexed: 12/11/2022]
Abstract
The Krebs cycle-derived metabolite itaconate and its derivatives suppress the inflammatory response in pro-inflammatory "M1" macrophages. However, alternatively activated "M2" macrophages can take up itaconate. We therefore examined the effect of itaconate and 4-octyl itaconate (OI) on M2 macrophage activation. We demonstrate that itaconate and OI inhibit M2 polarization and metabolic remodeling. Examination of IL-4 signaling revealed inhibition of JAK1 and STAT6 phosphorylation by both itaconate and OI. JAK1 activation was also inhibited by OI in response to IL-13, interferon-β, and interferon-γ in macrophages and in T helper 2 (Th2) cells. Importantly, JAK1 was directly modified by itaconate derivatives at multiple residues, including cysteines 715, 816, 943, and 1130. Itaconate and OI also inhibited JAK1 kinase activity. Finally, OI treatment suppressed M2 macrophage polarization and JAK1 phosphorylation in vivo. We therefore identify itaconate and OI as JAK1 inhibitors, suggesting a new strategy to inhibit JAK1 in M2 macrophage-driven diseases.
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13
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Wang S, Zhou Q, Zhang X, Wang P. Site‐Selective Itaconation of Complex Peptides by Photoredox Catalysis. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202111388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Siyao Wang
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules Shanghai Jiao Tong University No. 800, Dongchuan Rd Shanghai 200240 China
| | - QingQing Zhou
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules Shanghai Jiao Tong University No. 800, Dongchuan Rd Shanghai 200240 China
| | - Xiaheng Zhang
- School of Chemistry and Materials Science Hangzhou Institute for Advanced Study University of Chinese Academy of Sciences 1 Sub-lane Xiangshan Hangzhou 310024 China
| | - Ping Wang
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules Shanghai Jiao Tong University No. 800, Dongchuan Rd Shanghai 200240 China
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14
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Wang S, Zhou Q, Zhang X, Wang P. Site-Selective Itaconation of Complex Peptides by Photoredox Catalysis. Angew Chem Int Ed Engl 2022; 61:e202111388. [PMID: 34845804 DOI: 10.1002/anie.202111388] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Indexed: 12/20/2022]
Abstract
Site-selective peptide functionalization provides a straightforward and cost-effective access to diversify peptides for biological studies. Among many existing non-invasive peptide conjugations methodologies, photoredox catalysis has emerged as one of the powerful approaches for site-specific manipulation on native peptides. Herein, we report a highly N-termini-specific method to rapidly access itaconated peptides and their derivatives through a combination of transamination and photoredox conditions. This strategy exploits the facile reactivity of peptidyl-dihydropyridine in the complex peptide settings, complementing existing approaches for bioconjugations with excellent selectivity under mild conditions. Distinct from conventional methods, this method utilizes the highly reactive carbamoyl radical derived from a peptidyl-dihydropyridine. In addition, this itaconated peptide can be further functionalized as a Michael acceptor to access the corresponding peptide-protein conjugate.
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Affiliation(s)
- Siyao Wang
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, No. 800, Dongchuan Rd, Shanghai, 200240, China
| | - QingQing Zhou
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, No. 800, Dongchuan Rd, Shanghai, 200240, China
| | - Xiaheng Zhang
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, Hangzhou, 310024, China
| | - Ping Wang
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, No. 800, Dongchuan Rd, Shanghai, 200240, China
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15
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Chen Y, Qin W, Wang C. Functional Proteomics Driven by Chemical and Computational Approaches. CHINESE J CHEM 2022. [DOI: 10.1002/cjoc.202100785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ying Chen
- College of Chemistry and Molecular Engineering Peking University Beijing 100871 China
- Beijing National Laboratory for Molecular Sciences Peking University Beijing 100871 China
- Synthetic and Functional Biomolecules Center Peking University Beijing 100871 China
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Wei Qin
- Peking‐Tsinghua Center for Life Science Peking University Beijing 100871 China
- Beijing National Laboratory for Molecular Sciences Peking University Beijing 100871 China
- Synthetic and Functional Biomolecules Center Peking University Beijing 100871 China
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Chu Wang
- College of Chemistry and Molecular Engineering Peking University Beijing 100871 China
- Peking‐Tsinghua Center for Life Science Peking University Beijing 100871 China
- Beijing National Laboratory for Molecular Sciences Peking University Beijing 100871 China
- Synthetic and Functional Biomolecules Center Peking University Beijing 100871 China
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
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16
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Wong Fok Lung T, Chan LC, Prince A, Yeaman MR, Archer NK, Aman MJ, Proctor RA. Staphylococcus aureus adaptive evolution: Recent insights on how immune evasion, immunometabolic subversion and host genetics impact vaccine development. Front Cell Infect Microbiol 2022; 12:1060810. [PMID: 36636720 PMCID: PMC9831658 DOI: 10.3389/fcimb.2022.1060810] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 11/16/2022] [Indexed: 12/28/2022] Open
Abstract
Despite meritorious attempts, a S. aureus vaccine that prevents infection or mitigates severity has not yet achieved efficacy endpoints in prospective, randomized clinical trials. This experience underscores the complexity of host-S. aureus interactions, which appear to be greater than many other bacterial pathogens against which successful vaccines have been developed. It is increasingly evident that S. aureus employs strategic countermeasures to evade or exploit human immune responses. From entering host cells to persist in stealthy intracellular reservoirs, to sensing the environmental milieu and leveraging bacterial or host metabolic products to reprogram host immune responses, S. aureus poses considerable challenges for the development of effective vaccines. The fact that this pathogen causes distinct types of infections and can undergo transient genetic, transcriptional or metabolic adaptations in vivo that do not occur in vitro compounds challenges in vaccine development. Notably, the metabolic versatility of both bacterial and host immune cells as they compete for available substrates within specific tissues inevitably impacts the variable repertoire of gene products that may or may not be vaccine antigens. In this respect, S. aureus has chameleon phenotypes that have alluded vaccine strategies thus far. Nonetheless, a number of recent studies have also revealed important new insights into pathogenesis vulnerabilities of S. aureus. A more detailed understanding of host protective immune defenses versus S. aureus adaptive immune evasion mechanisms may offer breakthroughs in the development of effective vaccines, but at present this goal remains a very high bar. Coupled with the recent advances in human genetics and epigenetics, newer vaccine technologies may enable such a goal. If so, future vaccines that protect against or mitigate the severity of S. aureus infections are likely to emerge at the intersection of precision and personalized medicine. For now, the development of S. aureus vaccines or alternative therapies that reduce mortality and morbidity must continue to be pursued.
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Affiliation(s)
| | - Liana C Chan
- Department of Medicine, David Geffen School of Medicine at University of California Loss Angeles (UCLA), Los Angeles, CA, United States.,Divisions of Molecular Medicine and Infectious Diseases, Harbor-University of California Loss Angeles (UCLA) Medical Center, Torrance, CA, United States.,Lundquist Institute for Biomedical Innovation at Harbor-University of California Loss Angeles (UCLA) Medical Center, Torrance, CA, United States
| | - Alice Prince
- Department of Pediatrics, Columbia University, New York, NY, United States
| | - Michael R Yeaman
- Department of Medicine, David Geffen School of Medicine at University of California Loss Angeles (UCLA), Los Angeles, CA, United States.,Divisions of Molecular Medicine and Infectious Diseases, Harbor-University of California Loss Angeles (UCLA) Medical Center, Torrance, CA, United States.,Lundquist Institute for Biomedical Innovation at Harbor-University of California Loss Angeles (UCLA) Medical Center, Torrance, CA, United States
| | - Nathan K Archer
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - M Javad Aman
- Integrated BioTherapeutics, Rockville, MD, United States
| | - Richard A Proctor
- Department of Medicine and Medical Microbiology/Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
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