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Zou JX, Chua W, Ser Z, Wang SM, Chiang GSH, Sanmugam K, Tan BY, Sobota RM, Li H. Detection of Bacterial Neutral Ceramidase in Diabetic Foot Ulcers with an Optimized Substrate and Chemoenzymatic Probes. Angew Chem Int Ed Engl 2023; 62:e202307553. [PMID: 37340712 DOI: 10.1002/anie.202307553] [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: 05/30/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 06/22/2023]
Abstract
Ceramidases (CDases) are important in controlling skin barrier integrity by regulating ceramide composition and affording downstream signal molecules. While the functions of epidermal CDases are known, roles of neutral CDases secreted by skin-residing microbes are undefined. Here, we developed a one-step fluorogenic substrate, S-B, for specific detection of bacterial CDase activity and inhibitor screening. We identified a non-hydrolyzable substrate mimic, C6, as the best hit. Based on C6, we designed a photoaffinity probe, JX-1, which efficiently detects bacterial CDases. Using JX-1, we identified endogenous low-abundance PaCDase in a P. aeruginosa monoculture and in a mixed skin bacteria culture. Harnessing both S-B and JX-1, we found that CDase activity positively correlates with the relative abundance of P. aeruginosa and is negatively associated with wound area reduction in clinical diabetic foot ulcer patient samples. Overall, our study demonstrates that bacterial CDases are important regulators of skin ceramides and potentially play a role in wound healing.
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Affiliation(s)
- Jiao Xia Zou
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore
| | - Wisely Chua
- Molecular Engineering Lab, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
| | - Zheng Ser
- Functional Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
| | - Shi Mei Wang
- Functional Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
| | | | | | | | - Radoslaw M Sobota
- Functional Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
| | - Hao Li
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore
- Molecular Engineering Lab, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
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2
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Fang B, Shen Y, Peng B, Bai H, Wang L, Zhang J, Hu W, Fu L, Zhang W, Li L, Huang W. Small‐Molecule Quenchers for Förster Resonance Energy Transfer: Structure, Mechanism, and Applications. Angew Chem Int Ed Engl 2022; 61:e202207188. [DOI: 10.1002/anie.202207188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Bin Fang
- Frontiers Science Center for Flexible Electronics Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME) Northwestern Polytechnical University Xi'an 710072 China
- State Key Laboratory of Solidification Processing School of Materials Science and Engineering Northwestern Polytechnical University 127 West Youyi Road Xi'an 710072 China
| | - Yu Shen
- Frontiers Science Center for Flexible Electronics Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME) Northwestern Polytechnical University Xi'an 710072 China
| | - Bo Peng
- Frontiers Science Center for Flexible Electronics Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME) Northwestern Polytechnical University Xi'an 710072 China
| | - Hua Bai
- Frontiers Science Center for Flexible Electronics Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME) Northwestern Polytechnical University Xi'an 710072 China
| | - Limin Wang
- Frontiers Science Center for Flexible Electronics Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME) Northwestern Polytechnical University Xi'an 710072 China
| | - Jiaxin Zhang
- Frontiers Science Center for Flexible Electronics Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME) Northwestern Polytechnical University Xi'an 710072 China
| | - Wenbo Hu
- Frontiers Science Center for Flexible Electronics Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME) Northwestern Polytechnical University Xi'an 710072 China
| | - Li Fu
- Frontiers Science Center for Flexible Electronics Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME) Northwestern Polytechnical University Xi'an 710072 China
- State Key Laboratory of Solidification Processing School of Materials Science and Engineering Northwestern Polytechnical University 127 West Youyi Road Xi'an 710072 China
| | - Wei Zhang
- Teaching and Evaluation Center of Air Force Medical University Xi'an 710032 China
| | - Lin Li
- Frontiers Science Center for Flexible Electronics Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME) Northwestern Polytechnical University Xi'an 710072 China
- The Institute of Flexible Electronics (IFE, Future Technologies) Xiamen University Xiamen 361005, Fujian China
| | - Wei Huang
- Frontiers Science Center for Flexible Electronics Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME) Northwestern Polytechnical University Xi'an 710072 China
- The Institute of Flexible Electronics (IFE, Future Technologies) Xiamen University Xiamen 361005, Fujian China
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Fang B, Shen Y, Peng B, Bai H, Wang L, Zhang J, Hu W, Fu L, Zhang W, Li L, Huang W. Small Molecule Quenchers for Förster Resonance Energy Transfer: Structure, Mechanism and Applications. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202207188] [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)
- Bin Fang
- Northwestern Polytechnical University Frontiers Science Center for Flexible Electronics CHINA
| | - Yu Shen
- Northwestern Polytechnical University Frontiers Science Center for Flexible Electronics CHINA
| | - Bo Peng
- Northwestern Polytechnical University Frontiers Science Center for Flexible Electronics CHINA
| | - Hua Bai
- Northwestern Polytechnical University Frontiers Science Center for Flexible Electronics CHINA
| | - Limin Wang
- Northwestern Polytechnical University Frontiers Science Center for Flexible Electronics CHINA
| | - Jiaxin Zhang
- Northwestern Polytechnical University Frontiers Science Center for Flexible Electronics CHINA
| | - Wenbo Hu
- Northwestern Polytechnical University Frontiers Science Center for Flexible Electronics CHINA
| | - Li Fu
- Northwestern Polytechnical University Frontiers Science Center for Flexible Electronics CHINA
| | - Wei Zhang
- Air Force Medical University Teaching and Evaluation Center CHINA
| | - Lin Li
- Nanjing Tech University Institute of Advanced Materials 30 South Puzhu Road 210008 Nanjing CHINA
| | - Wei Huang
- Northwestern Polytechnical University Frontiers Science Center for Flexible Electronics CHINA
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4
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FRET events in fluorescent pentapeptides containing aliphatic triazolo amino acid scaffolds: Role of spacer lengths. J Photochem Photobiol A Chem 2019. [DOI: 10.1016/j.jphotochem.2019.04.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Giroud C, Du Y, Marin M, Min Q, Jui NT, Fu H, Melikyan GB. Screening and Functional Profiling of Small-Molecule HIV-1 Entry and Fusion Inhibitors. Assay Drug Dev Technol 2017; 15:53-63. [PMID: 28322598 DOI: 10.1089/adt.2017.777] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
HIV-1 entry and fusion with target cells is an important target for antiviral therapy. However, a few currently approved treatments are not effective as monotherapy due to the emergence of drug resistance. This consideration has fueled efforts to develop new bioavailable inhibitors targeting different steps of the HIV-1 entry process. Here, a high-throughput screen was performed of a large library of 100,000 small molecules for HIV-1 entry/fusion inhibitors, using a direct virus-cell fusion assay in a 384 half-well format. Positive hits were validated using a panel of functional assays, including HIV-1 specificity, cytotoxicity, and single-cycle infectivity assays. One compound-4-(2,5-dimethyl-pyrrol-1-yl)-2-hydroxy-benzoic acid (DPHB)-that selectively inhibited HIV-1 fusion was further characterized. Functional experiments revealed that DPHB caused irreversible inactivation of HIV-1 Env on cell-free virions and that this effect was related to binding to the third variable loop (V3) of the gp120 subunit of HIV-1 Env. Moreover, DPHB selectively inhibited HIV-1 strains that use CXCR4 or both CXCR4 and CCR5 co-receptors for entry, but not strains exclusively using CCR5. This selectivity was mapped to the gp120 V3 loop using chimeric Env glycoproteins. However, it was found that pure DPHB was not active against HIV-1 and that its degradation products (most likely polyanions) were responsible for inhibition of viral fusion. These findings highlight the importance of post-screening validation of positive hits and are in line with previous reports of the broad antiviral activity of polyanions.
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Affiliation(s)
- Charline Giroud
- 1 Department of Pediatrics Infectious Diseases, Emory University School of Medicine , Atlanta, Georgia
| | - Yuhong Du
- 2 Department of Pharmacology, Emory University School of Medicine , Atlanta, Georgia .,3 Emory Chemical Biology Discovery Center, Emory University School of Medicine , Atlanta, Georgia
| | - Mariana Marin
- 1 Department of Pediatrics Infectious Diseases, Emory University School of Medicine , Atlanta, Georgia
| | - Qui Min
- 2 Department of Pharmacology, Emory University School of Medicine , Atlanta, Georgia .,3 Emory Chemical Biology Discovery Center, Emory University School of Medicine , Atlanta, Georgia
| | - Nathan T Jui
- 4 Department of Chemistry, Emory University , Atlanta, Georgia
| | - Haian Fu
- 2 Department of Pharmacology, Emory University School of Medicine , Atlanta, Georgia .,3 Emory Chemical Biology Discovery Center, Emory University School of Medicine , Atlanta, Georgia .,5 Department of Hematology and Medical Oncology, Winship Cancer Institute , Atlanta, Georgia
| | - Gregory B Melikyan
- 1 Department of Pediatrics Infectious Diseases, Emory University School of Medicine , Atlanta, Georgia .,6 Children's Healthcare of Atlanta , Atlanta, Georgia
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Marin M, Du Y, Giroud C, Kim JH, Qui M, Fu H, Melikyan GB. High-Throughput HIV-Cell Fusion Assay for Discovery of Virus Entry Inhibitors. Assay Drug Dev Technol 2015; 13:155-66. [PMID: 25871547 DOI: 10.1089/adt.2015.639] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
HIV-1 initiates infection by merging its envelope membrane with the target cell membrane, a process that is mediated by the viral Env glycoprotein following its sequential binding to CD4 and coreceptors, CXCR4 or CCR5. Although HIV-1 fusion has been a target for antiviral therapy, the virus has developed resistance to drugs blocking the CCR5 binding or Env refolding steps of this process. This highlights the need for novel inhibitors. Here, we adapted and optimized an enzymatic HIV-cell fusion assay, which reports the transfer of virus-encapsulated β-lactamase into the cytoplasm, to high-throughput screening (HTS) with a 384-well format. The assay was robustly performed in HTS format and was validated by the pilot screen of a small library of pharmacologically active compounds. Several hits identified by screening included a prominent cluster of purinergic receptor antagonists. Functional studies demonstrated that P2X1 receptor antagonists selectively inhibited HIV-1 fusion without affecting the fusion activity of an unrelated virus that enters cells through an endocytic route. The inhibition of HIV-cell fusion by P2X1 antagonists was not through downmodulation of the cell surface expression of CD4 or coreceptors, thus implicating P2X1 receptor in the HIV-1 fusion step. The ability of these antagonists to inhibit viruses regardless of their coreceptor (CXCR4 or CCR5) preference indicates that fusion is blocked at a late step downstream of coreceptor binding. A future large-scale screening campaign for HIV-1 fusion inhibitors, using the above functional readout, will likely reveal novel classes of inhibitors and suggest potential targets for antiviral therapy.
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Affiliation(s)
- Mariana Marin
- 1 Division of Pediatric Infectious Diseases, Emory University Children's Center , Atlanta, Georgia
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Jadhav MP. High-throughput screening (HTS) for the identification of novel antiviral scaffolds. Clin Pharmacol Drug Dev 2014; 3:79-83. [PMID: 27128452 DOI: 10.1002/cpdd.99] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 12/09/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Manoj P Jadhav
- Division of Cardiovascular Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
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Ohayon S, Spasser L, Aharoni A, Brik A. Targeting deubiquitinases enabled by chemical synthesis of proteins. J Am Chem Soc 2012; 134:3281-9. [PMID: 22279964 DOI: 10.1021/ja2116712] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Ubiquitination/ubiquitylation is involved in a wide range of cellular processes in eukaryotes, such as protein degradation and DNA repair. Ubiquitination is a reversible post-translational modification, with the removal of the ubiquitin (Ub) protein being catalyzed by a family of enzymes known as deubiquitinases (DUBs). Approximately 100 DUBs are encoded in the human genome and are involved in a variety of regulatory processes, such as cell-cycle progression, tissue development, and differentiation. DUBs were, moreover, found to be associated with several diseases and as such are emerging as potential therapeutic targets. Several directions have been pursued in the search for lead anti-DUB compounds. However, none of these strategies have delivered inhibitors reaching advanced clinical stages due to several challenges in the discovery process, such as the absence of a highly sensitive and practically available high-throughput screening assay. In this study, we report on the design and preparation of a FRET-based assay for DUBs based on the application of our recent chemical method for the synthesis of Ub bioconjugates. In the assay, the ubiquitinated peptide was specifically labeled with a pair of FRET labels and used to screen a library comprising 1000 compounds against UCH-L3. Such analysis identified a novel and potent inhibitor able to inhibit this DUB in time-dependent manner with k(inact) = 0.065 min(-1) and K(i) = 0.8 μM. Our assay, which was also found suitable for the UCH-L1 enzyme, should assist in the ongoing efforts targeting the various components of the ubiquitin system and studying the role of DUBs in health and disease.
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Affiliation(s)
- Shimrit Ohayon
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
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A mammalian two-hybrid system-based assay for small-molecular HIV fusion inhibitors targeting gp41. Antiviral Res 2011; 90:54-63. [DOI: 10.1016/j.antiviral.2011.02.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Revised: 01/14/2011] [Accepted: 02/17/2011] [Indexed: 11/19/2022]
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10
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Chen X, Lu L, Qi Z, Lu H, Wang J, Yu X, Chen Y, Jiang S. Novel recombinant engineered gp41 N-terminal heptad repeat trimers and their potential as anti-HIV-1 therapeutics or microbicides. J Biol Chem 2010; 285:25506-15. [PMID: 20538590 DOI: 10.1074/jbc.m110.101170] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Peptides derived from N-terminal heptad repeat (NHR) of the HIV-1 gp41 are generally poor inhibitors of HIV-1 entry, because they tend to aggregate and do not form a trimeric coiled-coil. In this study, we have fused portions of gp41 NHR, e.g. N36 or N28, to the T4 fibritin trimerization domain, Foldon (Fd), thus constructing novel NHR trimers, designated N36Fd or N28Fd, which could be expressed in Escherichia coli cells. The purified N36Fd and N28Fd exhibited SDS-resistant trimeric coiled-coil conformation with improved alpha-helicity compared with the corresponding N-peptides. They could interact with a C-peptide (e.g. C34) to form stable six-helix bundle and possessed potent anti-HIV-1 activity against a broad spectrum of HIV-1 strains. N28Fd was effective against T20-resistant HIV-1 variants and more resistant to proteinase K compared with T20 (enfuvirtide), a C-peptide-based HIV fusion inhibitor. Therefore, N28Fd trimer has great potentials for further development as an affordable therapeutic or microbicide for treatment and prevention of HIV-1 infection.
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Affiliation(s)
- Xi Chen
- School of Life Sciences, Tsinghua University, Beijing 100084, China
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Nishikawa H, Nakamura S, Kodama E, Ito S, Kajiwara K, Izumi K, Sakagami Y, Oishi S, Ohkubo T, Kobayashi Y, Otaka A, Fujii N, Matsuoka M. Electrostatically constrained α-helical peptide inhibits replication of HIV-1 resistant to enfuvirtide. Int J Biochem Cell Biol 2009; 41:891-9. [DOI: 10.1016/j.biocel.2008.08.039] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2008] [Revised: 08/19/2008] [Accepted: 08/22/2008] [Indexed: 11/25/2022]
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Novel screening systems for HIV-1 fusion mediated by two extra-virion heptad repeats of gp41. Antiviral Res 2008; 80:71-6. [PMID: 18584890 PMCID: PMC7114109 DOI: 10.1016/j.antiviral.2008.05.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2007] [Revised: 03/19/2008] [Accepted: 05/05/2008] [Indexed: 11/20/2022]
Abstract
Entry of human immunodeficiency virus type 1 (HIV-1) into target cells is mediated by its envelope protein gp41 through membrane fusion. Interaction of two extra-virion heptad repeats (HRs) in the gp41 plays a pivotal role in the fusion, and its inhibitor, enfuvirtide (T-20), blocks HIV-1 entry. To identify agents that block HIV-1 fusion, two screening methods based on detection and quantification by the enzyme-linked immunosorbent assay (ELISA) principle have been established. One method uses an alkaline phosphatase (ALP)-conjugated antibody (Ab-ELISA) and the other uses an ALP-fused HR (F-ELISA) to detect and quantify the interaction of the two HRs. The F-ELISA was more simple and rapid, since no ALP-conjugated antibody reaction was required. Both ELISAs detected all the fusion inhibitors tested except for T-20. Interaction of the two HRs was observed in both ELISAs, even in the presence of 10% dimethyl sulfoxide. Ab-ELISA performed best in a pH ranging from 6 to 8, while F-ELISA performed best at a pH ranging from 7 to 8. These results indicate that both established ELISAs are suitable for the identification of HIV-1 fusion inhibitors.
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