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Deutscher RCE, Safa Karagöz M, Purder PL, Kolos JM, Meyners C, Oki Sugiarto W, Krajczy P, Tebbe F, Geiger TM, Ünal C, Hellmich UA, Steinert M, Hausch F. [4.3.1]Bicyclic FKBP Ligands Inhibit Legionella Pneumophila Infection by LpMip-Dependent and LpMip-Independent Mechanisms. Chembiochem 2023; 24:e202300442. [PMID: 37489700 DOI: 10.1002/cbic.202300442] [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: 06/14/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 07/26/2023]
Abstract
Legionella pneumophila is the causative agent of Legionnaires' disease, a serious form of pneumonia. Its macrophage infectivity potentiator (Mip), a member of a highly conserved family of FK506-binding proteins (FKBPs), plays a major role in the proliferation of the gram-negative bacterium in host organisms. In this work, we test our library of >1000 FKBP-focused ligands for inhibition of LpMip. The [4.3.1]-bicyclic sulfonamide turned out as a highly preferred scaffold and provided the most potent LpMip inhibitors known so far. Selected compounds were non-toxic to human cells, displayed antibacterial activity and block bacterial proliferation in cellular infection-assays as well as infectivity in human lung tissue explants. The results confirm [4.3.1]-bicyclic sulfonamides as anti-legionellal agents, although their anti-infective properties cannot be explained by inhibition of LpMip alone.
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Affiliation(s)
- Robin C E Deutscher
- Institute for Organic Chemistry and Biochemistry, Technical University Darmstadt, Peter-Grünberg-Straße 4, 64287, Darmstadt, Germany
| | - M Safa Karagöz
- Institut für Mikrobiologie, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - Patrick L Purder
- Institute for Organic Chemistry and Biochemistry, Technical University Darmstadt, Peter-Grünberg-Straße 4, 64287, Darmstadt, Germany
| | - Jürgen M Kolos
- Institute for Organic Chemistry and Biochemistry, Technical University Darmstadt, Peter-Grünberg-Straße 4, 64287, Darmstadt, Germany
| | - Christian Meyners
- Institute for Organic Chemistry and Biochemistry, Technical University Darmstadt, Peter-Grünberg-Straße 4, 64287, Darmstadt, Germany
| | - Wisely Oki Sugiarto
- Institute for Organic Chemistry and Biochemistry, Technical University Darmstadt, Peter-Grünberg-Straße 4, 64287, Darmstadt, Germany
| | - Patryk Krajczy
- Institute for Organic Chemistry and Biochemistry, Technical University Darmstadt, Peter-Grünberg-Straße 4, 64287, Darmstadt, Germany
| | - Frederike Tebbe
- Institute of Organic Chemistry & Macromolecular Chemistry (IOMC), Friedrich Schiller University Germany, Humboldtstraße 10, 07743, Jena, Germany
| | - Thomas M Geiger
- Institute for Organic Chemistry and Biochemistry, Technical University Darmstadt, Peter-Grünberg-Straße 4, 64287, Darmstadt, Germany
| | - Can Ünal
- Institut für Mikrobiologie, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - Ute A Hellmich
- Institute of Organic Chemistry & Macromolecular Chemistry (IOMC), Friedrich Schiller University Germany, Humboldtstraße 10, 07743, Jena, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University, Max-von-Laue-Str. 9, 60438, Frankurt/Main, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Michael Steinert
- Institut für Mikrobiologie, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany
- Helmholtz Centre for Infection Research, 38106, Braunschweig, Germany
| | - Felix Hausch
- Institute for Organic Chemistry and Biochemistry, Technical University Darmstadt, Peter-Grünberg-Straße 4, 64287, Darmstadt, Germany
- Centre for Synthetic Biology, Technical University of Darmstadt, 64287, Darmstadt, Germany
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2
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Hu JQ, Zhang A, Wang H, Niu L, Wang QX, Zhu LL, Li YZ, Wu C. Discovery and Biosynthesis of Glycosylated Cycloheximide from a Millipede-Associated Actinomycete. JOURNAL OF NATURAL PRODUCTS 2023; 86:340-345. [PMID: 36693198 DOI: 10.1021/acs.jnatprod.2c00951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Chemical redundancy of microbial natural products (NPs) underscores the importance to exploit new resources of microorganisms. Insect-associated microbes are prolific but largely underexplored sources of diverse NPs. Herein, we discovered the new compound α-l-rhamnosyl-actiphenol (1) from a millipede-associated Streptomyces sp. ML6, which is the first glycosylated cycloheximide-class natural product. Interestingly, bioinformatics analysis of the ML6 genome revealed that the biosynthesis of 1 involves a cooperation between two gene clusters (chx and rml) located distantly on the genome of ML6. We also carried out in vitro enzymatic glycosylation of cycloheximide using an exotic promiscuous glycosyltransferase BsGT-1, which resulted in the production of an additional cycloheximide glycoside cycloheximide 7-O-β-d-glucoside (5). Although the antifungal and cytotoxic activities of the new compounds 1 and 5 were attenuated relative to those of cycloheximide, our work not only enriches the chemical repertoire of the cycloheximide family but also provides new insights into the structure-activity relationship optimization and ecological roles of cycloheximide.
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Affiliation(s)
- Jia-Qi Hu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, People's Republic of China
| | - Ai Zhang
- Fetal Medicine Center, Qingdao Women and Children's Hospital, Qingdao University, 266071 Qingdao, People's Republic of China
| | - Han Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, People's Republic of China
| | - Luo Niu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, People's Republic of China
| | - Qing-Xia Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, People's Republic of China
| | - Le-Le Zhu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, People's Republic of China
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, People's Republic of China
| | - Changsheng Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, People's Republic of China
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3
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Scheuplein NJ, Bzdyl NM, Kibble EA, Lohr T, Holzgrabe U, Sarkar-Tyson M. Targeting Protein Folding: A Novel Approach for the Treatment of Pathogenic Bacteria. J Med Chem 2020; 63:13355-13388. [PMID: 32786507 DOI: 10.1021/acs.jmedchem.0c00911] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Infectious diseases are a major cause of morbidity and mortality worldwide, exacerbated by increasing antibiotic resistance in many bacterial species. The development of drugs with new modes of action is essential. A leading strategy is antivirulence, with the aim to target bacterial proteins that are important in disease causation and progression but do not affect growth, resulting in reduced selective pressure for resistance. Immunophilins, a superfamily of peptidyl-prolyl cis-trans isomerase (PPIase) enzymes have been shown to be important for virulence in a broad-spectrum of pathogenic bacteria. This Perspective will provide an overview of the recent advances made in understanding the role of each immunophilin family, cyclophilins, FK506 binding proteins (FKBPs), and parvulins in bacteria. Inhibitor design and medicinal chemistry strategies for development of novel drugs against bacterial FKBPs will be discussed. Furthermore, drugs against human cyclophilins and parvulins will be reviewed in their current indication as antiviral and anticancer therapies.
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Affiliation(s)
- Nicolas J Scheuplein
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Nicole M Bzdyl
- Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, 6009 Perth, Australia
| | - Emily A Kibble
- Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, 6009 Perth, Australia.,School of Veterinary and Life Sciences, Murdoch University, 6150 Murdoch, Australia
| | - Theresa Lohr
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Ulrike Holzgrabe
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Mitali Sarkar-Tyson
- Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, 6009 Perth, Australia
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4
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Targeting the Human 80S Ribosome in Cancer: From Structure to Function and Drug Design for Innovative Adjuvant Therapeutic Strategies. Cells 2020; 9:cells9030629. [PMID: 32151059 PMCID: PMC7140421 DOI: 10.3390/cells9030629] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/28/2020] [Accepted: 03/02/2020] [Indexed: 12/12/2022] Open
Abstract
The human 80S ribosome is the cellular nucleoprotein nanomachine in charge of protein synthesis that is profoundly affected during cancer transformation by oncogenic proteins and provides cancerous proliferating cells with proteins and therefore biomass. Indeed, cancer is associated with an increase in ribosome biogenesis and mutations in several ribosomal proteins genes are found in ribosomopathies, which are congenital diseases that display an elevated risk of cancer. Ribosomes and their biogenesis therefore represent attractive anti-cancer targets and several strategies are being developed to identify efficient and specific drugs. Homoharringtonine (HHT) is the only direct ribosome inhibitor currently used in clinics for cancer treatments, although many classical chemotherapeutic drugs also appear to impact on protein synthesis. Here we review the role of the human ribosome as a medical target in cancer, and how functional and structural analysis combined with chemical synthesis of new inhibitors can synergize. The possible existence of oncoribosomes is also discussed. The emerging idea is that targeting the human ribosome could not only allow the interference with cancer cell addiction towards protein synthesis and possibly induce their death but may also be highly valuable to decrease the levels of oncogenic proteins that display a high turnover rate (MYC, MCL1). Cryo-electron microscopy (cryo-EM) is an advanced method that allows the visualization of human ribosome complexes with factors and bound inhibitors to improve our understanding of their functioning mechanisms mode. Cryo-EM structures could greatly assist the foundation phase of a novel drug-design strategy. One goal would be to identify new specific and active molecules targeting the ribosome in cancer such as derivatives of cycloheximide, a well-known ribosome inhibitor.
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5
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Saleh AK, Soliman NA, Farrag AA, Ibrahim MM, El-Shinnawy NA, Abdel-Fattah YR. Statistical optimization and characterization of a biocellulose produced by local Egyptian isolate Komagataeibacter hansenii AS.5. Int J Biol Macromol 2019; 144:198-207. [PMID: 31843613 DOI: 10.1016/j.ijbiomac.2019.12.103] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 10/30/2019] [Accepted: 12/12/2019] [Indexed: 11/16/2022]
Abstract
Optimization of the culture parameters used for biocellulose (BC) production by a previously isolated bacterial strain (Komagataeibacter hansenii AS.5) was carried out. The effect of nine culture parameters on BC production was evaluated by implementing the Plackett-Burman design, and the results revealed that, the most significant variables affecting BC production were MgSO4, ethanol, pH and yeast extract. A three-level and four-factor Box-Behnken design was applied to determine the optimum level of each significant variable. According to the results of the Plackett-Burman (PBD) and Box-Behnken designs (BBD), the following medium composition and parameters were calculated to be optimum (g/l): glucose 25, yeast extract 13, MgSO4 0.15, KH2PO4 2, ethanol 7.18 ml/l, pH 5.5, inoclume size 7%, cultivation temperature 20 °C and incubation time 9 days. Characterization of purified BC was performed to determine the network morphology by scanning electron microscopy, crystallinity by X-ray diffraction, chemical structure and functional groups by Fourier-transform infrared spectroscopy, thermal stability by thermogravimetric analysis and mechanical properties such as Young's modulus, tensile strength and elongation at beak % of BC.
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Affiliation(s)
- Ahmed K Saleh
- Cellulose and Paper Department, National Research Centre, El-Tahrir St., Dokki, Giza, Egypt.
| | - Nadia A Soliman
- Bioprocess Development Department, Genetic Engineering and Biotechnology Research Institute, City for Scientific Research and Technological Applications, Alexandria, Egypt
| | - Ayman A Farrag
- Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Egypt
| | - Maha M Ibrahim
- Cellulose and Paper Department, National Research Centre, El-Tahrir St., Dokki, Giza, Egypt
| | - Nashwa A El-Shinnawy
- Zoology Department, Faculty of Women for Arts, Science and Education, Ain Shams University, Cairo, Egypt
| | - Yasser R Abdel-Fattah
- Bioprocess Development Department, Genetic Engineering and Biotechnology Research Institute, City for Scientific Research and Technological Applications, Alexandria, Egypt
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6
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Park Y, Koga Y, Su C, Waterbury AL, Johnny CL, Liau BB. Versatile Synthetic Route to Cycloheximide and Analogues That Potently Inhibit Translation Elongation. Angew Chem Int Ed Engl 2019; 58:5387-5391. [PMID: 30802354 DOI: 10.1002/anie.201901386] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Indexed: 02/05/2023]
Abstract
Cycloheximide (CHX) is an inhibitor of eukaryotic translation elongation that has played an essential role in the study of protein synthesis. Despite its ubiquity, few studies have been directed towards accessing synthetic CHX derivatives, even though such efforts may lead to protein synthesis inhibitors with improved or alternate properties. Described here is the total synthesis of CHX and analogues, and the establishment of structure-activity relationships (SAR) responsible for translation inhibition. The SAR studies aided the design of more potent compounds, one of which irreversibly blocks ribosomal elongation, preserves polysome profiles, and may be a broadly useful tool for investigating protein synthesis.
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Affiliation(s)
- Yongho Park
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
| | - Yumi Koga
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
| | - Cindy Su
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
| | - Amanda L Waterbury
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
| | - Christopher L Johnny
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
| | - Brian B Liau
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
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7
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Park Y, Koga Y, Su C, Waterbury AL, Johnny CL, Liau BB. Versatile Synthetic Route to Cycloheximide and Analogues That Potently Inhibit Translation Elongation. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201901386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yongho Park
- Department of Chemistry and Chemical BiologyHarvard University 12 Oxford Street Cambridge MA 02138 USA
| | - Yumi Koga
- Department of Chemistry and Chemical BiologyHarvard University 12 Oxford Street Cambridge MA 02138 USA
| | - Cindy Su
- Department of Chemistry and Chemical BiologyHarvard University 12 Oxford Street Cambridge MA 02138 USA
| | - Amanda L. Waterbury
- Department of Chemistry and Chemical BiologyHarvard University 12 Oxford Street Cambridge MA 02138 USA
| | - Christopher L. Johnny
- Department of Chemistry and Chemical BiologyHarvard University 12 Oxford Street Cambridge MA 02138 USA
| | - Brian B. Liau
- Department of Chemistry and Chemical BiologyHarvard University 12 Oxford Street Cambridge MA 02138 USA
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8
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Kolos JM, Voll AM, Bauder M, Hausch F. FKBP Ligands-Where We Are and Where to Go? Front Pharmacol 2018; 9:1425. [PMID: 30568592 PMCID: PMC6290070 DOI: 10.3389/fphar.2018.01425] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 11/19/2018] [Indexed: 12/24/2022] Open
Abstract
In recent years, many members of the FK506-binding protein (FKBP) family were increasingly linked to various diseases. The binding domain of FKBPs differs only in a few amino acid residues, but their biological roles are versatile. High-affinity ligands with selectivity between close homologs are scarce. This review will give an overview of the most prominent ligands developed for FKBPs and highlight a perspective for future developments. More precisely, human FKBPs and correlated diseases will be discussed as well as microbial FKBPs in the context of anti-bacterial and anti-fungal therapeutics. The last section gives insights into high-affinity ligands as chemical tools and dimerizers.
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Affiliation(s)
| | | | | | - Felix Hausch
- Department of Chemistry, Institute of Chemistry and Biochemistry, Darmstadt University of Technology, Darmstadt, Germany
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9
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Konstantinidou M, Kurpiewska K, Kalinowska-Tłuscik J, Dömling A. Glutarimide Alkaloids Through Multicomponent Reaction Chemistry. European J Org Chem 2018. [DOI: 10.1002/ejoc.201801276] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
| | - Katarzyna Kurpiewska
- Faculty of Chemistry; Jagiellonian University; 3 Ingardena Street 30-060 Krakow Poland
| | | | - Alexander Dömling
- Drug Design; University of Groningen; A. Deusinglaan 1 9713 AV Groningen The Netherlands
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10
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Pedro MP, Vilcaes AA, Gomez GA, Daniotti JL. Individual S-acylated cysteines differentially contribute to H-Ras endomembrane trafficking and acylation/deacylation cycles. Mol Biol Cell 2017; 28:962-974. [PMID: 28179458 PMCID: PMC5385944 DOI: 10.1091/mbc.e16-08-0603] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 01/09/2017] [Accepted: 01/30/2017] [Indexed: 11/18/2022] Open
Abstract
S-acylation/deacylation cycles and vesicular transport are critical for an adequate subcellular distribution of S-acylated Ras proteins. H-Ras is dually acylated on cysteines 181 and 184, but it is unknown how these residues individually contribute to H-Ras trafficking. In this study, we characterized the acylation and deacylation rates and membrane trafficking of monoacylated H-Ras mutants to analyze their contributions to H-Ras plasma membrane and endomembrane distribution. We demonstrated that dually acylated H-Ras interacts with acyl-protein thioesterases (APTs) 1 and 2 at the plasma membrane. Moreover, single-acylation mutants of H-Ras differed not only in their subcellular distribution, where both proteins localized to different extents at both the Golgi complex and plasma membrane, but also in their deacylation rates, which we showed to be due to different sensitivities to APT1 and APT2. Fluorescence photobleaching and photoactivation experiments also revealed that 1) although S-acylated, single-acylation mutants are incorporated with different efficiencies into Golgi complex to plasma membrane vesicular carriers, and 2) the different deacylation rates of single-acylated H-Ras influence differentially its overall exchange between different compartments by nonvesicular transport. Taken together, our results show that individual S-acylation sites provide singular information about H-Ras subcellular distribution that is required for GTPase signaling.
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Affiliation(s)
- Maria P Pedro
- Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, CONICET, and Departamento de Química Biológica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA, Córdoba, Argentina
| | - Aldo A Vilcaes
- Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, CONICET, and Departamento de Química Biológica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA, Córdoba, Argentina
| | - Guillermo A Gomez
- Division of Cell Biology and Molecular Medicine, Institute for Molecular Bioscience, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Jose L Daniotti
- Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, CONICET, and Departamento de Química Biológica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA, Córdoba, Argentina
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11
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Dunyak BM, Gestwicki JE. Peptidyl-Proline Isomerases (PPIases): Targets for Natural Products and Natural Product-Inspired Compounds. J Med Chem 2016; 59:9622-9644. [PMID: 27409354 DOI: 10.1021/acs.jmedchem.6b00411] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Peptidyl-proline isomerases (PPIases) are a chaperone superfamily comprising the FK506-binding proteins (FKBPs), cyclophilins, and parvulins. PPIases catalyze the cis/trans isomerization of proline, acting as a regulatory switch during folding, activation, and/or degradation of many proteins. These "clients" include proteins with key roles in cancer, neurodegeneration, and psychiatric disorders, suggesting that PPIase inhibitors could be important therapeutics. However, the active site of PPIases is shallow, solvent-exposed, and well conserved between family members, making selective inhibitor design challenging. Despite these hurdles, macrocyclic natural products, including FK506, rapamycin, and cyclosporin, bind PPIases with nanomolar or better affinity. De novo attempts to derive new classes of inhibitors have been somewhat less successful, often showcasing the "undruggable" features of PPIases. Interestingly, the most potent of these next-generation molecules tend to integrate features of the natural products, including macrocyclization or proline mimicry strategies. Here, we review recent developments and ongoing challenges in the inhibition of PPIases, with a focus on how natural products might inform the creation of potent and selective inhibitors.
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Affiliation(s)
- Bryan M Dunyak
- Department of Biological Chemistry, University of Michigan Medical School , 1150 W. Medical Center Drive, Ann Arbor, Michigan 48109, United States.,Department of Pharmaceutical Chemistry, University of California at San Francisco , 675 Nelson Rising Lane, San Francisco, California 94158, United States
| | - Jason E Gestwicki
- Department of Pharmaceutical Chemistry, University of California at San Francisco , 675 Nelson Rising Lane, San Francisco, California 94158, United States
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12
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Microbial peptidyl-prolyl cis/trans isomerases (PPIases): virulence factors and potential alternative drug targets. Microbiol Mol Biol Rev 2015; 78:544-71. [PMID: 25184565 DOI: 10.1128/mmbr.00015-14] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Initially discovered in the context of immunomodulation, peptidyl-prolyl cis/trans isomerases (PPIases) were soon identified as enzymes catalyzing the rate-limiting protein folding step at peptidyl bonds preceding proline residues. Intense searches revealed that PPIases are a superfamily of proteins consisting of three structurally distinguishable families with representatives in every described species of prokaryote and eukaryote and, recently, even in some giant viruses. Despite the clear-cut enzymatic activity and ubiquitous distribution of PPIases, reports on solely PPIase-dependent biological roles remain scarce. Nevertheless, they have been found to be involved in a plethora of biological processes, such as gene expression, signal transduction, protein secretion, development, and tissue regeneration, underscoring their general importance. Hence, it is not surprising that PPIases have also been identified as virulence-associated proteins. The extent of contribution to virulence is highly variable and dependent on the pleiotropic roles of a single PPIase in the respective pathogen. The main objective of this review is to discuss this variety in virulence-related bacterial and protozoan PPIases as well as the involvement of host PPIases in infectious processes. Moreover, a special focus is given to Legionella pneumophila macrophage infectivity potentiator (Mip) and Mip-like PPIases of other pathogens, as the best-characterized virulence-related representatives of this family. Finally, the potential of PPIases as alternative drug targets and first tangible results are highlighted.
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13
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Rasch J, Theuerkorn M, Ünal C, Heinsohn N, Tran S, Fischer G, Weiwad M, Steinert M. Novel Cycloheximide Derivatives Targeting the Moonlighting Protein Mip Exhibit Specific Antimicrobial Activity Against Legionella pneumophila. Front Bioeng Biotechnol 2015; 3:41. [PMID: 25870856 PMCID: PMC4376002 DOI: 10.3389/fbioe.2015.00041] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 03/15/2015] [Indexed: 12/28/2022] Open
Abstract
Macrophage infectivity potentiator (Mip) and Mip-like proteins are virulence factors in a wide range of pathogens including Legionella pneumophila. These proteins belong to the FK506 binding protein (FKBP) family of peptidyl-prolyl-cis/trans-isomerases (PPIases). In L. pneumophila, the PPIase activity of Mip is required for invasion of macrophages, transmigration through an in vitro lung–epithelial barrier, and full virulence in the guinea pig infection model. Additionally, Mip is a moonlighting protein that binds to collagen IV in the extracellular matrix. Here, we describe the development and synthesis of cycloheximide derivatives with adamantyl moieties as novel FKBP ligands, and analyze their effect on the viability of L. pneumophila and other bacteria. All compounds efficiently inhibited PPIase activity of the prototypic human FKBP12 as well as Mip with IC50-values as low as 180 nM and 1.7 μM, respectively. Five of these derivatives inhibited the growth of L. pneumophila at concentrations of 30–40 μM, but exhibited no effect on other tested bacterial species indicating a specific spectrum of antibacterial activity. The derivatives carrying a 3,5-dimethyladamantan-1-[yl]acetamide substitution (MT_30.32), and a 3-ethyladamantan-1-[yl]acetamide substitution (MT_30.51) had the strongest effects in PPIase- and liquid growth assays. MT_30.32 and MT_30.51 were also inhibitory in macrophage infection studies without being cytotoxic. Accordingly, by applying a combinatorial approach, we were able to generate novel, hybrid inhibitors consisting of cycloheximide and adamantane, two known FKBP inhibitors that interact with different parts of the PPIase domain, respectively. Interestingly, despite the proven Mip-inhibitory activity, the viability of a Mip-deficient strain was affected to the same degree as its wild type. Hence, we also propose that cycloheximide derivatives with adamantyl moieties are potent PPIase inhibitors with multiple targets in L. pneumophila.
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Affiliation(s)
- Janine Rasch
- Institut für Mikrobiologie, Technische Universität Braunschweig , Braunschweig , Germany
| | - Martin Theuerkorn
- Max Planck Institute of Biophysical Chemistry Göttingen BO Halle , Halle , Germany
| | - Can Ünal
- Institut für Mikrobiologie, Technische Universität Braunschweig , Braunschweig , Germany ; Türk-Alman Üniversitesi, Fen Fakültesi , Istanbul , Turkey
| | - Natascha Heinsohn
- Institut für Mikrobiologie, Technische Universität Braunschweig , Braunschweig , Germany
| | - Stefan Tran
- Institut für Mikrobiologie, Technische Universität Braunschweig , Braunschweig , Germany
| | - Gunter Fischer
- Max Planck Institute of Biophysical Chemistry Göttingen BO Halle , Halle , Germany ; Institut für Biochemie und Biotechnologie, Universität Halle-Wittenberg , Halle-Wittenberg , Germany
| | - Matthias Weiwad
- Max Planck Institute of Biophysical Chemistry Göttingen BO Halle , Halle , Germany ; Institut für Biochemie und Biotechnologie, Universität Halle-Wittenberg , Halle-Wittenberg , Germany
| | - Michael Steinert
- Institut für Mikrobiologie, Technische Universität Braunschweig , Braunschweig , Germany ; Helmholtz Centre for Infection Research , Braunschweig , Germany
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Ünal CM, Steinert M. FKBPs in bacterial infections. Biochim Biophys Acta Gen Subj 2014; 1850:2096-102. [PMID: 25529296 DOI: 10.1016/j.bbagen.2014.12.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 12/11/2014] [Accepted: 12/13/2014] [Indexed: 02/05/2023]
Abstract
BACKGROUND FK506-binding proteins (FKBPs) contain a domain with peptidyl-prolyl-cis/trans-isomerase (PPIase) activity and bind the immunosuppressive drugs FK506 and rapamycin. FKBPs belong to the immunophilin family and are found in eukaryotes and bacteria. SCOPE OF REVIEW In this review we describe two major groups of bacterial virulence-associated FKBPs, the trigger factor and Mip-like PPIases. Moreover, we discuss the contribution of host FKBPs in bacterial infection processes. MAJOR CONCLUSIONS Since PPIases are regarded as alternative antiinfective drug targets we highlight current research strategies utilizing pipecolinic acid and cycloheximide derivatives as well as substrate based inhibitors. GENERAL SIGNIFICANCE The current research strategies suggest a beneficial synergism of drug development and basic research. This article is part of a Special Issue entitled Proline-directed Foldases: Cell Signaling Catalysts and Drug Targets.
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Affiliation(s)
- Can M Ünal
- Türk-Alman Üniversitesi, Fen Fakültesi, Istanbul, Turkey; Technische Universität Braunschweig, Institut für Mikrobiologie, Braunschweig, Germany
| | - Michael Steinert
- Technische Universität Braunschweig, Institut für Mikrobiologie, Braunschweig, Germany; Helmholtz Centre for Infection Research, Braunschweig, Germany.
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15
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A structural biology approach enables the development of antimicrobials targeting bacterial immunophilins. Antimicrob Agents Chemother 2013; 58:1458-67. [PMID: 24366729 DOI: 10.1128/aac.01875-13] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Macrophage infectivity potentiators (Mips) are immunophilin proteins and essential virulence factors for a range of pathogenic organisms. We applied a structural biology approach to characterize a Mip from Burkholderia pseudomallei (BpML1), the causative agent of melioidosis. Crystal structure and nuclear magnetic resonance analyses of BpML1 in complex with known macrocyclics and other derivatives led to the identification of a key chemical scaffold. This scaffold possesses inhibitory potency for BpML1 without the immunosuppressive components of related macrocyclic agents. Biophysical characterization of a compound series with this scaffold allowed binding site specificity in solution and potency determinations for rank ordering the set. The best compounds in this series possessed a low-micromolar affinity for BpML1, bound at the site of enzymatic activity, and inhibited a panel of homologous Mip proteins from other pathogenic bacteria, without demonstrating toxicity in human macrophages. Importantly, the in vitro activity of BpML1 was reduced by these compounds, leading to decreased macrophage infectivity and intracellular growth of Burkholderia pseudomallei. These compounds offer the potential for activity against a new class of antimicrobial targets and present the utility of a structure-based approach for novel antimicrobial drug discovery.
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Liu F, Wang YQ, Meng L, Gu M, Tan RY. FK506-binding protein 12 ligands: a patent review. Expert Opin Ther Pat 2013; 23:1435-49. [DOI: 10.1517/13543776.2013.828695] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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17
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Aye Y, Long MJC, Stubbe J. Mechanistic studies of semicarbazone triapine targeting human ribonucleotide reductase in vitro and in mammalian cells: tyrosyl radical quenching not involving reactive oxygen species. J Biol Chem 2012; 287:35768-35778. [PMID: 22915594 DOI: 10.1074/jbc.m112.396911] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Triapine® (3-aminopyridine-2-carboxaldehyde thiosemicarbazone (3-AP)) is a drug in Phase II trials. One of its established cellular targets is the β(2) subunit of ribonucleotide reductase that requires a diferric-tyrosyl-radical [(Fe(III)(2)-Y·)(Fe(III)(2))] cofactor for de novo DNA biosynthesis. Several mechanisms for 3-AP inhibition of β(2) have been proposed; one involves direct iron chelation from β(2), whereas a second involves Y· destruction by reactive oxygen species formed in situ in the presence of O(2) and reductant by Fe(II)-(3-AP). Inactivation of β(2) can thus arise from cofactor destruction by loss of iron or Y·. In vitro kinetic data on the rates of (55)Fe and Y· loss from [((55)Fe(III)(2)-Y·)((55)Fe(III)(2))]-β(2) under aerobic and anaerobic conditions reveal that Y· loss alone is sufficient for rapid β(2) inactivation. Oxyblot(TM) and mass spectrometric analyses of trypsin-digested inhibited β(2), and lack of Y· loss from H(2)O(2) and O(2)(•) treatment together preclude reactive oxygen species involvement in Y· loss. Three mammalian cell lines treated with 5 μm 3-AP reveal Y· loss and β(2) inactivation within 30-min of 3-AP-exposure, analyzed by whole-cell EPR and lysate assays, respectively. Selective degradation of apo- over [(Fe(III)(2)-Y·)(Fe(III)(2))]-β(2) in lysates, similar iron-content in β(2) immunoprecipitated from 3-AP-treated and untreated [(55)Fe]-prelabeled cells, and prolonged (12 h) stability of the inhibited β(2) are most consistent with Y· loss being the predominant mode of inhibition, with β(2) remaining iron-loaded and stable. A model consistent with in vitro and cell-based biochemical studies is presented in which Fe(II)-(3-AP), which can be cycled with reductant, directly reduces Y· of the [(Fe(III)(2)-Y·)(Fe(III)(2))] cofactor of β(2).
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Affiliation(s)
- Yimon Aye
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Marcus J C Long
- Graduate Program in Biochemistry and Biophysics, Brandeis University, Waltham, Massachusetts 02454
| | - JoAnne Stubbe
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139; Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139.
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Gunn JS, Ehrlich HP. Evidence that translocation of collagen fibril segments plays a role in early intrinsic tendon repair. Plast Reconstr Surg 2012; 129:300e-306e. [PMID: 22286444 DOI: 10.1097/prs.0b013e31823aeb5a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Severed tendon repair advances with either a scar through extrinsic repair or regeneration through intrinsic repair. The authors examined whether intrinsic tendon repair reintroduces embryonic fibrillogenesis, whereby preformed collagen fibril segments are incorporated into growing collagen fibers at wound edges. METHODS Isolated tendons from 10-day-old chicken embryos were suspended in 1 mg/ml of the antibiotic gentamicin for 90 days, which released fibril segments that were fluorescently tagged with rhodamine. Tendons isolated from 14-day-old chicken embryos were wounded to half their diameter and then maintained as explants in stationary organ culture. Fluorescent-tagged fibril segments were introduced to wounded tendon explants in the presence of high concentrations of neomycin, an antibiotic; cycloheximide, a protein synthesis inhibitor; cytochalasin D, a disruptor of microfilaments; and colchicine, a disruptor of microtubules. At 24 hours, explants were viewed by means of fluorescent microscopy. RESULTS Untreated, wounded tendon explants showed the translocation of fluorescent-tagged fibril segments from the explant surface to accumulation at wound edges. In the presence of high concentrations of neomycin, cytochalasin D, or colchicine, fluorescent-tagged fibril segments failed to accumulate at wound edges and were retained on the explant surface. Inhibition of protein synthesis by cycloheximide did not alter the accumulation of fluorescent-tagged fibril segments at wound edges. CONCLUSIONS Inhibiting fluorescent-tagged fibril segment accumulation by antibiotics is consistent with their role in releasing fibril segments. Experimental findings show fibril segment translocation and accumulation at wound edges involves microfilaments and microtubules, but not protein synthesis. The experiments support the hypothesis that intrinsic tendon repair advances through the incorporation of fibril segments at wound edges.
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Affiliation(s)
- J Stephen Gunn
- Hershey, Pa. From the Division of Plastic Surgery, The Pennsylvania State University, College of Medicine
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The structure of a Burkholderia pseudomallei immunophilin-inhibitor complex reveals new approaches to antimicrobial development. Biochem J 2011; 437:413-22. [PMID: 21574961 DOI: 10.1042/bj20110345] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Mips (macrophage infectivity potentiators) are a subset of immunophilins associated with virulence in a range of micro-organisms. These proteins possess peptidylprolyl isomerase activity and are inhibited by drugs including rapamycin and tacrolimus. We determined the structure of the Mip homologue [BpML1 (Burkholderia pseudomallei Mip-like protein 1)] from the human pathogen and biowarfare threat B. pseudomallei by NMR and X-ray crystallography. The crystal structure suggests that key catalytic residues in the BpML1 active site have unexpected conformational flexibility consistent with a role in catalysis. The structure further revealed BpML1 binding to a helical peptide, in a manner resembling the physiological interaction of human TGFβRI (transforming growth factor β receptor I) with the human immunophilin FKBP12 (FK506-binding protein 12). Furthermore, the structure of BpML1 bound to the class inhibitor cycloheximide N-ethylethanoate showed that this inhibitor mimics such a helical peptide, in contrast with the extended prolyl-peptide mimicking shown by inhibitors such as tacrolimus. We suggest that Mips, and potentially other bacterial immunophilins, participate in protein-protein interactions in addition to their peptidylprolyl isomerase activity, and that some roles of Mip proteins in virulence are independent of their peptidylprolyl isomerase activity.
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Dezitter X, Masselot B, Tardivel M, Mereau-Richard C, Formstecher P, Idziorek T. Macromolecular synthesis inhibitors perturb glucocorticoid receptor trafficking. J Steroid Biochem Mol Biol 2011; 126:104-12. [PMID: 21569845 DOI: 10.1016/j.jsbmb.2011.04.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Revised: 04/21/2011] [Accepted: 04/22/2011] [Indexed: 11/17/2022]
Abstract
The ability of inhibitors of transcription and translation to prevent glucocorticoid-induced apoptosis has been interpreted to indicate that the cell death machinery requires de novo protein synthesis. The transcriptional inhibitors actinomycin D (Act D) and DRB as well as the translational inhibitors CHX and puromycin inhibited early loss of mitochondrial membrane integrity in a dose-dependent manner. This effect was not observed with the transcriptional inhibitor α-amanitin suggesting they may have additional effects. Their role in the glucocorticoid receptor (GR) intracellular trafficking was therefore investigated. Here, we show that Act D and CHX reduced glucocorticoid binding, GR turnover and impaired GR nuclear translocation. We performed the same experiments in different thymocyte subpopulations of Balb/c mice. At the highest dose tested, actinomycin D and cycloheximide abolished glucocorticoid-induced cell death of CD4+CD8+ and CD4+CD8-. In all subsets, Act D, DRB, as well as CHX and puromycin prevented receptor nuclear translocation, indicating a general alteration of GR trafficking. Overall, our data support a direct effect of macromolecular inhibitors on GR activation and trafficking. Finally, direct alterations of the functional properties of the glucocorticoid receptor might be responsible for cell death prevention by actinomycin D, DRB, cycloheximide and puromycin.
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21
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Zeng X, Small DP, Wan W. Statistical optimization of culture conditions for bacterial cellulose production by Acetobacter xylinum BPR 2001 from maple syrup. Carbohydr Polym 2011. [DOI: 10.1016/j.carbpol.2011.02.034] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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22
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Ahearn IM, Tsai FD, Court H, Zhou M, Jennings BC, Ahmed M, Fehrenbacher N, Linder ME, Philips MR. FKBP12 binds to acylated H-ras and promotes depalmitoylation. Mol Cell 2011; 41:173-85. [PMID: 21255728 DOI: 10.1016/j.molcel.2011.01.001] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Revised: 09/07/2010] [Accepted: 11/24/2010] [Indexed: 11/19/2022]
Abstract
A cycle of palmitoylation/depalmitoylation of H-Ras mediates bidirectional trafficking between the Golgi apparatus and the plasma membrane, but nothing is known about how this cycle is regulated. We show that the prolyl isomerase (PI) FKBP12 binds to H-Ras in a palmitoylation-dependent fashion and promotes depalmitoylation. A variety of inhibitors of the PI activity of FKBP12, including FK506, rapamycin, and cycloheximide, increase steady-state palmitoylation. FK506 inhibits retrograde trafficking of H-Ras from the plasma membrane to the Golgi in a proline 179-dependent fashion, augments early GTP loading of Ras in response to growth factors, and promotes H-Ras-dependent neurite outgrowth from PC12 cells. These data demonstrate that FKBP12 regulates H-Ras trafficking by promoting depalmitoylation through cis-trans isomerization of a peptidyl-prolyl bond in proximity to the palmitoylated cysteines.
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Affiliation(s)
- Ian M Ahearn
- Department of Medicine, NYU Langone School of Medicine, 550 First Avenue, New York, NY 10016, USA. 0016, USA
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Peptide Bond cis/trans Isomerases: A Biocatalysis Perspective of Conformational Dynamics in Proteins. Top Curr Chem (Cham) 2011; 328:35-67. [DOI: 10.1007/128_2011_151] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Misaki R, Morimatsu M, Uemura T, Waguri S, Miyoshi E, Taniguchi N, Matsuda M, Taguchi T. Palmitoylated Ras proteins traffic through recycling endosomes to the plasma membrane during exocytosis. ACTA ACUST UNITED AC 2010; 191:23-9. [PMID: 20876282 PMCID: PMC2953436 DOI: 10.1083/jcb.200911143] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Palmitoylation directs Ras proteins to the correct intracellular organelles for trafficking and activity. Ras proteins regulate cell growth, death, and differentiation, and it is well established that this functional versatility is accomplished through their different subcellular localizations. Palmitoylated H- and N-Ras are believed to localize at the perinuclear Golgi and plasma membrane (PM). Notably, however, recycling endosomes (REs) also localize to a perinuclear region, which is often indistinguishable from the Golgi. In this study, we show that active palmitoylated Ras proteins mainly localize intracellularly at REs and that REs act as a way station along the post-Golgi exocytic pathway to the PM. H-Ras requires two palmitoyl groups for RE targeting. The lack of either or both palmitoyl groups leads to the mislocalization of the mutant proteins to the endoplasmic reticulum, Golgi apparatus, or the PM. Therefore, we demonstrate that palmitoylation directs Ras proteins to the correct intracellular organelles for trafficking and activity.
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Affiliation(s)
- Ryo Misaki
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
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25
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Shi YN, Zhou YP, Long CL, Li ML, Wang YH, Li XY, Guo R, Wang HS. Cycloheximide Derivatives from the Fruits ofDipteronia dyeriana. Helv Chim Acta 2009. [DOI: 10.1002/hlca.200900007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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26
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Kiralj R, Ferreira M. Extensive Chemometric Investigations of the Multidrug Resistance in Strains of the Phytopathogenic FungusPenicillium Digitatum. ACTA ACUST UNITED AC 2008. [DOI: 10.1002/qsar.200630160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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27
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Kiralj R, Ferreira MMC. Chemometric analysis of the multidrug resistance in strains of Penicillium digitatum. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2008; 19:55-70. [PMID: 18311634 DOI: 10.1080/10629360701844118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Multidrug resistance activities pECr50 of diverse strains of pathogenic fungus Penicillium digitatum against seven toxicants were studied by Principal Component Analysis (PCA) and Hierarchical Cluster Analysis (HCA). Fungal growth data (radii, circumferences, surface areas of fungal colonies, radius differences and ratios) in absence and presence of toxicants were used to derive eight new descriptors for 35 fungal strains. This data set was studied by PCA and HCA, and was correlated with the genome descriptor PCR for expression of gene CYP51 by Partial Least Squares (PLS) regression. Both analyses of pECr50 data and of fungal growth data have identified baseline resistance character, origin and target fruits of the fungal strains. In addition, the analysis of fungal growth data shows that fungal growth morphology is multivariate by nature, meaning that experimental data can be explored more intensely than in usual practice. Fungal growth is directly related to the production of enzyme P45014DM as the main resistance mechanism of P. digitatum against demethylation inhibitors. This is visible from a parsimonious PLS model (two principal components, Q2 = 0.985, R2 = 0.991, SEV = 0.028), validated with eight strains in the external validation set (Q2ev = 0.982, R2ev = 0.990, SECev = 0.025). Chemometric methods in exploring bioassay data are promising approaches to obtain useful information on fungal resistance and to apply these findings in practice.
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Affiliation(s)
- R Kiralj
- Laboratório de Quimiometria Teórica e Aplicada, Instituto de Química, Universidade Estadual de Campinas, Campinas, SP, Brazil
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Joshi PB, Hirst M, Malcolm T, Parent J, Mitchell D, Lund K, Sadowski I. Identification of protein interaction antagonists using the repressed transactivator two-hybrid system. Biotechniques 2007; 42:635-44. [PMID: 17515203 DOI: 10.2144/000112434] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The repressed transactivator (RTA) yeast two-hybrid system was developed to enable genetic identification of interactions with transcriptional activator proteins. We have devised modifications of this system that enable its use in screening for inhibitors of protein interactions from small molecule compound libraries. We show that inhibition of protein interactions can be measured by monitoring growth in selective medium containing 3-aminotriazole (3-AT) and using this assay have identified inhibitors of four independent protein interactions in screens with a 23,000 small molecule compound library. Compounds found to inhibit one of the tested interactions between FKBP12 and the transforming growth factor β receptor (TGFβ-R) were validated in vivo and found to inhibit calcineurin-dependent signaling in T cells. One of these compounds was also found to cause elevated basal expression of a TGFβ-R/SMAD-dependent reporter gene. These results demonstrate the capability of the RTA small molecule screening assay for discovery of potentially novel therapeutic compounds.
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Pecot MY, Malhotra V. The Golgi apparatus maintains its organization independent of the endoplasmic reticulum. Mol Biol Cell 2006; 17:5372-80. [PMID: 17050735 PMCID: PMC1679697 DOI: 10.1091/mbc.e06-06-0565] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Under artificial conditions Golgi enzymes have the capacity to rapidly accumulate in the endoplasmic reticulum (ER). These observations prompted the idea that Golgi enzymes constitutively recycle through the ER. We have tested this hypothesis under physiological conditions through use of a procedure that captures Golgi enzymes in the ER. In the presence of rapamycin, which induces a tight association between FKBP (FK506-binding protein) and FRAP (FKBP-rapamycin-associated protein), an FKBP-tagged Golgi enzyme can be trapped when it visits the ER by an ER-retained protein fused to FRAP. We find that although FKBP-ERGIC-53 of the ER-Golgi intermediate compartment (ERGIC) rapidly cycles through the ER (30 min), FKBP-Golgi enzyme chimeras remain stably associated with Golgi membranes. We also demonstrate that Golgi dispersion upon nocodazole treatment mainly occurs through a mechanism that does not involve the recycling of Golgi membranes through the ER. Our findings suggest that the Golgi apparatus, as defined by its collection of resident enzymes, exists independent of the ER.
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Affiliation(s)
- Matthew Y. Pecot
- Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093
| | - Vivek Malhotra
- Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093
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30
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Abstract
Designed peptidyl-prolyl isomerase (PPIase) inhibitors of Pin1, cyclophilin (CyP), and FK506 binding protein (FKBP) are reviewed. Emphasis is placed on the design, structure, and biological activity of the inhibitors. While CyP and FKBP inhibitors have been explored fairly thoroughly, inhibitors of the relatively new Pin1 cell cycle regulator are in their infancy. Ligands designed for Pin1 and CyP have primarily been ground state analogues: alkenes and bicyclic compounds. For FKBP, more of the focus has been on analogues of bonds at the reactive center, the prolyl amide, because of the idea that the alpha-ketoamide of FK506 is an analogue of the twisted amide in the transition state.
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Affiliation(s)
- Xiaodong J Wang
- Department of Chemistry, Virginia Tech, Blacksburg, VA 24060, USA
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31
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Klemm D, Schumann D, Kramer F, Heßler N, Hornung M, Schmauder HP, Marsch S. Nanocelluloses as Innovative Polymers in Research and Application. POLYSACCHARIDES II 2006. [DOI: 10.1007/12_097] [Citation(s) in RCA: 306] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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32
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Edlich F, Weiwad M, Erdmann F, Fanghänel J, Jarczowski F, Rahfeld JU, Fischer G. Bcl-2 regulator FKBP38 is activated by Ca2+/calmodulin. EMBO J 2005; 24:2688-99. [PMID: 15990872 PMCID: PMC1176465 DOI: 10.1038/sj.emboj.7600739] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2005] [Accepted: 06/10/2005] [Indexed: 01/06/2023] Open
Abstract
FKBP-type peptidyl prolyl cis/trans isomerases (PPIases) are folding helper enzymes involved in the control of functional regrowth of damaged sciatic, cortical cholinergic, dopaminergic and 5-HT neurones. Here, we show that the constitutively inactive human FK506-binding protein 38 (FKBP38) is capable of responding directly to intracellular Ca2+ rise through formation of a heterodimeric Ca2+/calmodulin/FKBP38 complex. Only complex formation creates an enzymatically active FKBP, displaying affinity for Bcl-2 mediated through the PPIase site. Association between Bcl-2 and the active site of Ca2+/calmodulin/FKBP38 regulates Bcl-2 function and thereby participates in the promotion of apoptosis in neuronal tissues. FKBP38 proapoptotic function mediated by this interaction is abolished by either potent inhibitors of the PPIase activity of the Ca2+/calmodulin/FKBP38 complex or RNA interference-mediated depletion of FKBP38, promoting neuronal cell survival.
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Affiliation(s)
- Frank Edlich
- Max-Planck Research Unit for Enzymology of Protein Folding, Halle/Saale, Germany
| | - Matthias Weiwad
- Max-Planck Research Unit for Enzymology of Protein Folding, Halle/Saale, Germany
| | - Frank Erdmann
- Max-Planck Research Unit for Enzymology of Protein Folding, Halle/Saale, Germany
| | - Jörg Fanghänel
- Max-Planck Research Unit for Enzymology of Protein Folding, Halle/Saale, Germany
| | - Franziska Jarczowski
- Max-Planck Research Unit for Enzymology of Protein Folding, Halle/Saale, Germany
| | - Jens-Ulrich Rahfeld
- Max-Planck Research Unit for Enzymology of Protein Folding, Halle/Saale, Germany
| | - Gunter Fischer
- Max-Planck Research Unit for Enzymology of Protein Folding, Halle/Saale, Germany
- Enzymologie der Peptidbindung, Max-Planck-Gesellschaft in Max-Planck Research Unit for Enzymology of Protein Folding, Weinbergweg 22, 06120 Halle/Saale, Germany. Tel.: +49 345 5522800; Fax: +49 345 5511972; E-mail:
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Sun F, Li P, Ding Y, Wang L, Bartlam M, Shu C, Shen B, Jiang H, Li S, Rao Z. Design and structure-based study of new potential FKBP12 inhibitors. Biophys J 2003; 85:3194-201. [PMID: 14581219 PMCID: PMC1303595 DOI: 10.1016/s0006-3495(03)74737-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Based on the structure of FKBP12 complexed with FK506 or rapamycin, with computer-aided design, two neurotrophic ligands, (3R)-4-(p-Toluenesulfonyl)-1,4-thiazane-3-carboxylic acid-L-Leucine ethyl ester and (3R)-4-(p-Toluenesulfonyl)-1,4-thiazane-3-carboxylic acid-L-phenylalanine benzyl ester, were designed and synthesized. Fluorescence experiments were used to detect the binding affinity between FKBP12 and these two ligands. Complex structures of FKBP12 with these two ligands were obtained by x-ray crystallography. In comparing FKBP12-rapamycin complex and FKBP12-FK506 complex as well as FKBP12-GPI-1046 solution structure with these new complexes, significant volume and surface area effects and obvious contact changes were detected which are expected to cause their different binding energies-showing these two novel ligands will become more effective neuron regeneration drugs than GPI-1046, which is currently undergoing phase II clinical trail as a neurotrophic drug. Analysis of volume and surface area effects also gives a new clue for structure-based drug design.
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Affiliation(s)
- Fei Sun
- Laboratory of Structural Biology, Tsinghua University, Beijing, China
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Dugave C, Demange L. Cis-trans isomerization of organic molecules and biomolecules: implications and applications. Chem Rev 2003; 103:2475-532. [PMID: 12848578 DOI: 10.1021/cr0104375] [Citation(s) in RCA: 753] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Christophe Dugave
- CEA/Saclay, Département d'Ingénierie et d'Etudes des Protéines (DIEP), Bâtiment 152, 91191 Gif-sur-Yvette, France.
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Mackrill JJ, O'Driscoll S, Lai FA, McCarthy TV. Analysis of type 1 ryanodine receptor-12 kDa FK506-binding protein interaction. Biochem Biophys Res Commun 2001; 285:52-7. [PMID: 11437371 DOI: 10.1006/bbrc.2001.5125] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Although dissociation of the 12 kDa FK506 binding protein (FKBP12)-type 1 ryanodine receptor (RyR1) complex by macrolide immunosuppressants is well documented, effects of many solutes and drugs have not been quantitated. In the current study, the influence of these on binding between solubilised RyR1 and an FKBP12-glutathione-S-transferase fusion protein was analysed using a novel assay. Association between these two proteins is stable, and is not greatly altered by changes in temperature, pH, cations, and endogenous solutes over physiological ranges. Ascomycin, an FK506 analogue, was identified for the first time as a drug which can disrupt the FKBP12-RyR1 complex.
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Affiliation(s)
- J J Mackrill
- Department of Biochemistry, University College Cork, National University of Ireland, Cork, Ireland.
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Grabley S, Thiericke R, Sattler I. Tools for drug discovery: natural product-based libraries. ERNST SCHERING RESEARCH FOUNDATION WORKSHOP 2001:217-52. [PMID: 11077611 DOI: 10.1007/978-3-662-04042-3_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- S Grabley
- Hans-Knöll-Institut für Naturstoff-Forschung e.V., Jena, Germany
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Parat MO, Fox PL. Palmitoylation of caveolin-1 in endothelial cells is post-translational but irreversible. J Biol Chem 2001; 276:15776-82. [PMID: 11278313 DOI: 10.1074/jbc.m006722200] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Caveolin-1 is a palmitoylated protein involved in assembly of signaling molecules in plasma membrane subdomains termed caveolae and in intracellular cholesterol transport. Three cysteine residues in the C terminus of caveolin-1 are subject to palmitoylation, which is not necessary for caveolar targeting of caveolin-1. Protein palmitoylation is a post-translational and reversible modification that may be regulated and that in turn may regulate conformation, membrane association, protein-protein interactions, and intracellular localization of the target protein. We have undertaken a detailed analysis of [(3)H]palmitate incorporation into caveolin-1 in aortic endothelial cells. The linkage of palmitate to caveolin-1 was hydroxylamine-sensitive and thus presumably a thioester bond. However, contrary to expectations, palmitate incorporation was blocked completely by the protein synthesis inhibitors cycloheximide and puromycin. In parallel experiments to show specificity, palmitoylation of aortic endothelial cell-specific nitric-oxide synthase was unaffected by these reagents. Inhibitors of protein trafficking, brefeldin A and monensin, blocked caveolin-1 palmitoylation, indicating that the modification was not cotranslational but rather required caveolin-1 transport from the endoplasmic reticulum and Golgi to the plasma membrane. In addition, immunophilin chaperones that form complexes with caveolin-1, i.e. FK506-binding protein 52, cyclophilin A, and cyclophilin 40, were not necessary for caveolin-1 palmitoylation because agents that bind immunophilins did not inhibit palmitoylation. Pulse-chase experiments showed that caveolin-1 palmitoylation is essentially irreversible because the release of [(3)H]palmitate was not significant even after 24 h. These results show that [(3)H]palmitate incorporation is limited to newly synthesized caveolin-1, not because incorporation only occurs during synthesis but because the continuous presence of palmitate on caveolin-1 prevents subsequent repalmitoylation.
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Affiliation(s)
- M O Parat
- Department of Cell Biology, Cleveland Clinic Foundation, The Lerner Research Institute, Cleveland, Ohio 44195, USA
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Abstract
It is widely believed that calcium plays a primary role in the development of neuronal cell injury in different pathological states of the brain. Disturbances of calcium homeostasis may be induced in three different subcellular compartments, the cytoplasm, mitochondria or the endoplasmic reticulum (ER). The traditional calcium hypothesis holds that neuronal cell injury is induced by a marked increase in cytoplasmic calcium activity during stress (e.g., cerebral ischemia). Recently, this hypothesis has been modified, taking into account that under different experimental conditions the extent of cell injury does not correlate closely with calcium load or total calcium influx into the cell, and that neuronal cell injury has been found to be associated with both increases and decreases of cytoplasmic calcium activity. The mitochondrial calcium hypothesis is based on the observation that after a severe form of stress there is a massive influx of calcium ions into mitochondria, which may lead to production of free radicals, opening of the mitochondrial permeability transition (MPT) pore and disturbances of energy metabolism. However, it has still to be established whether drugs such as cyclosporin A are neuroprotective through their effect on MPT or through the blocking of processes upstream of MPT. The ER calcium hypothesis arose from the observation that ER calcium stores are depleted after severe forms of stress, and that the response of cells to disturbances of ER calcium homeostasis (activation of the expression of genes coding for ER resident stress proteins and suppression of the initiation of protein synthesis) resembles their response to a severe form of stress (e.g., transient ischemia) implying common underlying mechanisms. Elucidating the exact mechanisms of calcium toxicity and identifying the subcellular compartment playing the most important role in this pathological process will help to evaluate strategies for specific therapeutic intervention.
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Affiliation(s)
- W Paschen
- Department of Experimental Neurology, Max-Planck-Institute for Neurological Research, Köln, Germany.
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