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Yeboah SK, Sintim HO. PDE-stable 2'3'-cGAMP analogues, containing 5'-S-phosphorothioester linkage, as STING agonists. RSC Med Chem 2024; 15:1508-1514. [PMID: 38784462 PMCID: PMC11110794 DOI: 10.1039/d3md00593c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 01/03/2024] [Indexed: 05/25/2024] Open
Abstract
The stimulator of interferon genes (STING) has emerged as a promising target for cancer immunotherapy. 2'3'-cGAMP, a natural agonist of STING, shows anticancer activity via stimulation of immune cells but it is susceptible to degradation in vivo by hydrolytic enzymes. Consequently, the cyclic dinucleotide analogues that are being evaluated in the clinic as immunotherapies contain the hydrolytically stable phosphorothioate moiety, whereby the sulfur moiety is exo to the phosphate containing ring. The synthesis of these phosphorothioates however produces diastereomers, which presents separation challenges. An alternative phosphorothioate (referred to as endo-S-phosphorothioate) whereby the sulfur atom is endo to the cyclic phosphate ring (i.e. 5'-S-phosphorothioester linkage) would not have chirality at phosphorus and hence not pose diastereomer separation problems. Herein, we report the design and synthesis of novel 5'-endo-phosphorothioate substituted 2'3'cGAMP analogues that are hydrolytically stable towards both ectonucleotide phosphodiesterase I (ENPP1, a mammalian phosphodiesterase) and poxvirus immune nucleases (poxin, a phosphodiesterase in Poxvirus) but retains STING-TBK1-IRF activation, comparable to clinical candidate, ADU-S100 in THP1 monocytes.
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Affiliation(s)
- Simpa K Yeboah
- Department of Chemistry 560 Oval Drive West Lafayette Indiana 47907-2084 USA
- Institute for Drug Discovery, Purdue University 720 Clinic Drive West Lafayette IN 47907 USA
| | - Herman O Sintim
- Department of Chemistry 560 Oval Drive West Lafayette Indiana 47907-2084 USA
- Institute for Drug Discovery, Purdue University 720 Clinic Drive West Lafayette IN 47907 USA
- Purdue Institute of Inflammation, Immunology, and Infectious Disease West Lafayette IN 47907 USA
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2
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Tian H, Li W, Chen C, Yu H, Yuan H. Antibacterial Activity and Mechanism of Oxidized Bacterial Nanocellulose with Different Carboxyl Content. Macromol Biosci 2023; 23:e2200459. [PMID: 36575859 DOI: 10.1002/mabi.202200459] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/20/2022] [Indexed: 12/29/2022]
Abstract
Oxidized bacterial nanocellulose (OBC) is reported to prevent microbial growth, but its antibacterial characteristics and mechanism are still unclear. Here, the antibacterial mechanism of OBC is explored by detecting and assessing the interaction of OBC with different carboxyl content on Staphylococcus aureus and Escherichia coli. The results show that OBC has strong antibacterial activity and antibiofilm activity against S. aureus and E. coli, which is positively correlated with the carboxyl content of OBC. After OBC treatment, the bacteria adhesion is inhibited and the cell membrane is destroyed leading to increased permeability. Further investigation reveals that the concentration of cyclic diguanosine monophosphate (c-di-GMP) that induced biofilm formation is significantly decreased to 1.81 pmol mg-1 after OBC treatment. In addition, OBC inactivates mature biofilms, with inactivation rates up to 79.3%. This study suggests that OBC has excellent antibacterial and antiadhesion properties, which can increase the cell membrane permeability and inhibit c-di-GMP formation. In addition, OBC also has a strong inactivation effect on mature biofilm, which can be used as an effective antibiofilm agent.
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Affiliation(s)
- Huaixiang Tian
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Haiquan Road 100, Shanghai, 201418, China
| | - Wei Li
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Haiquan Road 100, Shanghai, 201418, China
| | - Chen Chen
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Haiquan Road 100, Shanghai, 201418, China
| | - Haiyan Yu
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Haiquan Road 100, Shanghai, 201418, China
| | - Haibin Yuan
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Haiquan Road 100, Shanghai, 201418, China
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3
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Singh A, Amod A, Pandey P, Bose P, Pingali MS, Shivalkar S, Varadwaj P, Sahoo A, Samanta S. Bacterial biofilm infections, their resistance to antibiotics therapy and current treatment strategies. Biomed Mater 2022; 17. [PMID: 35105823 DOI: 10.1088/1748-605x/ac50f6] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 02/01/2022] [Indexed: 11/11/2022]
Abstract
Nearly 80% of human chronic infections are caused due to bacterial biofilm formation. This is the most leading cause for failure of medical implants resulting in high morbidity and mortality. In addition, biofilms are also known to cause serious problems in food industry. Biofilm impart enhanced antibiotic resistance and become recalcitrant to host immune responses leading to persistent and recurrent infections. It makes the clinical treatment for biofilm infections very difficult. Reduced penetration of antibiotic molecules through EPS, mutation of the target site, accumulation of antibiotic degrading enzymes, enhanced expression of efflux pump genes are the probable causes for antibiotics resistance. Accordingly, strategies like administration of topical antibiotics and combined therapy of antibiotics with antimicrobial peptides are considered for alternate options to overcome the antibiotics resistance. A number of other remediation strategies for both biofilm inhibition and dispersion of established biofilm have been developed. The metallic nanoparticles and their oxides have recently gained a tremendous thrust as antibiofilm therapy for their unique features. This present comprehensive review gives the understanding of antibiotic resistance mechanisms of biofilm and provides an overview of various currently available biofilm remediation strategies, focusing primarily on the applications of metallic nanoparticles and their oxides.
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Affiliation(s)
- Anirudh Singh
- Indian Institute of Information Technology Allahabad, Allahabad, UP, India, Allahabad, Uttar Pradesh, 211012, INDIA
| | - Ayush Amod
- Indian Institute of Information Technology Allahabad, UP, India, Allahabad, Uttar Pradesh, 211012, INDIA
| | | | - Pranay Bose
- KIIT University, Bhubaneswar, Odisha, India, Bhubaneswar, Orissa, 751024, INDIA
| | - M Shivapriya Pingali
- Indian Institute of Information Technology Allahabad, UP, India, Allahabad, Uttar Pradesh, 211012, INDIA
| | - Saurabh Shivalkar
- Applied Sciences, IIIT Allahabad, UP, India, Allahabad, 211012, INDIA
| | - Pritish Varadwaj
- Applied Sciences, Indian Institute of Information Technology Allahabad, Allahabad, India, Allahabad, Uttar Pradesh, 211012, INDIA
| | - Amaresh Sahoo
- Applied Sciences, Indian Institute of Information Technology Allahabad, Allahabad, UP, India, Allahabad, Uttar Pradesh, 211012, INDIA
| | - Sintu Samanta
- Applied Sciences, Indian Institute of Information Technology Allahabad, Allahabad, India, Allahabad, Uttar Pradesh, 211012, INDIA
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4
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Biofilm control by interfering with c-di-GMP metabolism and signaling. Biotechnol Adv 2022; 56:107915. [PMID: 35101567 DOI: 10.1016/j.biotechadv.2022.107915] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 12/28/2021] [Accepted: 01/23/2022] [Indexed: 01/30/2023]
Abstract
Biofilm formation and biofilm-induced biodeterioration of surfaces have deeply affected the life of our community. Cyclic dimeric guanosine monophosphate (c-di-GMP) is a small nucleic acid signal molecule in bacteria, which functions as a second messenger mediating a wide range of bacterial processes, such as cell motility, biofilm formation, virulence expression, and cell cycle progression. C-di-GMP regulated phenotypes are triggered by a variety of determinants, such as metabolic cues and stress factors that affect c-di-GMP synthesis, the transduction and conduction of signals by specific effectors, and their actions on terminal targets. Therefore, understanding of the regulatory mechanisms of c-di-GMP would greatly benefit the control of the relevant bacterial processes, particularly for the development of anti-biofilm technologies. Here, we discuss the regulatory determinants of c-di-GMP signaling, identify the corresponding chemical inhibitors as anti-biofilm agents, and shed light on further perspectives in the metabolic regulation of c-di-GMP through chemical and biological approaches. This Review will advance the development of anti-biofilm policies applied in the industries of medicine, environment and engineering.
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5
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Kumari P, Som A. Comparative molecular dynamics simulation analysis of G20 and C92 mutations in c-di-GMP I riboswitch and the wild type with docked c-di-GMP ligand. Bioinformation 2021; 17:721-726. [PMID: 35540701 PMCID: PMC9049102 DOI: 10.6026/97320630017721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 08/30/2021] [Accepted: 08/30/2021] [Indexed: 11/23/2022] Open
Abstract
Riboswitch, a bacterial regulatory RNA consists of an aptamer (specific ligand binding unit) and an expression platform (gene expression modulation unit), which act as a potential drug target as it regulates critical genes. Therefore, it is of interest to glean information on the binding of c-di-GMP ligand to mutated conserved G20 and C92 residues of cyclic diguanosine monophosphate I (c-di-GMP I) riboswitch using molecular dynamics simulation. The result shows that the binding energy of wild/native type riboswitch-ligand complex (3IRW) is lower than the mutant complexes suggesting that the binding affinity for c-di-GMP ligand decreases in case of mutant riboswitches. The hydrogen bonding interactions analysis also showed a high number of hydrogen bonds formation in the wild type riboswitch-ligand complex as compared to the mutant complexes illustrating stronger interaction of ligand to wild type riboswitch than the mutants. The simulation result shows that the mutations affected riboswitch-ligand interactions. The residues G14, G21, C46, A47, and U92 were identified as the key residues which contributed effectively to the binding of c-di-GMP I riboswitch with the natural ligand.
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Affiliation(s)
- Priyanka Kumari
- Centre of Bioinformatics, Institute of Interdisciplinary Studies, University of Allahabad, Prayagraj – 211002, India
| | - Anup Som
- Centre of Bioinformatics, Institute of Interdisciplinary Studies, University of Allahabad, Prayagraj – 211002, India
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6
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Richter AM, Possling A, Malysheva N, Yousef KP, Herbst S, von Kleist M, Hengge R. Local c-di-GMP Signaling in the Control of Synthesis of the E. coli Biofilm Exopolysaccharide pEtN-Cellulose. J Mol Biol 2020; 432:4576-4595. [PMID: 32534064 PMCID: PMC7397504 DOI: 10.1016/j.jmb.2020.06.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 05/20/2020] [Accepted: 06/08/2020] [Indexed: 12/17/2022]
Abstract
In many bacteria, the biofilm-promoting second messenger c-di-GMP is produced and degraded by multiple diguanylate cyclases (DGC) and phosphodiesterases (PDE), respectively. High target specificity of some of these enzymes has led to theoretical concepts of "local" c-di-GMP signaling. In Escherichia coli K-12, which has 12 DGCs and 13 PDEs, a single DGC, DgcC, is specifically required for the biosynthesis of the biofilm exopolysaccharide pEtN-cellulose without affecting the cellular c-di-GMP pool, but the mechanistic basis of this target specificity has remained obscure. DGC activity of membrane-associated DgcC, which is demonstrated in vitro in nanodiscs, is shown to be necessary and sufficient to specifically activate cellulose biosynthesis in vivo. DgcC and a particular PDE, PdeK (encoded right next to the cellulose operon), directly interact with cellulose synthase subunit BcsB and with each other, thus establishing physical proximity between cellulose synthase and a local source and sink of c-di-GMP. This arrangement provides a localized, yet open source of c-di-GMP right next to cellulose synthase subunit BcsA, which needs allosteric activation by c-di-GMP. Through mathematical modeling and simulation, we demonstrate that BcsA binding from the low cytosolic c-di-GMP pool in E. coli is negligible, whereas a single c-di-GMP molecule that is produced and released in direct proximity to cellulose synthase increases the probability of c-di-GMP binding to BcsA several hundred-fold. This local c-di-GMP signaling could provide a blueprint for target-specific second messenger signaling also in other bacteria where multiple second messenger producing and degrading enzymes exist.
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Affiliation(s)
- Anja M Richter
- Institute of Biology/Microbiology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany; Department of Materials and the Environment, Bundesanstalt für Materialforschung und -Prüfung, 12205 Berlin, Germany
| | - Alexandra Possling
- Institute of Biology/Microbiology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Nadezhda Malysheva
- Department of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany; MF1 Bioinformatics, Robert-Koch-Institut, 13353 Berlin, Germany
| | - Kaveh P Yousef
- Department of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany
| | - Susanne Herbst
- Institute of Biology/Microbiology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Max von Kleist
- Department of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany; MF1 Bioinformatics, Robert-Koch-Institut, 13353 Berlin, Germany
| | - Regine Hengge
- Institute of Biology/Microbiology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany.
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7
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Qvortrup K, Hultqvist LD, Nilsson M, Jakobsen TH, Jansen CU, Uhd J, Andersen JB, Nielsen TE, Givskov M, Tolker-Nielsen T. Small Molecule Anti-biofilm Agents Developed on the Basis of Mechanistic Understanding of Biofilm Formation. Front Chem 2019; 7:742. [PMID: 31737611 PMCID: PMC6838868 DOI: 10.3389/fchem.2019.00742] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 10/17/2019] [Indexed: 01/12/2023] Open
Abstract
Microbial biofilms are the cause of persistent infections associated with various medical implants and distinct body sites such as the urinary tract, lungs, and wounds. Compared with their free living counterparts, bacteria in biofilms display a highly increased resistance to immune system activities and antibiotic treatment. Therefore, biofilm infections are difficult or impossible to treat with our current armory of antibiotics. The challenges associated with biofilm infections have urged researchers to pursue a better understanding of the molecular mechanisms that are involved in the formation and dispersal of biofilms, and this has led to the identification of several steps that could be targeted in order to eradicate these challenging infections. Here we describe mechanisms that are involved in the regulation of biofilm development in Pseudomonas aeruginosa, Escherichia coli, and Acinetobacter baumannii, and provide examples of chemical compounds that have been developed to specifically inhibit these processes. These compounds include (i) pilicides and curlicides which inhibit the initial steps of biofilm formation by E. coli; (ii) compounds that interfere with c-di-GMP signaling in P. aeruginosa and E. coli; and (iii) compounds that inhibit quorum-sensing in P. aeruginosa and A. baumannii. In cases where compound series have a defined molecular target, we focus on elucidating structure activity relationship (SAR) trends within the particular compound series.
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Affiliation(s)
- Katrine Qvortrup
- Department of Chemistry, Technical University of Denmark, Lyngby, Denmark
| | - Louise Dahl Hultqvist
- Department of Immunology and Microbiology, Costerton Biofilm Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Martin Nilsson
- Department of Immunology and Microbiology, Costerton Biofilm Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tim Holm Jakobsen
- Department of Immunology and Microbiology, Costerton Biofilm Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Jesper Uhd
- Department of Chemistry, Technical University of Denmark, Lyngby, Denmark
| | - Jens Bo Andersen
- Department of Immunology and Microbiology, Costerton Biofilm Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thomas E Nielsen
- Department of Immunology and Microbiology, Costerton Biofilm Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Michael Givskov
- Department of Immunology and Microbiology, Costerton Biofilm Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Tim Tolker-Nielsen
- Department of Immunology and Microbiology, Costerton Biofilm Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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8
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Opoku-Temeng C, Zhou J, Zheng Y, Su J, Sintim HO. Cyclic dinucleotide (c-di-GMP, c-di-AMP, and cGAMP) signalings have come of age to be inhibited by small molecules. Chem Commun (Camb) 2016; 52:9327-42. [PMID: 27339003 DOI: 10.1039/c6cc03439j] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Bacteria utilize nucleotide-based second messengers to regulate a myriad of physiological processes. Cyclic dinucleotides have emerged as central regulators of bacterial physiology, controlling processes ranging from cell wall homeostasis to virulence production, and so far over thousands of manuscripts have provided biological insights into c-di-NMP signaling. The development of small molecule inhibitors of c-di-NMP signaling has significantly lagged behind. Recent developments in assays that allow for high-throughput screening of inhibitors suggest that the time is right for a concerted effort to identify inhibitors of these fascinating second messengers. Herein, we review c-di-NMP signaling and small molecules that have been developed to inhibit cyclic dinucleotide-related enzymes.
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Affiliation(s)
- Clement Opoku-Temeng
- Department of Chemistry, Center for Drug Discovery, Purdue University, West Lafayette, IN 47907, USA.
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9
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Ren GX, Fan S, Guo XP, Chen S, Sun YC. Differential Regulation of c-di-GMP Metabolic Enzymes by Environmental Signals Modulates Biofilm Formation in Yersinia pestis. Front Microbiol 2016; 7:821. [PMID: 27375563 PMCID: PMC4891359 DOI: 10.3389/fmicb.2016.00821] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 05/16/2016] [Indexed: 11/13/2022] Open
Abstract
Cyclic diguanylate (c-di-GMP) is essential for Yersinia pestis biofilm formation, which is important for flea-borne blockage-dependent plague transmission. Two diguanylate cyclases (DGCs), HmsT and HmsD and one phosphodiesterase (PDE), HmsP are responsible for the synthesis and degradation of c-di-GMP in Y. pestis. Here, we systematically analyzed the effect of various environmental signals on regulation of the biofilm phenotype, the c-di-GMP levels, and expression of HmsT, HmsD, and HmsP in Y. pestis. Biofilm formation was higher in the presence of non-lethal high concentration of CaCl2, MgCl2, CuSO4, sucrose, sodium dodecyl sulfate, or dithiothreitol, and was lower in the presence of FeCl2 or NaCl. In addition, we found that HmsD plays a major role in biofilm formation in acidic or redox environments. These environmental signals differentially regulated expression of HmsT, HmsP and HmsD, resulting in changes in the intracellular levels of c-di-GMP in Y. pestis. Our results suggest that bacteria can sense various environmental signals, and differentially regulate activity of DGCs and PDEs to coordinately regulate and adapt metabolism of c-di-GMP and biofilm formation to changing environments.
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Affiliation(s)
- Gai-Xian Ren
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College Beijing, China
| | - Sai Fan
- Institute of Nutrition and Food Hygiene, Beijing Centre for Disease Control and Prevention Beijing, China
| | - Xiao-Peng Guo
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College Beijing, China
| | - Shiyun Chen
- Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences Wuhan, China
| | - Yi-Cheng Sun
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College Beijing, China
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10
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Machtel P, Bąkowska-Żywicka K, Żywicki M. Emerging applications of riboswitches - from antibacterial targets to molecular tools. J Appl Genet 2016; 57:531-541. [PMID: 27020791 PMCID: PMC5061826 DOI: 10.1007/s13353-016-0341-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 01/25/2016] [Accepted: 01/29/2016] [Indexed: 01/01/2023]
Abstract
The ability to precisely regulate gene expression is one of the most important features of the living cells as it enables the adaptation and survival in different environmental conditions. The majority of regulatory mechanisms involve protein action, however, multiple genes are controlled by nucleic acids. Among RNA-based regulators, the riboswitches present a large group of specific domains within messenger RNAs able to respond to small metabolites, tRNA, secondary messengers, ions, vitamins or amino acids. A simple, accurate, and efficient mechanism of action as well as easiness in handling and engineering make the riboswitches a potent practical tool in industry, medicine, pharmacy or environmental protection. Hereby, we summarize the current achievements and challenges in designing and practical employment of the riboswitch-based tools.
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Affiliation(s)
- Piotr Machtel
- Department of RNA Biology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poznań, Poland
| | - Kamilla Bąkowska-Żywicka
- Department of RNA Biology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poznań, Poland
| | - Marek Żywicki
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614, Poznań, Poland.
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11
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Fei N, Häussinger D, Blümli S, Laventie BJ, Bizzini LD, Zimmermann K, Jenal U, Gillingham D. Catalytic carbene transfer allows the direct customization of cyclic purine dinucleotides. Chem Commun (Camb) 2015; 50:8499-502. [PMID: 24946836 DOI: 10.1039/c4cc01919a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We describe a simple method for the direct modification of nucleobases in cyclic purine dinucleotides, important signalling molecules in both prokaryotes and eukaryotes. The method tolerates all members of the cyclic dinucleotide family and could be used to modulate their function or introduce useful side-chains such as fluorophores and photo-crosslinking groups.
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Affiliation(s)
- Na Fei
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056, Basel, Switzerland.
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12
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Roembke BT, Zhou J, Zheng Y, Sayre D, Lizardo A, Bernard L, Sintim HO. A cyclic dinucleotide containing 2-aminopurine is a general fluorescent sensor for c-di-GMP and 3',3'-cGAMP. MOLECULAR BIOSYSTEMS 2014; 10:1568-75. [PMID: 24705858 DOI: 10.1039/c3mb70518h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Cyclic dinucleotides have emerged as second messengers that regulate diverse processes in bacteria, as well as regulating the production of type I interferons in metazoans. Fluorescent sensors for these important second messengers are highly sought-after for high-throughput inhibitor discovery, yet most sensors reported to date are not amenable for high-throughput screening purposes. Herein, we demonstrate that a new analog, 3',3'-cG(d2AP)MP, which is a 2-aminopurine (2AP)-containing cyclic dinucleotide, self-associates in the presence of Mn(2+) with an association constant of 120,000 M(-1). 3'3'-cG(d2AP)MP can also form a heterodimer with cGAMP, activator of immune regulator, STING, or the bacterial biofilm regulator, c-di-GMP in the presence of Mn(II). Upon dimer formation, the fluorescence of 3',3'-cG(d2AP)MP is quenched and this provides a convenient method to monitor the enzymatic processing of both DGC and PDE enzymes, opening up several opportunities for the discovery of inhibitors of nucleotide signaling.
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Affiliation(s)
- Benjamin T Roembke
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA.
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13
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Luo Y, Chen B, Zhou J, Sintim HO, Dayie TK. E88, a new cyclic-di-GMP class I riboswitch aptamer from Clostridium tetani, has a similar fold to the prototypical class I riboswitch, Vc2, but differentially binds to c-di-GMP analogs. MOLECULAR BIOSYSTEMS 2014; 10:384-90. [PMID: 24430255 DOI: 10.1039/c3mb70467j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
C-di-GMP has emerged as a ubiquitous second messenger, which regulates the transition between sessile and motile lifestyles and virulence factor expression in many pathogenic bacteria using both RNA riboswitches and protein effectors. We recently showed that two additional class I c-di-GMP riboswitch aptamers (Ct-E88 and Cb-17B) bind c-di-GMP with nanomolar affinity, and that Ct-E88 RNA binds 2'-F-c-di-GMP 422 times less tightly than class I Vc2 RNA. Based on sequence comparison, it was concluded that the global folds of Ct-E88 and Vc2 RNAs were similar and that differences in ligand binding were probably due to differences in binding site architectures. Herein, we utilized EMSA, aptamer sensing spinach modules, SAXS and 1D NMR titration to study the conformational transitions of Ct-E88. We conclude that whereas the global folds of the bound states of Vc2 and Ct-E88 RNAs are similar, the unbound states are different and this could explain differences in ligand affinities between these class I c-di-GMP riboswitches.
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Affiliation(s)
- Yiling Luo
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA.
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