1
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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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Rohilla A, Singh AK, Koleske B, Srikrishna G, Bishai WR. Structure-based virtual screening and in vitro validation of inhibitors of cyclic dinucleotide phosphodiesterases ENPP1 and CdnP. Microbiol Spectr 2024; 12:e0201223. [PMID: 38095464 PMCID: PMC10783014 DOI: 10.1128/spectrum.02012-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 11/21/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE In this paper, we describe novel inhibitors of cyclic dinucleotide phosphodiesterase enzymes from Mycobacterium tuberculosis (M.tb) (CdnP) and mammals (ENPP1). The phosphodiesterase enzymes hydrolyze cyclic dinucleotides, such as 2',3'-cyclic GMP-AMP and c-di-AMP, which are stimulator of interferon gene (STING) agonists. By blocking the hydrolysis of STING agonists, the cyclic GMP-AMP synthase (cGAS)-STING-IRF3 pathway is potentiated. There is strong evidence in tuberculosis and in cancer biology that potentiation of the cGAS-STING-IRF3 pathway leads to improved M.tb clearance and also improved antitumor responses in cancer. In addition to the identification of novel inhibitors and their biochemical characterization, we provide proof-of-concept evidence that our E-3 inhibitor potentiates the cGAS-STING-IRF3 pathway in both macrophage cell lines and also in primary human monocyte-derived macrophages.
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Affiliation(s)
- Akshay Rohilla
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Alok Kumar Singh
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Benjamin Koleske
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Geetha Srikrishna
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - William R. Bishai
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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3
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Pfreundt U, Słomka J, Schneider G, Sengupta A, Carrara F, Fernandez V, Ackermann M, Stocker R. Controlled motility in the cyanobacterium Trichodesmium regulates aggregate architecture. Science 2023; 380:830-835. [PMID: 37228200 DOI: 10.1126/science.adf2753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 04/25/2023] [Indexed: 05/27/2023]
Abstract
The ocean's nitrogen is largely fixed by cyanobacteria, including Trichodesmium, which forms aggregates comprising hundreds of filaments arranged in organized architectures. Aggregates often form upon exposure to stress and have ecological and biophysical characteristics that differ from those of single filaments. Here, we report that Trichodesmium aggregates can rapidly modulate their shape, responding within minutes to changes in environmental conditions. Combining video microscopy and mathematical modeling, we discovered that this reorganization is mediated by "smart reversals" wherein gliding filaments reverse when their overlap with other filaments diminishes. By regulating smart reversals, filaments control aggregate architecture without central coordination. We propose that the modulation of gliding motility at the single-filament level is a determinant of Trichodesmium's aggregation behavior and ultimately of its biogeochemical role in the ocean.
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Affiliation(s)
- Ulrike Pfreundt
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zürich, Switzerland
| | - Jonasz Słomka
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zürich, Switzerland
| | - Giulia Schneider
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zürich, Switzerland
| | - Anupam Sengupta
- Physics of Living Matter, Department of Physics and Materials Science, University of Luxembourg, Luxembourg City, Grand Duchy of Luxembourg
| | - Francesco Carrara
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zürich, Switzerland
| | - Vicente Fernandez
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zürich, Switzerland
| | - Martin Ackermann
- Department of Environmental Systems Sciences, Microbial Systems Ecology Group, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, Zürich, Switzerland
- Department of Environmental Microbiology, Eawag: Swiss Federal Institute of Aquatic Sciences, Dübendorf, Switzerland
| | - Roman Stocker
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zürich, Switzerland
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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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Chemical evolution of cyclic dinucleotides: Perspective of the analogs and their preparation. Tetrahedron 2021. [DOI: 10.1016/j.tet.2021.132096] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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6
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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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7
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Tsukamoto M, Oyama KI. Recent application of acidic 1,3-azolium salts as promoters in the solution-phase synthesis of nucleosides and nucleotides. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2018.03.074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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8
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Zhou J, Opoku-Temeng C, Sintim HO. Fluorescent 2-Aminopurine c-di-GMP and GpG Analogs as PDE Probes. Methods Mol Biol 2018; 1657:245-261. [PMID: 28889299 DOI: 10.1007/978-1-4939-7240-1_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
c-di-GMP is widely recognized as an important ubiquitous signaling molecule in bacteria. c-di-GMP phosphodiesterases (PDEs) regulate the intracellular concentration of c-di-GMP and some could be potential drug targets. Here, we describe a class of dinucleotide probes suitable for monitoring the enzymatic activities of c-di-GMP PDEs in real time. Such probes contain fluorescent nucleobases and can be readily cleaved by PDEs, resulting in a change in fluorescence. Fluorescent cyclic and linear dinucleotide probes could be used in diverse applications, such as confirming the activity of an expressed PDE or oligoribonuclease (Orns) or identifying inhibitors of PDEs or Orns using high-throughput screening formats.
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Affiliation(s)
- Jie Zhou
- Purdue Institute for Drug Discovery, Purdue University, 500 Oval Drive, West Lafayette, IN, 47907, USA.,Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Clement Opoku-Temeng
- Purdue Institute for Drug Discovery, Purdue University, 500 Oval Drive, West Lafayette, IN, 47907, USA.,Biochemistry Graduate Program, University of Maryland, College Park, MD, 20742, USA.,Department of Chemistry, Center for Drug Discovery, Purdue University, West Lafayette, IN, 47907, USA
| | - Herman O Sintim
- Purdue Institute for Drug Discovery, Purdue University, 500 Oval Drive, West Lafayette, IN, 47907, USA. .,Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA. .,Purdue Institute of Inflammation, Immunology and Infectious Disease, West Lafayette, IN, 47907, USA.
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9
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Opoku-Temeng C, Sintim HO. Targeting c-di-GMP Signaling, Biofilm Formation, and Bacterial Motility with Small Molecules. Methods Mol Biol 2018; 1657:419-430. [PMID: 28889311 DOI: 10.1007/978-1-4939-7240-1_31] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacteria possess several signaling molecules that regulate distinct phenotypes. Cyclic di-GMP (c-di-GMP) has emerged as a ubiquitous second messenger that regulates bacterial virulence, cell cycle, motility, and biofilm formation. The link between c-di-GMP signaling and biofilm formation affords novel strategies for treatment of biofilm-associated infections, which is a major public health problem. The complex c-di-GMP signaling pathway creates a hurdle in the development of small molecule modulators. Nonetheless, some progress has been made in this regard and inhibitors of c-di-GMP metabolizing enzymes that affect biofilm formation and motility have been documented. Herein we discuss the components of c-di-GMP signaling, their correlation with biofilm formation as well as motility and reported small molecule inhibitors of c-di-GMP signaling.
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Affiliation(s)
- Clement Opoku-Temeng
- Purdue Institute for Drug Discovery, Purdue University, 500 Oval Drive, West Lafayette, IN, 47907, USA.,Biochemistry Graduate Program, University of Maryland, College Park, MD, 20742, USA.,Department of Chemistry, Center for Drug Discovery, Purdue University, West Lafayette, IN, 47907, USA
| | - Herman O Sintim
- Purdue Institute for Drug Discovery, Purdue University, 500 Oval Drive, West Lafayette, IN, 47907, USA. .,Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA. .,Purdue Institute of Inflammation, Immunology and Infectious Disease, West Lafayette, IN, 47907, USA.
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10
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Discovering Selective Diguanylate Cyclase Inhibitors: From PleD to Discrimination of the Active Site of Cyclic-di-GMP Phosphodiesterases. Methods Mol Biol 2018; 1657:431-453. [PMID: 28889312 DOI: 10.1007/978-1-4939-7240-1_32] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
One of the most important signals involved in controlling biofilm formation is represented by the intracellular second messenger 3',5'-cyclic diguanylic acid (c-di-GMP). Since the pathways involved in c-di-GMP biosynthesis and breakdown are found only in bacteria, targeting c-di-GMP metabolism represents an attractive strategy for the development of biofilm-disrupting drugs. Here, we present the workflow required to perform a structure-based design of inhibitors of diguanylate cyclases, the enzymes responsible for c-di-GMP biosynthesis. Downstream of the virtual screening process, detailed in the first part of the chapter, we report the step-by-step protocols required to test the positive hits in vitro and to validate their selectivity, thus minimizing possible off-target effects.
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11
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Pal C, Chakraborty TK. Synthesis of Amide-Linked Cyclic Dinucleotide Analogues with Pyrimidine Bases. ASIAN J ORG CHEM 2017. [DOI: 10.1002/ajoc.201700260] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Chandan Pal
- Department of Organic Chemistry; Indian Institute of Science; Bangalore- 560012 India
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12
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Zhou J, Zheng Y, Roembke BT, Robinson S, Opoku-Temeng C, Sayre DA, Sintim HO. Fluorescent analogs of cyclic and linear dinucleotides as phosphodiesterase and oligoribonuclease activity probes. RSC Adv 2017. [DOI: 10.1039/c6ra25394f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
2-Aminopurine or etheno adenosine cyclic dinucleotide probes can report the activity of cyclic dinucleotide PDEs or oligoribonucleases.
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Affiliation(s)
- Jie Zhou
- Purdue Institute for Drug Discovery
- Purdue University
- West Lafayette
- USA
- Department of Chemistry
| | - Yue Zheng
- Purdue Institute for Drug Discovery
- Purdue University
- West Lafayette
- USA
- Department of Chemistry and Biochemistry
| | - Benjamin T. Roembke
- Department of Chemistry and Biochemistry
- University of Maryland
- College Park
- USA
| | - Sarah M. Robinson
- Department of Chemistry and Biochemistry
- University of Maryland
- College Park
- USA
| | - Clement Opoku-Temeng
- Purdue Institute for Drug Discovery
- Purdue University
- West Lafayette
- USA
- Department of Chemistry and Biochemistry
| | - David A. Sayre
- Department of Chemistry and Biochemistry
- University of Maryland
- College Park
- USA
| | - Herman O. Sintim
- Purdue Institute for Drug Discovery
- Purdue University
- West Lafayette
- USA
- Department of Chemistry
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13
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Inhibition of innate immune cytosolic surveillance by an M. tuberculosis phosphodiesterase. Nat Chem Biol 2016; 13:210-217. [PMID: 28106876 DOI: 10.1038/nchembio.2254] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 10/05/2016] [Indexed: 12/18/2022]
Abstract
Mycobacterium tuberculosis infection leads to cytosolic release of the bacterial cyclic dinucleotide (CDN) c-di-AMP and a host-generated CDN, cGAMP, both of which trigger type I interferon (IFN) expression in a STING-dependent manner. Here we report that M. tuberculosis has developed a mechanism to inhibit STING activation and the type I IFN response via the bacterial phosphodiesterase (PDE) CdnP, which mediates hydrolysis of both bacterial-derived c-di-AMP and host-derived cGAMP. Mutation of cdnP attenuates M. tuberculosis virulence, as does loss of a host CDN PDE known as ENPP1. CdnP is inhibited by both US Food and Drug Administration (FDA)-approved PDE inhibitors and nonhydrolyzable dinucleotide mimetics specifically designed to target the enzyme. These findings reveal a crucial role of CDN homeostasis in governing the outcome of M. tuberculosis infection as well as a unique mechanism of subversion of the host's cytosolic surveillance pathway (CSP) by a bacterial PDE that may serve as an attractive antimicrobial target.
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14
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Computational understanding and experimental characterization of twice-as-smart quadruplex ligands as chemical sensors of bacterial nucleotide second messengers. Sci Rep 2016; 6:33888. [PMID: 27667717 PMCID: PMC5036188 DOI: 10.1038/srep33888] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 09/05/2016] [Indexed: 12/20/2022] Open
Abstract
A twice-as-smart ligand is a small molecule that experiences a structural switch upon interaction with its target (i.e., smart ligand) that concomitantly triggers its fluorescence (i.e., smart probe). Prototypes of twice-as-smart ligands were recently developed to track and label G-quadruplexes: these higher-order nucleic acid structures originate in the assembly of four guanine(G)-rich DNA or RNA strands, whose stability is imparted by the formation and the self-assembly of G-quartets. The first prototypes of twice-as-smart quadruplex ligands were designed to exploit the self-association of quartets, being themselves synthetic G-quartets. While their quadruplex recognition capability has been thoroughly documented, some doubts remain about the precise photophysical mechanism that underlies their peculiar spectroscopic properties. Here, we uncovered this mechanism via complete theoretical calculations. Collected information was then used to develop a novel application of twice-as-smart ligands, as efficient chemical sensors of bacterial signaling pathways via the fluorescent detection of naturally occurring extracellular quadruplexes formed by cyclic dimeric guanosine monophosphate (c-di-GMP).
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15
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Zheng Y, Tsuji G, Opoku-Temeng C, Sintim HO. Inhibition of P. aeruginosa c-di-GMP phosphodiesterase RocR and swarming motility by a benzoisothiazolinone derivative. Chem Sci 2016; 7:6238-6244. [PMID: 30034764 PMCID: PMC6024209 DOI: 10.1039/c6sc02103d] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 06/15/2016] [Indexed: 01/18/2023] Open
Abstract
Various important cellular processes in bacteria are controlled by c-di-GMP, such as motility, biofilm formation and virulence factors production. C-di-GMP is synthesized from two molecules of GTP by diguanylate cyclases (DGCs) and its actions are terminated by EAL or HD-GYP domain phosphodiesterases (PDEs), which hydrolyze c-di-GMP to linear pGpG or GMP. Thus far the majority of efforts have been dedicated to the development of inhibitors of DGCs but not PDEs. This is probably because the old view was that inhibiting any c-di-GMP PDE would lead to biofilm formation, an undesirable phenotype. Recent data however suggest that some PDEs only change the localized (not global) concentration of c-di-GMP to increase bacterial virulence and do not affect biofilm formation. A challenge therefore is to be able to develop selective PDE inhibitors that inhibit virulence-associated PDEs but not inhibit PDEs that regulate bacterial biofilm formation. Using high throughput docking experiments to screen a library of 250 000 commercially available compounds against E. coli YahA (also called PdeL), a benzoisothiazolinone derivative was found to bind to the c-di-GMP binding site of YahA with favorable energetics. Paradoxically the in silico identified inhibitor (a benzoisothiazolinone derivative) did not inhibit the hydrolysis of c-di-GMP by YahA, the model PDE that was used in the docking, but instead inhibited RocR, which is a PDE from the opportunistic pathogen P. aeruginosa (PA). RocR promotes bacterial virulence but not biofilm dispersal, making it an ideal PDE to target for anti-virulence purposes. This newly identified RocR ligand displayed some selectivity and did not inhibit other P. aeruginosa PDEs, such as DipA, PvrR and PA4108. DipA, PvrR and PA4108 are key enzymes that reduce global c-di-GMP concentration and promote biofilm dispersal; therefore the identification of an inhibitor of a PA PDE, such as RocR, that does not inhibit major PDEs that modulate global c-di-GMP is an important step towards the development of selective c-di-GMP PDEs that could have interesting biomedical applications. The identified RocR ligand could also inhibit P. aeruginosa (PAO1) swarming but not swimming or biofilm formation. Rhamnolipid production was decreased, explaining the inhibition of swarming.
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Affiliation(s)
- Yue Zheng
- Department of Chemistry , Purdue University , 560 Oval Drive , West Lafayette , IN 47907 , USA .
- Center for Drug Discovery , Purdue University , 720 Clinic Drive , West Lafayette , IN 47907 , USA
- Graduate Program in Biochemistry , University of Maryland , College Park , MD 20742 , USA
| | - Genichiro Tsuji
- Department of Chemistry , Purdue University , 560 Oval Drive , West Lafayette , IN 47907 , USA .
- Center for Drug Discovery , Purdue University , 720 Clinic Drive , West Lafayette , IN 47907 , USA
| | - Clement Opoku-Temeng
- Department of Chemistry , Purdue University , 560 Oval Drive , West Lafayette , IN 47907 , USA .
- Center for Drug Discovery , Purdue University , 720 Clinic Drive , West Lafayette , IN 47907 , USA
- Graduate Program in Biochemistry , University of Maryland , College Park , MD 20742 , USA
| | - Herman O Sintim
- Department of Chemistry , Purdue University , 560 Oval Drive , West Lafayette , IN 47907 , USA .
- Center for Drug Discovery , Purdue University , 720 Clinic Drive , West Lafayette , IN 47907 , USA
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16
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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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17
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Meehan RE, Torgerson CD, Gaffney BL, Jones RA, Strobel SA. Nuclease-Resistant c-di-AMP Derivatives That Differentially Recognize RNA and Protein Receptors. Biochemistry 2016; 55:837-49. [PMID: 26789423 DOI: 10.1021/acs.biochem.5b00965] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The ability of bacteria to sense environmental cues and adapt is essential for their survival. The use of second-messenger signaling molecules to translate these cues into a physiological response is a common mechanism employed by bacteria. The second messenger 3'-5'-cyclic diadenosine monophosphate (c-di-AMP) has been linked to a diverse set of biological processes involved in maintaining cell viability and homeostasis, as well as pathogenicity. A complex network of both protein and RNA receptors inside the cell activates specific pathways and mediates phenotypic outputs in response to c-di-AMP. Structural analysis of these RNA and protein receptors has revealed the different recognition elements employed by these effectors to bind the same small molecule. Herein, using a series of c-di-AMP analogues, we probed the interactions made with a riboswitch and a phosphodiesterase protein to identify the features important for c-di-AMP binding and recognition. We found that the ydaO riboswitch binds c-di-AMP in two discrete sites with near identical affinity and a Hill coefficient of 1.6. The ydaO riboswitch distinguishes between c-di-AMP and structurally related second messengers by discriminating against an amine at the C2 position more than a carbonyl at the C6 position. We also identified phosphate-modified analogues that bind both the ydaO RNA and GdpP protein with high affinity, whereas symmetrically modified ribose analogues exhibited a substantial decrease in ydaO affinity but retained high affinity for GdpP. These ligand modifications resulted in increased resistance to enzyme-catalyzed hydrolysis by the GdpP enzyme. Together, these data suggest that these c-di-AMP analogues could be useful as chemical tools to specifically target subsections of second-messenger signaling pathways.
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Affiliation(s)
| | | | - Barbara L Gaffney
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey , Piscataway, New Jersey 08854, United States
| | - Roger A Jones
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey , Piscataway, New Jersey 08854, United States
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18
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Fernicola S, Torquati I, Paiardini A, Giardina G, Rampioni G, Messina M, Leoni L, Del Bello F, Petrelli R, Rinaldo S, Cappellacci L, Cutruzzolà F. Synthesis of Triazole-Linked Analogues of c-di-GMP and Their Interactions with Diguanylate Cyclase. J Med Chem 2015; 58:8269-84. [PMID: 26426545 DOI: 10.1021/acs.jmedchem.5b01184] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cyclic di-GMP (c-di-GMP) is a widespread second messenger that plays a key role in bacterial biofilm formation. The compound's ability to assume multiple conformations allows it to interact with a diverse set of target macromolecules. Here, we analyzed the binding mode of c-di-GMP to the allosteric inhibitory site (I-site) of diguanylate cyclases (DGCs) and compared it to the conformation adopted in the catalytic site of the EAL phosphodiesterases (PDEs). An array of novel molecules has been designed and synthesized by simplifying the native c-di-GMP structure and replacing the charged phosphodiester backbone with an isosteric nonhydrolyzable 1,2,3-triazole moiety. We developed the first neutral small molecule able to selectively target DGCs discriminating between the I-site of DGCs and the active site of PDEs; this molecule represents a novel tool for mechanistic studies, particularly on those proteins bearing both DGC and PDE modules, and for future optimization studies to target DGCs in vivo.
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Affiliation(s)
- Silvia Fernicola
- Department of Biochemical Sciences, Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University of Rome , 00185 Rome, Italy
| | - Ilaria Torquati
- Medicinal Chemistry Unit, School of Pharmacy, University of Camerino , 62032 Camerino, MC, Italy
| | - Alessandro Paiardini
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome , 00185 Rome, Italy
| | - Giorgio Giardina
- Department of Biochemical Sciences, Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University of Rome , 00185 Rome, Italy
| | | | - Marco Messina
- Department of Science, University Roma Tre , 00154 Rome, Italy
| | - Livia Leoni
- Department of Science, University Roma Tre , 00154 Rome, Italy
| | - Fabio Del Bello
- Medicinal Chemistry Unit, School of Pharmacy, University of Camerino , 62032 Camerino, MC, Italy
| | - Riccardo Petrelli
- Medicinal Chemistry Unit, School of Pharmacy, University of Camerino , 62032 Camerino, MC, Italy
| | - Serena Rinaldo
- Department of Biochemical Sciences, Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University of Rome , 00185 Rome, Italy
| | - Loredana Cappellacci
- Medicinal Chemistry Unit, School of Pharmacy, University of Camerino , 62032 Camerino, MC, Italy
| | - Francesca Cutruzzolà
- Department of Biochemical Sciences, Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University of Rome , 00185 Rome, Italy
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19
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In Silico Discovery and In Vitro Validation of Catechol-Containing Sulfonohydrazide Compounds as Potent Inhibitors of the Diguanylate Cyclase PleD. J Bacteriol 2015; 198:147-56. [PMID: 26416830 DOI: 10.1128/jb.00742-15] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 09/21/2015] [Indexed: 12/29/2022] Open
Abstract
UNLABELLED Biofilm formation is responsible for increased antibiotic tolerance in pathogenic bacteria. Cyclic di-GMP (c-di-GMP) is a widely used second-messenger signal that plays a key role in bacterial biofilm formation. c-di-GMP is synthesized by diguanylate cyclases (DGCs), a conserved class of enzymes absent in mammals and hence considered attractive molecular targets for the development of antibiofilm agents. Here, the results of a virtual screening approach aimed at identifying small-molecule inhibitors of the DGC PleD from Caulobacter crescentus are described. A three-dimensional (3D) pharmacophore model, derived from the mode of binding of GTP to the active site of PleD, was exploited to screen the ZINC database of compounds. Seven virtual hits were tested in vitro for their ability to inhibit the activity of purified PleD by using circular dichroism spectroscopy. Two drug-like molecules with a catechol moiety and a sulfonohydrazide scaffold were shown to competitively inhibit PleD at the low-micromolar range (50% inhibitory concentration [IC50] of ∼11 μM). Their predicted binding mode highlighted key structural features presumably responsible for the efficient inhibition of PleD by both hits. These molecules represent the most potent in vitro inhibitors of PleD identified so far and could therefore result in useful leads for the development of novel classes of antimicrobials able to hamper biofilm formation. IMPORTANCE Biofilm-mediated infections are difficult to eradicate, posing a threatening health issue worldwide. The capability of bacteria to form biofilms is almost universally stimulated by the second messenger c-di-GMP. This evidence has boosted research in the last decade for the development of new antibiofilm strategies interfering with c-di-GMP metabolism. Here, two potent inhibitors of c-di-GMP synthesis have been identified in silico and characterized in vitro by using the well-characterized DGC enzyme PleD from C. crescentus as a structural template and molecular target. Given that the protein residues implied as crucial for enzyme inhibition are found to be highly conserved among DGCs, the outcome of this study could pave the way for the future development of broad-spectrum antibiofilm compounds.
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20
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Fujino T. Cyclic Dinucleotide and Its Analogues: Synthesis and Function. J SYN ORG CHEM JPN 2015. [DOI: 10.5059/yukigoseikyokaishi.73.278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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21
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Sharma IM, Petchiappan A, Chatterji D. Quorum sensing and biofilm formation in mycobacteria: Role of c-di-GMP and methods to study this second messenger. IUBMB Life 2014; 66:823-34. [DOI: 10.1002/iub.1339] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2014] [Accepted: 12/04/2014] [Indexed: 12/18/2022]
Affiliation(s)
- Indra Mani Sharma
- Molecular Biophysics Unit; Indian Institute of Science; Bangalore Karnataka India
| | - Anushya Petchiappan
- Molecular Biophysics Unit; Indian Institute of Science; Bangalore Karnataka India
| | - Dipankar Chatterji
- Molecular Biophysics Unit; Indian Institute of Science; Bangalore Karnataka India
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22
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A novel method for the synthesis of sulfur substituted-cyclopyrophosphate of cADPR analogs. CHINESE CHEM LETT 2014. [DOI: 10.1016/j.cclet.2014.07.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Kinzie CR, Steele AD, Pasciolla SM, Wuest WM. Synthesis of cyclic dimeric methyl morpholinoside—a common synthetic precursor to cyclic dinucleotide analogs. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.07.038] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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24
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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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25
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Fujino T, Okada K, Isobe H. Conformational restriction of cyclic dinucleotides with triazole-linked cyclophane analogues. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.03.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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26
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Lieberman OJ, Orr MW, Wang Y, Lee VT. High-throughput screening using the differential radial capillary action of ligand assay identifies ebselen as an inhibitor of diguanylate cyclases. ACS Chem Biol 2014; 9:183-92. [PMID: 24134695 DOI: 10.1021/cb400485k] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The rise of bacterial resistance to traditional antibiotics has motivated recent efforts to identify new drug candidates that target virulence factors or their regulatory pathways. One such antivirulence target is the cyclic-di-GMP (cdiGMP) signaling pathway, which regulates biofilm formation, motility, and pathogenesis. Pseudomonas aeruginosa is an important opportunistic pathogen that utilizes cdiGMP-regulated polysaccharides, including alginate and pellicle polysaccharide (PEL), to mediate virulence and antibiotic resistance. CdiGMP activates PEL and alginate biosynthesis by binding to specific receptors including PelD and Alg44. Mutations that abrogate cdiGMP binding to these receptors prevent polysaccharide production. Identification of small molecules that can inhibit cdiGMP binding to the allosteric sites on these proteins could mimic binding defective mutants and potentially reduce biofilm formation or alginate secretion. Here, we report the development of a rapid and quantitative high-throughput screen for inhibitors of protein-cdiGMP interactions based on the differential radial capillary action of ligand assay (DRaCALA). Using this approach, we identified ebselen as an inhibitor of cdiGMP binding to receptors containing an RxxD domain including PelD and diguanylate cyclases (DGC). Ebselen reduces diguanylate cyclase activity by covalently modifying cysteine residues. Ebselen oxide, the selenone analogue of ebselen, also inhibits cdiGMP binding through the same covalent mechanism. Ebselen and ebselen oxide inhibit cdiGMP regulation of biofilm formation and flagella-mediated motility in P. aeruginosa through inhibition of diguanylate cyclases. The identification of ebselen provides a proof-of-principle that a DRaCALA high-throughput screening approach can be used to identify bioactive agents that reverse regulation of cdiGMP signaling by targeting cdiGMP-binding domains.
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Affiliation(s)
- Ori J. Lieberman
- Department
of Cell Biology and Molecular Genetics, University of Maryland College Park, 3114 Bioscience Research Building, College
Park, Maryland 20742, United States
- Maryland Pathogen Research Institute, Bioscience Research Building, College Park, Maryland 20742, United States
| | - Mona W. Orr
- Department
of Cell Biology and Molecular Genetics, University of Maryland College Park, 3114 Bioscience Research Building, College
Park, Maryland 20742, United States
- Maryland Pathogen Research Institute, Bioscience Research Building, College Park, Maryland 20742, United States
| | - Yan Wang
- Proteomics
Core Facility, College of Computer, Mathematical and Natural Science, University of Maryland College Park, 0111 Biology Psychology Building College Park, Maryland 20742, United States
| | - Vincent T. Lee
- Department
of Cell Biology and Molecular Genetics, University of Maryland College Park, 3114 Bioscience Research Building, College
Park, Maryland 20742, United States
- Maryland Pathogen Research Institute, Bioscience Research Building, College Park, Maryland 20742, United States
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27
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Clivio P, Coantic-Castex S, Guillaume D. (3'-5')-Cyclic dinucleotides: synthetic strategies and biological potential. Chem Rev 2013; 113:7354-401. [PMID: 23767818 DOI: 10.1021/cr300011s] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Pascale Clivio
- UMR 6229, Institut de Chimie Moléculaire de Reims, CNRS-Université de Reims Champagne Ardenne , UFR Médecine-Pharmacie, 51 Rue Cognacq Jay, 51096 Reims Cedex, France
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28
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Zhou J, Watt S, Wang J, Nakayama S, Sayre DA, Lam YF, Lee VT, Sintim HO. Potent suppression of c-di-GMP synthesis via I-site allosteric inhibition of diguanylate cyclases with 2'-F-c-di-GMP. Bioorg Med Chem 2013; 21:4396-404. [PMID: 23685177 DOI: 10.1016/j.bmc.2013.04.050] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2013] [Revised: 04/10/2013] [Accepted: 04/19/2013] [Indexed: 11/29/2022]
Abstract
Cyclic-di-GMP (c-di-GMP) is a central regulator of bacterial behavior. Various studies have implicated c-di-GMP in biofilm formation and virulence factor production in multitudes of bacteria. Hence it is expected that the disruption of c-di-GMP signaling could provide an effective means to disrupt biofilm and/or virulence factor formation in several bacteria of clinical relevance. C-di-GMP achieves the regulation of bacterial phenotype via binding to several effector molecules including transcription factors, enzymes and riboswitches. Crystal structure analyses of c-di-GMP effector molecules, in complex with the ligand, reveal that various classes of c-di-GMP receptors recognize this dinucleotide using different sets of recognition elements. Therefore, it is plausible that different analogues of c-di-GMP could be used to selectively modulate a specific class of c-di-GMP binding receptors, and hence modulate the bacterial phenotype. Thus far only a detailed study of the differential binding of c-di-GMP analogues to riboswitches, but not proteins, has been reported. In this report, we prepared various 2'-modified analogues of c-di-GMP and studied both polymorphisms of these analogues using DOSY NMR and the binding to several effector proteins, such as PilZ-containing proteins, diguanylate cyclases (DGC) containing I-sites, and phoshphodiesterases (PDE). 2'-Modification of c-di-GMP did not adversely affect the propensity to form higher aggregates, such as octameric forms, in the presence of potassium salts. Interestingly, we find that the selective binding to different classes of c-di-GMP binding proteins could be achieved with the 2'-modified analogues and that 2'-F analogue of c-di-GMP binds to the I-site of DGCs better (four times) than the native dinucleotide, c-di-GMP, whereas c-di-GMP binds to PDEs better (10 times) than 2'-F-c-di-GMP. 2'-F-c-di-GMP potently inhibits c-di-GMP synthesis by DGCs and hence raises the potential that cell permeable analogues of 2'-F-c-di-GMP could be used to disrupt c-di-GMP signaling in bacteria.
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Affiliation(s)
- Jie Zhou
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
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29
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Guzzo CR, Dunger G, Salinas RK, Farah CS. Structure of the PilZ-FimXEAL-c-di-GMP Complex Responsible for the Regulation of Bacterial Type IV Pilus Biogenesis. J Mol Biol 2013; 425:2174-97. [PMID: 23507310 DOI: 10.1016/j.jmb.2013.03.021] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 03/02/2013] [Accepted: 03/11/2013] [Indexed: 10/27/2022]
Abstract
Signal transduction pathways mediated by cyclic-bis(3'→5')-dimeric GMP (c-di-GMP) control many important and complex behaviors in bacteria. C-di-GMP is synthesized through the action of GGDEF domains that possess diguanylate cyclase activity and is degraded by EAL or HD-GYP domains with phosphodiesterase activity. There is mounting evidence that some important c-di-GMP-mediated pathways require protein-protein interactions between members of the GGDEF, EAL, HD-GYP and PilZ protein domain families. For example, interactions have been observed between PilZ and the EAL domain from FimX of Xanthomonas citri (Xac). FimX and PilZ are involved in the regulation of type IV pilus biogenesis via interactions of the latter with the hexameric PilB ATPase associated with the bacterial inner membrane. Here, we present the crystal structure of the ternary complex made up of PilZ, the FimX EAL domain (FimXEAL) and c-di-GMP. PilZ interacts principally with the lobe region and the N-terminal linker helix of the FimXEAL. These interactions involve a hydrophobic surface made up of amino acids conserved in a non-canonical family of PilZ domains that lack intrinsic c-di-GMP binding ability and strand complementation that joins β-sheets from both proteins. Interestingly, the c-di-GMP binds to isolated FimXEAL and to the PilZ-FimXEAL complex in a novel conformation encountered in c-di-GMP-protein complexes in which one of the two glycosidic bonds is in a rare syn conformation while the other adopts the more common anti conformation. The structure points to a means by which c-di-GMP and PilZ binding could be coupled to FimX and PilB conformational states.
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Affiliation(s)
- Cristiane R Guzzo
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Avenida Professor Lineu Prestes 748, São Paulo SP 05508-000, Brazil; Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Avenida Professor Lineu Prestes 1374, São Paulo SP 05508-900, Brazil
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30
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Stelitano V, Brandt A, Fernicola S, Franceschini S, Giardina G, Pica A, Rinaldo S, Sica F, Cutruzzolà F. Probing the activity of diguanylate cyclases and c-di-GMP phosphodiesterases in real-time by CD spectroscopy. Nucleic Acids Res 2013; 41:e79. [PMID: 23358823 PMCID: PMC3627566 DOI: 10.1093/nar/gkt028] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Bacteria react to adverse environmental stimuli by clustering into organized communities called biofilms. A remarkably sophisticated control system based on the dinucleotide 3'-5' cyclic diguanylic acid (c-di-GMP) is involved in deciding whether to form or abandon biofilms. The ability of c-di-GMP to form self-intercalated dimers is also thought to play a role in this complex regulation. A great advantage in the quest of elucidating the catalytic properties of the enzymes involved in c-di-GMP turnover (diguanylate cyclases and phosphodiesterases) would come from the availability of an experimental approach for in vitro quantification of c-di-GMP in real-time. Here, we show that c-di-GMP can be detected and quantified by circular dichroism (CD) spectroscopy in the low micromolar range. The method is based on the selective ability of manganese ions to induce formation of the intercalated dimer of the c-di-GMP dinucleotide in solution, which displays an intense sigmoidal CD spectrum in the near-ultraviolet region. This characteristic spectrum originates from the stacking interaction of the four mutually intercalated guanines, as it is absent in the other cyclic dinucleotide 3'-5' cyclic adenilic acid (c-di-AMP). Thus, near-ultraviolet CD can be used to effectively quantify in real-time the activity of diguanylate cyclases and phosphodiesterases in solution.
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Affiliation(s)
- Valentina Stelitano
- Istituto Pasteur-Fondazione Cenci Bolognetti, Department of Biochemical Sciences, Sapienza University of Rome, 00185 Rome, Italy
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31
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Shanahan CA, Gaffney BL, Jones RA, Strobel SA. Identification of c-di-GMP derivatives resistant to an EAL domain phosphodiesterase. Biochemistry 2013; 52:365-77. [PMID: 23256840 DOI: 10.1021/bi301510v] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The bacterial second messenger signaling molecule bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) controls important biological processes such as biofilm formation, virulence response, and motility. This second messenger is sensed by macromolecular targets inside the cell, both protein and RNA, which induce specific phenotypic responses critical for bacterial survival. One class of enzymes responsible for regulating the intracellular concentration of c-di-GMP, and therefore the physiological behavior of the cell, consists of the EAL domain phosphodiesterases, which degrade the second messenger to its linear form, pGpG. Here, we investigate how base and backbone modifications of c-di-GMP affect the rate of cyclic dinucleotide degradation by an EAL domain protein (CC3396 from Caulobacter crescentus). The doubly substituted thiophosphate analogue is highly resistant to hydrolysis by this metabolizing enzyme but can still bind c-di-GMP riboswitch targets. We used these findings to develop a novel ribosyl phosphate-modified derivative of c-di-GMP containing 2'-deoxy and methylphosphonate substitutions that is charge neutral and demonstrate that this analogue is also resistant to EAL domain-catalyzed degradation. This suggests a general strategy for designing c-di-GMP derivatives with increased enzymatic stability that also possess desirable properties for development as chemical probes of c-di-GMP signaling.
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Affiliation(s)
- Carly A Shanahan
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, USA
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32
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Roembke BT, Wang J, Nakayama S, Zhou J, Sintim HO. Octameric G8 c-di-GMP is an efficient peroxidase and this suggests that an open G-tetrad site can effectively enhance hemin peroxidation reactions. RSC Adv 2013. [DOI: 10.1039/c3ra23308a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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33
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Römling U, Balsalobre C. Biofilm infections, their resilience to therapy and innovative treatment strategies. J Intern Med 2012; 272:541-61. [PMID: 23025745 DOI: 10.1111/joim.12004] [Citation(s) in RCA: 546] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Biofilm formation of microorganisms causes persistent tissue and foreign body infections resistant to treatment with antimicrobial agents. Up to 80% of human bacterial infections are biofilm associated; such infections are most frequently caused by Staphylococcus epidermidis, Pseudomonas aeruginosa, Staphylococcus aureus and Enterobacteria such as Escherichia coli. The accurate diagnosis of biofilm infections is often difficult, which prevents the appropriate choice of treatment. As biofilm infections significantly contribute to patient morbidity and substantial healthcare costs, novel strategies to treat these infections are urgently required. Nucleotide second messengers, c-di-GMP, (p)ppGpp and potentially c-di-AMP, are major regulators of biofilm formation and associated antibiotic tolerance. Consequently, different components of these signalling networks might be appropriate targets for antibiofilm therapy in combination with antibiotic treatment strategies. In addition, cyclic di-nucleotides are microbial-associated molecular patterns with an almost universal presence. Their conserved structures sensed by the eukaryotic host have a widespread effect on the immune system. Thus, cyclic di-nucleotides are also potential immunotherapeutic agents to treat antibiotic-resistant bacterial infections.
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Affiliation(s)
- U Römling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
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34
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Zhou J, Sayre DA, Wang J, Pahadi N, Sintim HO. Endo-S-c-di-GMP analogues-polymorphism and binding studies with class I riboswitch. Molecules 2012; 17:13376-89. [PMID: 23143150 PMCID: PMC6269045 DOI: 10.3390/molecules171113376] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 10/30/2012] [Accepted: 11/01/2012] [Indexed: 11/17/2022] Open
Abstract
C-di-GMP, a cyclic guanine dinucleotide, has been shown to regulate biofilm formation as well as virulence gene expression in a variety of bacteria. Analogues of c-di-GMP have the potential to be used as chemical probes to study c-di-GMP signaling and could even become drug leads for the development of anti-biofilm compounds. Herein we report the synthesis and biophysical studies of a series of c-di-GMP analogues, which have both phosphate and sugar moieties simultaneously modified (called endo-S-c-di-GMP analogues). We used computational methods to predict the relative orientation of the guanine nucleobases in c-di-GMP and analogues. DOSY NMR of the endo-S-c-di-GMP series showed that the polymorphism of c-di-GMP can be tuned with conservative modifications to the phosphate and sugar moieties (conformational steering). Binding studies with Vc2 RNA (a class I c-di-GMP riboswitch) revealed that conservative modifications to the phosphate and 2'-positions of c-di-GMP dramatically affected binding to class I riboswitch.
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Affiliation(s)
| | | | | | | | - Herman O. Sintim
- Author to whom correspondence should be addressed; ; Tel.: +1-301-405-0633; Fax: +1-301-314-9121
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35
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Shanahan CA, Strobel SA. The bacterial second messenger c-di-GMP: probing interactions with protein and RNA binding partners using cyclic dinucleotide analogs. Org Biomol Chem 2012; 10:9113-29. [PMID: 23108253 DOI: 10.1039/c2ob26724a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The ability of bacteria to adapt to a changing environment is essential for their survival. One mechanism used to facilitate behavioral adaptations is the second messenger signaling molecule bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP). c-di-GMP is widespread throughout the bacterial domain and plays a vital role in regulating the transition between the motile planktonic lifestyle and the sessile biofilm forming state. This second messenger also controls the virulence response of pathogenic organisms and is thought to be connected to quorum sensing, the process by which bacteria communicate with each other. The intracellular concentration of c-di-GMP is tightly regulated by the opposing enzymatic activities of diguanlyate cyclases and phosphodiesterases, which synthesize and degrade the second messenger, respectively. The change in the intracellular concentration of c-di-GMP is directly sensed by downstream targets of the second messenger, both protein and RNA, which induce the appropriate phenotypic response. This review will summarize our current state of knowledge of c-di-GMP signaling in bacteria with a focus on protein and RNA binding partners of the second messenger. Efforts towards the synthesis of c-di-GMP and its analogs are discussed as well as studies aimed at targeting these macromolecular effectors with chemically synthesized cyclic dinucleotide analogs.
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Affiliation(s)
- Carly A Shanahan
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
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Kalia D, Merey G, Nakayama S, Zheng Y, Zhou J, Luo Y, Guo M, Roembke BT, Sintim HO. Nucleotide, c-di-GMP, c-di-AMP, cGMP, cAMP, (p)ppGpp signaling in bacteria and implications in pathogenesis. Chem Soc Rev 2012; 42:305-41. [PMID: 23023210 DOI: 10.1039/c2cs35206k] [Citation(s) in RCA: 261] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
For an organism to survive, it must be able to sense its environment and regulate physiological processes accordingly. Understanding how bacteria integrate signals from various environmental factors and quorum sensing autoinducers to regulate the metabolism of various nucleotide second messengers c-di-GMP, c-di-AMP, cGMP, cAMP and ppGpp, which control several key processes required for adaptation is key for efforts to develop agents to curb bacterial infections. In this review, we provide an update of nucleotide signaling in bacteria and show how these signals intersect or integrate to regulate the bacterial phenotype. The intracellular concentrations of nucleotide second messengers in bacteria are regulated by synthases and phosphodiesterases and a significant number of these metabolism enzymes had been biochemically characterized but it is only in the last few years that the effector proteins and RNA riboswitches, which regulate bacterial physiology upon binding to nucleotides, have been identified and characterized by biochemical and structural methods. C-di-GMP, in particular, has attracted immense interest because it is found in many bacteria and regulate both biofilm formation and virulence factors production. In this review, we discuss how the activities of various c-di-GMP effector proteins and riboswitches are modulated upon c-di-GMP binding. Using V. cholerae, E. coli and B. subtilis as models, we discuss how both environmental factors and quorum sensing autoinducers regulate the metabolism and/or processing of nucleotide second messengers. The chemical syntheses of the various nucleotide second messengers and the use of analogs thereof as antibiofilm or immune modulators are also discussed.
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Affiliation(s)
- Dimpy Kalia
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
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Chin KH, Kuo WT, Yu YJ, Liao YT, Yang MT, Chou SH. Structural polymorphism of c-di-GMP bound to an EAL domain and in complex with a type II PilZ-domain protein. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1380-92. [PMID: 22993092 DOI: 10.1107/s0907444912030594] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 07/04/2012] [Indexed: 12/21/2022]
Abstract
Cyclic di-GMP (c-di-GMP) is a novel secondary-messenger molecule that is involved in regulating a plethora of important bacterial activities through binding to an unprecedented array of effectors. Proteins with a canonical PilZ domain that bind c-di-GMP play crucial roles in regulating flagellum-based motility. In contrast, noncanonical type II PilZ domains that do not effectively bind c-di-GMP regulate twitching motility, which is dependent on type IV pili (T4P). Recent data indicate that T4P biogenesis is initiated via the interaction of a noncanonical type II PilZ protein with the GGDEF/EAL-domain protein FimX and the pilus motor protein PilB at high c-di-GMP concentrations. However, the molecular details of such interactions remain to be elucidated. In this manuscript, the first hetero-complex crystal structure between a type II PilZ protein and the EAL domain of the FimX protein (FimX(EAL)) from Xanthomonas campestris pv. campestris (Xcc) in the presence of c-di-GMP is reported. This work reveals two novel conformations of monomeric c-di-GMP in the XccFimX(EAL)-c-di-GMP and XccFimX(EAL)-c-di-GMP-XccPilZ complexes, as well as a unique interaction mode of a type II PilZ domain with FimX(EAL). These findings indicate that c-di-GMP is sufficiently flexible to adjust its conformation to match the corresponding recognition motifs of different cognate effectors. Together, these results represent a first step towards an understanding of how T4P biogenesis is controlled by c-di-GMP at the molecular level and also of the ability of c-di-GMP to bind to a wide variety of effectors.
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Affiliation(s)
- Ko-Hsin Chin
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan
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Sharma IM, Dhanaraman T, Mathew R, Chatterji D. Synthesis and characterization of a fluorescent analogue of cyclic di-GMP. Biochemistry 2012; 51:5443-53. [PMID: 22715917 DOI: 10.1021/bi3003617] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Cyclic di-GMP (c-di-GMP), a ubiquitous bacterial second messenger, has emerged as a key controller of several biological processes. Numbers of reports that deal with the mechanistic aspects of this second messenger have appeared in the literature. However, the lack of a reporter tag attached to the c-di-GMP at times limits the understanding of further details. In this study, we have chemically coupled N-methylisatoic anhydride (MANT) with c-di-GMP, giving rise to Mant-(c-di-GMP) or MANT-CDG. We have characterized the chemical and physical properties and spectral behavior of MANT-CDG. The fluorescence of MANT-CDG is sensitive to changes in the microenvironment, which helped us study its interaction with three different c-di-GMP binding proteins (a diguanylate cyclase, a phosphodiesterase, and a PilZ domain-containing protein). In addition, we have shown here that MANT-CDG can inhibit diguanylate cyclase activity; however, it is hydrolyzed by c-di-GMP specific phosphodiesterase. Taken together, our data suggest that MANT-CDG behaves like native c-di-GMP, and this study raises the possibility that MANT-CDG will be a valuable research tool for the in vitro characterization of c-di-GMP signaling factors.
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Affiliation(s)
- Indra Mani Sharma
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
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Ryan RP, Tolker-Nielsen T, Dow JM. When the PilZ don't work: effectors for cyclic di-GMP action in bacteria. Trends Microbiol 2012; 20:235-42. [PMID: 22444828 DOI: 10.1016/j.tim.2012.02.008] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Revised: 02/16/2012] [Accepted: 02/23/2012] [Indexed: 01/25/2023]
Abstract
The second messenger cyclic di-GMP has emerged as a central regulator of many important bacterial processes including biofilm formation and virulence. Although the pathways of cyclic di-GMP synthesis and degradation have been established, the mechanisms by which this second messenger exerts its action on diverse cellular functions remain relatively poorly understood. Recent studies report considerable advances in identifying different classes of cyclic di-GMP effectors; these include the PilZ protein domain, transcription factors, proteins involved in RNA processing and riboswitches. Here, we review this range of cyclic di-GMP effectors and the biological processes that they govern using examples from several different bacteria.
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Affiliation(s)
- Robert P Ryan
- BIOMERIT Research Centre, Department of Microbiology, Biosciences Institute, University College Cork, Cork, Ireland.
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Veliath E, Kim S, Gaffney BL, Jones RA. Synthesis and characterization of C8 analogs of c-di-GMP. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2012; 30:961-78. [PMID: 22060558 DOI: 10.1080/15257770.2011.624567] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
We have synthesized five analogs of c-di-GMP with different substituents at the guanine C8 position, to study their effects on the metal-dependent polymorphism we had previously demonstrated for the parent compound. Of these, only the K(+) salt of c-di-Br-GMP, 2, forms higher order complexes, predominantly two different syn octamolecular ones. Its Na(+) salt, as well as both the K(+) and Na(+) salts of c-di-thio-GMP, 3, c-di-methylthio-GMP, 4, c-di-phenyl-GMP, 5, and c-di-acetylphenyl-GMP, 6, all form primarily a syn bimolecular structure.
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Affiliation(s)
- Elizabeth Veliath
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
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Gentner M, Allan MG, Zaehringer F, Schirmer T, Grzesiek S. Oligomer formation of the bacterial second messenger c-di-GMP: reaction rates and equilibrium constants indicate a monomeric state at physiological concentrations. J Am Chem Soc 2011; 134:1019-29. [PMID: 22142443 DOI: 10.1021/ja207742q] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cyclic diguanosine-monophosphate (c-di-GMP) is a bacterial signaling molecule that triggers a switch from motile to sessile bacterial lifestyles. This mechanism is of considerable pharmaceutical interest, since it is related to bacterial virulence, biofilm formation, and persistence of infection. Previously, c-di-GMP has been reported to display a rich polymorphism of various oligomeric forms at millimolar concentrations, which differ in base stacking and G-quartet interactions. Here, we have analyzed the equilibrium and exchange kinetics between these various forms by NMR spectroscopy. We find that the association of the monomer into a dimeric form is in fast exchange (<milliseconds) with an equilibrium constant of about 1 mM. At concentrations above 100 μM, higher oligomers are formed in the presence of cations. These are presumably tetramers and octamers, with octamers dominating above about 0.5 mM. Thus, at the low micromolar concentrations of the cellular environment and in the absence of additional compounds that stabilize oligomers, c-di-GMP should be predominantly monomeric. This finding has important implications for the understanding of c-di-GMP recognition by protein receptors. In contrast to the monomer/dimer exchange, formation and dissociation of higher oligomers occurs on a time scale of several hours to days. The time course can be described quantitatively by a simple kinetic model where tetramers are intermediates of octamer formation. The extremely slow oligomer dissociation may generate severe artifacts in biological experiments when c-di-GMP is diluted from concentrated stock solution. We present a simple method to quantify c-di-GMP monomers and oligomers from UV spectra and a procedure to dissolve the unwanted oligomers by an annealing step.
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Affiliation(s)
- Martin Gentner
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
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Luo Y, Zhou J, Watt SK, Lee VT, Dayie TK, Sintim HO. Differential binding of 2'-biotinylated analogs of c-di-GMP with c-di-GMP riboswitches and binding proteins. MOLECULAR BIOSYSTEMS 2011; 8:772-8. [PMID: 22182995 DOI: 10.1039/c2mb05338a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
C-di-GMP has emerged as a signalling molecule that regulates a variety of processes in several bacteria; therefore there is interest in the development of biotinylated analogs for the identification of binding partners. No detailed study has been done to evaluate if biotinylated analogs of c-di-GMP are capable of binding to c-di-GMP receptors. Herein, we evaluate the binding of commercially available 2'-biotinylated c-di-GMP and phosphorothioate 2'-biotinylated c-di-GMP, prepared via a facile solid-phase synthesis, to several c-di-GMP receptors. Docking, using Autodock vina software, as well as experimental studies of these analogs, with c-di-GMP class I and II riboswitches and binding proteins, reveal that some, but not all, c-di-GMP receptors can tolerate the 2'-modification of c-di-GMP with biotin.
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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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Abstract
The secondary messenger cyclic di-GMP coordinately regulates the transition between motility/sessility/virulence in bacterial populations and upon adaptation to novel habitats. Thereby, multiple independent regulatory circuits regulate a diversity of targets. This specific output response is surprising considering the diverse physiological processes regulated by this signalling molecule, which range from transcription to proteolysis and clearly demonstrates the presence of sophisticated developmental programmes in these so-called simple organisms.
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Affiliation(s)
- Ute Römling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
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