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Swetha R, Sharma A, Singh R, Ganeshpurkar A, Kumar D, Kumar A, Singh SK. Combined ligand-based and structure-based design of PDE 9A inhibitors against Alzheimer's disease. Mol Divers 2022; 26:2877-2892. [PMID: 35932437 DOI: 10.1007/s11030-022-10504-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 07/22/2022] [Indexed: 10/16/2022]
Abstract
PDE9 enzyme hydrolyzes cGMP, which is involved in the regulation of synaptic plasticity through the NMDA pathway (a well-known excitotoxic target for AD) via activation of calcium/calmodulin-dependent neuronal NO synthases in the postsynaptic neurons. The inhibition of PDE9 leads to elevated cGMP levels, causing enhanced NMDA signaling and thus contributing to an increase in synaptic plasticity and stabilization. Therefore, it could be considered a pertinent target for AD drug discovery. PF-04447943 and BI-409306 targeting PDE9 are undergoing clinical trials (Phase II). The present study encompasses a pharmacophoric approach to identify potent PDE9 inhibitors using various computational methods. Pharmacophores generated from the PDB 6A3N yielded 37,554 virtual hits, which underwent drug likeliness and PAINS filtering to arrive at a few virtual leads. The leads were further subjected to extra precision docking, ADMET predictions, and molecular dynamics. The final hits, ZINC000001305675 and ZINC000000377099, showed superior docking scores of - 10.90 and - 10.30 kcal/mol and satisfactory predicted ADMET scores. The hits were subjected to molecular dynamics (MD) studies, wherein they formed stable complexes with PDE9 protein and had ligand RMSDs within acceptable limits. The processes involved in the combined ligand and structure-based strategies.
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Affiliation(s)
- Rayala Swetha
- Pharmaceutical Chemistry Research Laboratory 1, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, India
| | - Anjali Sharma
- Pharmaceutical Chemistry Research Laboratory 1, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, India
| | - Ravi Singh
- Pharmaceutical Chemistry Research Laboratory 1, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, India
| | - Ankit Ganeshpurkar
- Department of Pharmaceutical Chemistry, Poona College of Pharmacy, Bharti Vidyapeeth University, Pune, India
| | | | - Ashok Kumar
- Pharmaceutical Chemistry Research Laboratory 1, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, India
| | - Sushil K Singh
- Pharmaceutical Chemistry Research Laboratory 1, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, India.
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2
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Rasmussen M, Welinder C, Schwede F, Ekström P. The stereospecific interaction sites and target specificity of cGMP analogs in mouse cortex. Chem Biol Drug Des 2021; 99:206-221. [PMID: 34687134 DOI: 10.1111/cbdd.13976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 09/29/2021] [Accepted: 10/16/2021] [Indexed: 11/30/2022]
Abstract
cGMP interactors play a role in several pathologies and may be targets for cGMP analog-based drugs, but the success of targeting depends on the biochemical stereospecificity between the cGMP-analog and the interactor. The stereospecificity between general cGMP analogs-or such that are selectivity-modified to obtain, for example, inhibitory actions on a specific target, like the cGMP-dependent protein kinase-have previously been investigated. However, the importance of stereospecificity for cGMP-analog binding to interactors is not known. We, therefore, applied affinity chromatography on mouse cortex proteins utilizing analogs with cyclic phosphate (8-AET-cGMP, 2-AH-cGMP, 2'-AHC-cGMP) and selectivity-modified analogs with sulfur-containing cyclic phosphorothioates (Rp/Sp-8-AET-cGMPS, Rp/Sp-2'-AHC-cGMPS) immobilized to agaroses. The results illustrate the cGMP analogs' stereospecific binding for PKG, PKA regulatory subunits and PKA catalytic subunits, PDEs, and EPAC2 and the involvement of these in various KEGG pathways. For the seven agaroses, PKG, PKA regulatory subunits, and PKA catalytic subunits were more prone to be enriched by 2-AH-, 8-AET-, Rp-8-AET-, and Sp-8-AET-cGMP, whereas PDEs and EPAC2 were more likely to be enriched by 2-AH-, Rp-2'-AHC-, and Rp-8-AET-cGMP. Our findings help elucidate the stereospecific-binding sites essential for the interaction between individual cGMP analogs and cGMP-binding proteins, as well as the cGMP analogs' target specificity, which are two crucial parameters in drug design.
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Affiliation(s)
- Michel Rasmussen
- Faculty of Medicine, Department of Clinical Sciences Lund, Ophthalmology, Lund University, Lund, Sweden
| | - Charlotte Welinder
- Faculty of Medicine, Department of Clinical Sciences Lund, Oncology, Lund University, Lund, Sweden
| | - Frank Schwede
- BIOLOG Life Science Institute GmbH & Co. KG, Bremen, Germany
| | - Per Ekström
- Faculty of Medicine, Department of Clinical Sciences Lund, Ophthalmology, Lund University, Lund, Sweden
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3
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Photoreceptor Phosphodiesterase (PDE6): Structure, Regulatory Mechanisms, and Implications for Treatment of Retinal Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1371:33-59. [PMID: 34170501 DOI: 10.1007/5584_2021_649] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The photoreceptor phosphodiesterase (PDE6) is a member of large family of Class I phosphodiesterases responsible for hydrolyzing the second messengers cAMP and cGMP. PDE6 consists of two catalytic subunits and two inhibitory subunits that form a tetrameric protein. PDE6 is a peripheral membrane protein that is localized to the signal-transducing compartment of rod and cone photoreceptors. As the central effector enzyme of the G-protein coupled visual transduction pathway, activation of PDE6 catalysis causes a rapid decrease in cGMP levels that results in closure of cGMP-gated ion channels in the photoreceptor plasma membrane. Because of its importance in the phototransduction pathway, mutations in PDE6 genes result in various retinal diseases that currently lack therapeutic treatment strategies due to inadequate knowledge of the structure, function, and regulation of this enzyme. This review focuses on recent progress in understanding the structure of the regulatory and catalytic domains of the PDE6 holoenzyme, the central role of the multi-functional inhibitory γ-subunit, the mechanism of activation by the heterotrimeric G protein, transducin, and future directions for pharmacological interventions to treat retinal degenerative diseases arising from mutations in the PDE6 genes.
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4
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Rana MN, Lu J, Xue E, Ruan J, Liu Y, Zhang L, Dhar R, Li Y, Hu Z, Zhou J, Ma W, Tang H. PDE9 Inhibitor PF-04447943 Attenuates DSS-Induced Colitis by Suppressing Oxidative Stress, Inflammation, and Regulating T-Cell Polarization. Front Pharmacol 2021; 12:643215. [PMID: 33967779 PMCID: PMC8098793 DOI: 10.3389/fphar.2021.643215] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 02/12/2021] [Indexed: 12/24/2022] Open
Abstract
Ulcerative colitis (UC) is a form of inflammatory bowel disease, which manifests as irritation or swelling and sores in the large intestine in a relapsing and remitting manner. In a dextran sulfate sodium sulfate (DSS)-induced UC model in female mice, we found that the levels of cyclic guanosine monophosphate (cGMP) are reduced, while the expression of phosphodiesterase 9A (PDE9A) is highest among all phosphodiesterase (PDEs). Since PDE9 has the highest affinity toward cGMP, we evaluated the selective PDE9 inhibitor PF-04447943 (PF) as a potential candidate for UC treatment. PF has been extensively studies in cognitive function and in sickle cell disease, but not in models for inflammatory bowel disease (IBD). Therefore, we used female C57BL/6 mice treated with 3% DSS alone or co-treated with PF or sulfasalazine (SASP) to study the body weight, colon length, histopathology, and measure superoxide dismutase (SOD), malondialdehyde (MDA), and cGMP level, as well as cytokines such as tumor necrosis factor-alpha (TNF-α), interleukin-6 (IL-6), interleukin-17 (IL-17), interleukin-12/23 (IL-12/23), interleukin-10 (IL-10), and pathways including nuclear factor kappa B (NF-κB), signal transducer and activator of transcription 3 (STAT3), and inflammasome activation. In addition, the number of dendritic cells (DC) and regulatory T cells (Treg cell) was assessed in the spleen, lymph node, and colon using flow cytometry. DSS reduced the number of goblet cells, decreased colon lengths and body weights, all of them were attenuated by PF treatment. It also suppressed the elevated level of inflammatory cytokines and increased level the anti-inflammatory cytokine, IL-10. PF treatment also reduced the DSS-induced inflammation by suppressing oxidative stress, NF-κB, STAT3, and inflammasome activation, by upregulating nuclear factor erythroid 2-related factor 2 (Nrf-2) and its downstream proteins via extracellular signal-regulated kinase (ERK) phosphorylation. Importantly, PF reversed imbalance in Treg/T helper 17 cells (Th17) cells ratio, possibly by regulating dendritic cells and Treg developmental process. In summary, this study shows the protective effect of a PDE9A inhibitor in ulcerative colitis by suppressing oxidative stress and inflammation as well as reversing the Treg/Th17 cells imbalance.
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Affiliation(s)
- Mohammad Nasiruddin Rana
- Department of Pharmacology, School of Basic Medical Sciences, Zhejiang University, Hangzhou, China
| | - Jie Lu
- Clinical Laboratory, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Enfu Xue
- Department of Pharmacology, School of Basic Medical Sciences, Zhejiang University, Hangzhou, China
| | - Jingjing Ruan
- Department of Pharmacology, School of Basic Medical Sciences, Zhejiang University, Hangzhou, China
| | - Yuting Liu
- Department of Pharmacology, School of Basic Medical Sciences, Zhejiang University, Hangzhou, China
| | - Lejun Zhang
- Department of Pharmacology, School of Basic Medical Sciences, Zhejiang University, Hangzhou, China
| | - Rana Dhar
- Department of Pharmacology, School of Basic Medical Sciences, Zhejiang University, Hangzhou, China
| | - Yajun Li
- Department of Pharmacology, School of Basic Medical Sciences, Zhejiang University, Hangzhou, China
| | - Zhengqiang Hu
- Department of Pharmacology, School of Basic Medical Sciences, Zhejiang University, Hangzhou, China
| | - Jie Zhou
- Department of Anesthesiology, Tongde Hospital of Zhejiang Province, Hangzhou, China
| | - Wangqian Ma
- Department of Gastroenterology, Second Affiliated Hospital, Zhejiang University College of Medicine, Hangzhou, China
| | - Huifang Tang
- Department of Pharmacology, School of Basic Medical Sciences, Zhejiang University, Hangzhou, China
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Morris ER, Caswell SJ, Kunzelmann S, Arnold LH, Purkiss AG, Kelly G, Taylor IA. Crystal structures of SAMHD1 inhibitor complexes reveal the mechanism of water-mediated dNTP hydrolysis. Nat Commun 2020; 11:3165. [PMID: 32576829 PMCID: PMC7311409 DOI: 10.1038/s41467-020-16983-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 06/03/2020] [Indexed: 12/29/2022] Open
Abstract
SAMHD1 regulates cellular 2'-deoxynucleoside-5'-triphosphate (dNTP) homeostasis by catalysing the hydrolysis of dNTPs into 2'-deoxynucleosides and triphosphate. In CD4+ myeloid lineage and resting T-cells, SAMHD1 blocks HIV-1 and other viral infections by depletion of the dNTP pool to a level that cannot support replication. SAMHD1 mutations are associated with the autoimmune disease Aicardi-Goutières syndrome and hypermutated cancers. Furthermore, SAMHD1 sensitises cancer cells to nucleoside-analogue anti-cancer therapies and is linked with DNA repair and suppression of the interferon response to cytosolic nucleic acids. Nevertheless, despite its requirement in these processes, the fundamental mechanism of SAMHD1-catalysed dNTP hydrolysis remained unknown. Here, we present structural and enzymological data showing that SAMHD1 utilises an active site, bi-metallic iron-magnesium centre that positions a hydroxide nucleophile in-line with the Pα-O5' bond to catalyse phosphoester bond hydrolysis. This precise molecular mechanism for SAMHD1 catalysis, reveals how SAMHD1 down-regulates cellular dNTP and modulates the efficacy of nucleoside-based anti-cancer and anti-viral therapies.
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Affiliation(s)
- Elizabeth R Morris
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Sarah J Caswell
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,AstraZeneca, 50F49, Mereside, Alderley Park, Macclesfield, Cheshire, SK10 4TG, UK
| | - Simone Kunzelmann
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Laurence H Arnold
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Pelago Bioscience, Banvaktsvägen 20, 171 48, Solna, Sweden
| | - Andrew G Purkiss
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Geoff Kelly
- The Medical Research Council Biomedical NMR Centre, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Ian A Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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6
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Synthesis and degradation of cAMP in Giardia lamblia: possible role and characterization of a nucleotidyl cyclase with a single cyclase homology domain. Biochem J 2017; 474:4001-4017. [PMID: 29054977 DOI: 10.1042/bcj20170590] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 10/17/2017] [Accepted: 10/19/2017] [Indexed: 01/25/2023]
Abstract
Despite its importance in the regulation of growth and differentiation processes of a variety of organisms, the mechanism of synthesis and degradation of cAMP (cyclic AMP) has not yet been described in Giardia lamblia In this work, we measured significant quantities of cAMP in trophozoites of G. lamblia incubated in vitro and later detected how it increases during the first hours of encystation, and how it then returns to basal levels at 24 h. Through an analysis of the genome of G. lamblia, we found sequences of three putative enzymes - one phosphodiesterase (gPDE) and two nucleotidyl cyclases (gNC1 and gNC2) - that should be responsible for the regulation of cAMP in G. lamblia Later, an RT-PCR assay confirmed that these three genes are expressed in trophozoites. The bioinformatic analysis indicated that gPDE is a transmembrane protein of 154 kDa, with a single catalytic domain in the C-terminal end; gNC1 is predicted to be a transmembrane protein of 74 kDa, with only one class III cyclase homology domain (CHD) at the C-terminal end; and gNC2 should be a transmembrane protein of 246 kDa, with two class III CHDs. Finally, we cloned and enriched the catalytic domain of gNC1 (gNC1cd) from bacteria. After that, we confirmed that gNC1cd has adenylyl cyclase (AC) activity. This enzymatic activity depends on the presence of Mn2+ and Ca2+, but no significant activity was displayed in the presence of Mg2+ Additionally, the AC activity of gNC1cd is competitively inhibited with GTP, so it is highly possible that gNC1 has guanylyl cyclase activity as well.
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7
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Çifci G, Aviyente V, Akten ED, Monard G. Assessing protein-ligand binding modes with computational tools: the case of PDE4B. J Comput Aided Mol Des 2017; 31:563-575. [PMID: 28534194 DOI: 10.1007/s10822-017-0024-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 05/13/2017] [Indexed: 01/31/2023]
Abstract
In a first step in the discovery of novel potent inhibitor structures for the PDE4B family with limited side effects, we present a protocol to rank newly designed molecules through the estimation of their IC[Formula: see text] values. Our protocol is based on reproducing the linear relationship between the logarithm of experimental IC[Formula: see text] values [[Formula: see text](IC[Formula: see text])] and their calculated binding free energies ([Formula: see text]). From 13 known PDE4B inhibitors, we show here that (1) binding free energies obtained after a docking process by AutoDock are not accurate enough to reproduce this linear relationship; (2) MM-GB/SA post-processing of molecular dynamics (MD) trajectories of the top ranked AutoDock pose improves the linear relationship; (3) by taking into account all representative structures obtained by AutoDock and by averaging MM-GB/SA computations on a series of 40 independent MD trajectories, a linear relationship between [Formula: see text](IC[Formula: see text]) and the lowest [Formula: see text] is achieved with [Formula: see text].
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Affiliation(s)
- Gülşah Çifci
- Department of Chemistry, Boğaziçi University, 34342, Bebek, Istanbul, Turkey
| | - Viktorya Aviyente
- Department of Chemistry, Boğaziçi University, 34342, Bebek, Istanbul, Turkey
| | - E Demet Akten
- Bioinformatics and Genetic, Kadir Has University, 34083, Cibali, Istanbul, Turkey
| | - Gerald Monard
- Université de Lorraine, UMR 7565 SRSMC, Boulevard des Aiguillettes, B.P. 70239, 54506, Vandoeuvre-les-Nancy, France. .,CNRS, UMR 7565 SRSMC, Boulevard des Aiguillettes, B.P. 70239, 54506, Vandoeuvre-les-Nancy, France.
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8
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Li N, Chen X, Zhu B, Ramírez-Alcántara V, Canzoneri JC, Lee K, Sigler S, Gary B, Li Y, Zhang W, Moyer MP, Salter EA, Wierzbicki A, Keeton AB, Piazza GA. Suppression of β-catenin/TCF transcriptional activity and colon tumor cell growth by dual inhibition of PDE5 and 10. Oncotarget 2016; 6:27403-15. [PMID: 26299804 PMCID: PMC4694998 DOI: 10.18632/oncotarget.4741] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 07/13/2015] [Indexed: 12/12/2022] Open
Abstract
Previous studies suggest the anti-inflammatory drug, sulindac inhibits tumorigenesis by a COX independent mechanism involving cGMP PDE inhibition. Here we report that the cGMP PDE isozymes, PDE5 and 10, are elevated in colon tumor cells compared with normal colonocytes, and that inhibitors and siRNAs can selectively suppress colon tumor cell growth. Combined treatment with inhibitors or dual knockdown suppresses tumor cell growth to a greater extent than inhibition from either isozyme alone. A novel sulindac derivative, ADT-094 was designed to lack COX-1/-2 inhibitory activity but have improved potency to inhibit PDE5 and 10. ADT-094 displayed >500 fold higher potency to inhibit colon tumor cell growth compared with sulindac by activating cGMP/PKG signaling to suppress proliferation and induce apoptosis. Combined inhibition of PDE5 and 10 by treatment with ADT-094, PDE isozyme-selective inhibitors, or by siRNA knockdown also suppresses β-catenin, TCF transcriptional activity, and the levels of downstream targets, cyclin D1 and survivin. These results suggest that dual inhibition of PDE5 and 10 represents novel strategy for developing potent and selective anticancer drugs.
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Affiliation(s)
- Nan Li
- Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Xi Chen
- Drug Discovery Research Center, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA
| | - Bing Zhu
- Drug Discovery Research Center, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA
| | - Verónica Ramírez-Alcántara
- Drug Discovery Research Center, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA
| | - Joshua C Canzoneri
- Drug Discovery Research Center, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA
| | - Kevin Lee
- Drug Discovery Research Center, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA
| | - Sara Sigler
- Drug Discovery Research Center, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA
| | - Bernard Gary
- Drug Discovery Research Center, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA
| | - Yonghe Li
- Drug Discovery Division, Southern Research, Birmingham, Alabama, USA
| | - Wei Zhang
- Drug Discovery Division, Southern Research, Birmingham, Alabama, USA
| | | | - E Alan Salter
- Department of Chemistry, University of South Alabama, Mobile, Alabama, USA
| | - Andrzej Wierzbicki
- Department of Chemistry, University of South Alabama, Mobile, Alabama, USA
| | - Adam B Keeton
- Drug Discovery Research Center, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA
| | - Gary A Piazza
- Drug Discovery Research Center, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA
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Grigorenko BL, Knyazeva MA, Nemukhin AV. Analysis of proton wires in the enzyme active site suggests a mechanism of c-di-GMP hydrolysis by the EAL domain phosphodiesterases. Proteins 2016; 84:1670-1680. [PMID: 27479508 DOI: 10.1002/prot.25108] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 06/30/2016] [Accepted: 07/25/2016] [Indexed: 11/08/2022]
Abstract
We report for the first time a hydrolysis mechanism of the cyclic dimeric guanosine monophosphate (c-di-GMP) by the EAL domain phosphodiesterases as revealed by molecular simulations. A model system for the enzyme-substrate complex was prepared on the base of the crystal structure of the EAL domain from the BlrP1 protein complexed with c-di-GMP. The nucleophilic hydroxide generated from the bridging water molecule appeared in a favorable position for attack on the phosphorus atom of c-di-GMP. The most difficult task was to find a pathway for a proton transfer to the O3' atom of c-di-GMP to promote the O3'P bond cleavage. We show that the hydrogen bond network extended over the chain of water molecules in the enzyme active site and the Glu359 and Asp303 side chains provides the relevant proton wires. The suggested mechanism is consistent with the structural, mutagenesis, and kinetic experimental studies on the EAL domain phosphodiesterases. Proteins 2016; 84:1670-1680. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Bella L Grigorenko
- Chemistry Department, M.V. Lomonosov Moscow State University, 1-3 Leninskiye Gory, Moscow, 119991, Russia.,N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygin Street, Moscow, 119334, Russia
| | - Marina A Knyazeva
- Chemistry Department, M.V. Lomonosov Moscow State University, 1-3 Leninskiye Gory, Moscow, 119991, Russia
| | - Alexander V Nemukhin
- Chemistry Department, M.V. Lomonosov Moscow State University, 1-3 Leninskiye Gory, Moscow, 119991, Russia. .,N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygin Street, Moscow, 119334, Russia.
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10
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Li Z, Wu Y, Feng LJ, Wu R, Luo HB. Ab Initio QM/MM Study Shows a Highly Dissociated SN2 Hydrolysis Mechanism for the cGMP-Specific Phosphodiesterase-5. J Chem Theory Comput 2014; 10:5448-57. [DOI: 10.1021/ct500761d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Zhe Li
- School of Pharmaceutical
Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Yinuo Wu
- School of Pharmaceutical
Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Ling-Jun Feng
- School of Pharmaceutical
Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Ruibo Wu
- School of Pharmaceutical
Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Hai-Bin Luo
- School of Pharmaceutical
Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China
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11
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12
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Barberot C, Boisson J, Gérard S, Khartabil H, Thiriot E, Monard G, Hénon E. AlgoGen: A tool coupling a linear-scaling quantum method with a genetic algorithm for exploring non-covalent interactions. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2013.11.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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13
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Cyclic di-GMP: the first 25 years of a universal bacterial second messenger. Microbiol Mol Biol Rev 2013; 77:1-52. [PMID: 23471616 DOI: 10.1128/mmbr.00043-12] [Citation(s) in RCA: 1219] [Impact Index Per Article: 110.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Twenty-five years have passed since the discovery of cyclic dimeric (3'→5') GMP (cyclic di-GMP or c-di-GMP). From the relative obscurity of an allosteric activator of a bacterial cellulose synthase, c-di-GMP has emerged as one of the most common and important bacterial second messengers. Cyclic di-GMP has been shown to regulate biofilm formation, motility, virulence, the cell cycle, differentiation, and other processes. Most c-di-GMP-dependent signaling pathways control the ability of bacteria to interact with abiotic surfaces or with other bacterial and eukaryotic cells. Cyclic di-GMP plays key roles in lifestyle changes of many bacteria, including transition from the motile to the sessile state, which aids in the establishment of multicellular biofilm communities, and from the virulent state in acute infections to the less virulent but more resilient state characteristic of chronic infectious diseases. From a practical standpoint, modulating c-di-GMP signaling pathways in bacteria could represent a new way of controlling formation and dispersal of biofilms in medical and industrial settings. Cyclic di-GMP participates in interkingdom signaling. It is recognized by mammalian immune systems as a uniquely bacterial molecule and therefore is considered a promising vaccine adjuvant. The purpose of this review is not to overview the whole body of data in the burgeoning field of c-di-GMP-dependent signaling. Instead, we provide a historic perspective on the development of the field, emphasize common trends, and illustrate them with the best available examples. We also identify unresolved questions and highlight new directions in c-di-GMP research that will give us a deeper understanding of this truly universal bacterial second messenger.
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14
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Stelitano V, Giardina G, Paiardini A, Castiglione N, Cutruzzolà F, Rinaldo S. C-di-GMP hydrolysis by Pseudomonas aeruginosa HD-GYP phosphodiesterases: analysis of the reaction mechanism and novel roles for pGpG. PLoS One 2013; 8:e74920. [PMID: 24066157 PMCID: PMC3774798 DOI: 10.1371/journal.pone.0074920] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 08/07/2013] [Indexed: 12/03/2022] Open
Abstract
In biofilms, the bacterial community optimizes the strategies to sense the environment and to communicate from cell to cell. A key player in the development of a bacterial biofilm is the second messenger c-di-GMP, whose intracellular levels are modulated by the opposite activity of diguanylate cyclases and phosphodiesterases. Given the huge impact of bacterial biofilms on human health, understanding the molecular details of c-di-GMP metabolism represents a critical step in the development of novel therapeutic approaches against biofilms. In this study, we present a detailed biochemical characterization of two c-di-GMP phosphodiesterases of the HD-GYP subtype from the human pathogen Pseudomonas aeruginosa, namely PA4781 and PA4108. Upstream of the catalytic HD-GYP domain, PA4781 contains a REC domain typical of two-component systems, while PA4108 contains an uncharacterized domain of unknown function. Our findings shed light on the activity and catalytic mechanism of these phosphodiesterases. We show that both enzymes hydrolyse c-di-GMP in a two-step reaction via the linear intermediate pGpG and that they produce GMP in vitro at a surprisingly low rate. In addition, our data indicate that the non-phosphorylated REC domain of PA4781 prevents accessibility of c-di-GMP to the active site. Both PA4108 and phosphorylated PA4781 are also capable to use pGpG as an alternative substrate and to hydrolyse it into GMP; the affinity of PA4781 for pGpG is one order of magnitude higher than that for c-di-GMP. These results suggest that these enzymes may not work (primarily) as genuine phosphodiesterases. Moreover, the unexpected affinity of PA4781 for pGpG may indicate that pGpG could also act as a signal molecule in its own right, thus further widening the c-di-GMP-related signalling scenario.
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Affiliation(s)
- Valentina Stelitano
- Istituto Pasteur-Fondazione Cenci Bolognetti, Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - Giorgio Giardina
- Istituto Pasteur-Fondazione Cenci Bolognetti, Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | | | - Nicoletta Castiglione
- Istituto Pasteur-Fondazione Cenci Bolognetti, Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - Francesca Cutruzzolà
- Istituto Pasteur-Fondazione Cenci Bolognetti, Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
- * E-mail:
| | - Serena Rinaldo
- Istituto Pasteur-Fondazione Cenci Bolognetti, Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
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15
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Synthesis, docking study and relaxant effect of 2-alkyl and 2-naphthylchromones on rat aorta and guinea-pig trachea through phosphodiesterase inhibition. Bioorg Chem 2013; 50:17-25. [PMID: 23933402 DOI: 10.1016/j.bioorg.2013.07.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 05/29/2013] [Accepted: 07/12/2013] [Indexed: 11/23/2022]
Abstract
Chromone (4), which form the base structure of various flavonoids isolated as natural products, is capable of relaxing smooth muscle. This is relevant to the treatment of high blood pressure, asthma and chronic obstructive pulmonary disease. The former disorder involves the contraction of vascular smooth muscle (VSM), and the latter two bronchoconstriction of airway smooth muscle (ASM). One of the principal mechanisms by which flavonoids relax muscle tissue is the inhibition of phosphodiesterases (PDEs), present in both VSM and ASM. Therefore, a study was designed to analyze the structure-activity relationship of chromone derivatives in vaso- and bronchorelaxation through the inhibition of PDE. Docking studies showed that these chromones bind at the catalytic site of PDEs. Consequently, we synthesized analogs of chromones substituted at position C-2 with alkyl and naphthyl groups. These compounds were synthesized from 2-hydroxyacetophenone and acyl chlorides in the presence of DBU and pyridine, modifying the methodology reported for the synthesis of 3-acylchromones by changing the reaction temperature from 80 to 30°C and using methylene chloride as solvent, yielding the corresponding phenolic esters 10a-10h. These compounds were cyclized with an equivalent of DBU, pyridine as solvent, and heated at reflux temperature, yielding the chromones 11a-11h. Evaluation of the vasorelaxant effect of 4, 11a-11h on rat aorta demonstrated that potency decreases with branched alkyl groups. Whereas the EC50 of compound 11d (substituted by an n-hexyl group) was 8.64±0.39 μM, that of 11f (substituted by an isobutyl group) was 14.58±0.64 μM. Contrarily, the effectiveness of the compound is directly proportional to the length of the alkyl chain, as evidenced by the increase in maximal effect of compound 11c versus 11d (66% versus 100%) and 11e versus 11f (60% versus 96%). With an aromatic group like naphthyl as the C-2 substituent, the effectiveness was only 43%. All compounds tested on guinea pig trachea showed less than 55% effectiveness. Compounds 4, 11a-11h were evaluated as PDE inhibitors in vitro, with 11d showing the greatest effect (73%), corroborating the importance of a long alkyl chain, which inhibits the decomposition of cGMP. Docking studies showed that the compound 11d was selective for the inhibition of PDE-5.
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16
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Oxidation reactivity of zinc–cysteine clusters in metallothionein. J Biol Inorg Chem 2013; 18:333-42. [DOI: 10.1007/s00775-013-0977-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 01/06/2013] [Indexed: 12/24/2022]
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17
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Lau JKC, Cheng YK. An update view on the substrate recognition mechanism of phosphodiesterases: a computational study of PDE10 and PDE4 bound with cyclic nucleotides. Biopolymers 2012; 97:910-22. [PMID: 22899366 DOI: 10.1002/bip.22104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Early studies strongly implied that the specificity of cyclic nucleotide phosphodiesterases (PDEs) toward its endogenous substrates can be uniquely determined by the amido orientation of the invariant glutamine locating in the binding pocket of the enzyme. However, recently solved crystal structures of PDE4 (cAMP specific) and PDE10 (dual specific) in the presence of endogenous substrates have revealed that their invariant glutamine orientations are very similar despite exhibiting different substrate specificities proven physiologically. To understand this subtle specificity issue in the PDE family, here several experimentally inaccessible PDE-substrate complex models have been studied computationally, and the results are juxtaposed and compared in detail. Modeling results show that PDE10 in fact favors cAMP energetically but still can bind to cGMP owing to the robust hydrogen-bond network in the vicinity of the invariant glutamine side chain. PDE4 fails to accommodate cGMP is correlated to the weakening of this same hydrogen-bond network but not owing to any steric strain in the binding pocket. An Asn residue in the binding pocket of PDE4 has enhanced the specificity of the binding to cAMP sideway as observed in our computer simulation. Further to the previously studied syn- versus anti-conformational specificity of cAMP in PDE10, the unexpected substrate-binding mode in PDE10 versus PDE4 as reported here strongly suggested that there are remaining uncertainties in the substrate orientation and recognition mechanism in the PDE families. The molecular details of the binding pocket observed in this study provide hints for more optimal PDE4 and PDE10 inhibitor design.
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Affiliation(s)
- Justin Kai-Chi Lau
- Department of Chemistry, The Hong Kong Baptist University, Kowloon, Hong Kong.
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18
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CAO XIAORAN, LIU CHENGBU, LIU YONGJUN. THEORETICAL STUDIES ON THE MECHANISM OF CYCLIC NUCLEOTIDE MONOPHOSPHATE HYDROLYSIS WITHIN PHOSPHODIESTERASES. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2012. [DOI: 10.1142/s021963361250037x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
As the only metabolizing enzyme for the degradation of second messenger cAMP and cGMP, phosphodiesterase (PDE) has been the clinical target of various human diseases. But the hydrolysis procedure of PDE is still unclear. To investigate the mechanism of PDE catalysis, three types of PDE (PDE4d, PDE5a and PDE10a) were selected and studied by using molecular dynamics (MD) simulation and quantum mechanics (QM) calculation methods. MD Simulation results indicate that different PDEs share a similar hydrolysis area in the active sites, and the phosphate parts of cyclic nucleotides take the same orientation and are partly surrounded by water molecules. Based on the statistical data of MD simulation, the QM calculation models were built. The calculation results indicate that in aqueous solution, the nucleophile hydroxide ion that attacks the phosphor atom of the cyclic nucleotide in the hydrolysis may migrate between the two metal ions in the active site. To help the ring-open reaction, it is the water molecule that provides proton to the O3′ atom of cyclic nucleotide, and generates another hydroxide ion complexed with the metal ion.
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Affiliation(s)
- XIAORAN CAO
- Key lab of Colloid Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, P. R. China
| | - CHENGBU LIU
- Key lab of Colloid Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, P. R. China
| | - YONGJUN LIU
- Key lab of Colloid Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, P. R. China
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19
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Chen X, Zhao X, Xiong Y, Liu J, Zhan CG. Fundamental reaction pathway and free energy profile for hydrolysis of intracellular second messenger adenosine 3',5'-cyclic monophosphate (cAMP) catalyzed by phosphodiesterase-4. J Phys Chem B 2011; 115:12208-19. [PMID: 21973014 PMCID: PMC3209513 DOI: 10.1021/jp205509w] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
As important drug targets for a variety of human diseases, cyclic nucleotide phosphodiesterases (PDEs) are a superfamily of enzymes sharing a similar catalytic site. We have performed pseudobond first-principles quantum mechanical/molecular mechanical-free energy perturbation (QM/MM-FE) and QM/MM-Poisson-Boltzmann surface area (PBSA) calculations to uncover the detailed reaction mechanism for PDE4-catalyzed hydrolysis of adenosine 3',5'-cyclic monophosphate (cAMP). This is the first report on QM/MM reaction-coordinate calculations including the protein environment of any PDE-catalyzed reaction system, demonstrating a unique catalytic reaction mechanism. The QM/MM-FE and QM/MM-PBSA calculations revealed that the PDE4-catalyzed hydrolysis of cAMP consists of two reaction stages: cAMP hydrolysis (stage 1) and bridging hydroxide ion regeneration (stage 2). The stage 1 includes the binding of cAMP in the active site, nucleophilic attack of the bridging hydroxide ion on the phosphorus atom of cAMP, cleavage of O3'-P phosphoesteric bond of cAMP, protonation of the departing O3' atom, and dissociation of hydrolysis product (AMP). The stage 2 includes the binding of solvent water molecules with the metal ions in the active site and regeneration of the bridging hydroxide ion. The dissociation of the hydrolysis product is found to be rate-determining for the enzymatic reaction process. The calculated activation Gibbs free energy of ≥16.0 and reaction free energy of -11.1 kcal/mol are in good agreement with the experimentally derived activation free energy of 16.6 kcal/mol and reaction free energy of -11.5 kcal/mol, suggesting that the catalytic mechanism obtained from this study is reliable and provides a solid base for future rational drug design.
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Affiliation(s)
- Xi Chen
- Key Laboratory of Pesticide & Chemical Biology of the Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, P. R. China
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone street, Lexington, KY 40536
| | - Xinyun Zhao
- College of Chemistry and Materials Science, South-Central University for Nationalities, Wuhan, Hubei 430074, P. R. China
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone street, Lexington, KY 40536
| | - Ying Xiong
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone street, Lexington, KY 40536
| | - Junjun Liu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone street, Lexington, KY 40536
| | - Chang-Guo Zhan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone street, Lexington, KY 40536
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20
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Combined ligand based pharmacophore modeling, virtual screening methods to identify critical chemical features of novel potential inhibitors for phosphodiesterase-5. J Taiwan Inst Chem Eng 2011. [DOI: 10.1016/j.jtice.2011.02.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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21
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Vorontsov II, Minasov G, Kiryukhina O, Brunzelle JS, Shuvalova L, Anderson WF. Characterization of the deoxynucleotide triphosphate triphosphohydrolase (dNTPase) activity of the EF1143 protein from Enterococcus faecalis and crystal structure of the activator-substrate complex. J Biol Chem 2011; 286:33158-66. [PMID: 21757692 PMCID: PMC3190883 DOI: 10.1074/jbc.m111.250456] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The EF1143 protein from Enterococcus faecalis is a distant homolog of deoxynucleotide triphosphate triphosphohydrolases (dNTPases) from Escherichia coli and Thermus thermophilus. These dNTPases are important components in the regulation of the dNTP pool in bacteria. Biochemical assays of the EF1143 dNTPase activity demonstrated nonspecific hydrolysis of all canonical dNTPs in the presence of Mn(2+). In contrast, with Mg(2+) hydrolysis required the presence of dGTP as an effector, activating the degradation of dATP and dCTP with dGTP also being consumed in the reaction with dATP. The crystal structure of EF1143 and dynamic light scattering measurements in solution revealed a tetrameric oligomer as the most probable biologically active unit. The tetramer contains four dGTP specific allosteric regulatory sites and four active sites. Examination of the active site with the dATP substrate suggests an in-line nucleophilic attack on the α-phosphate center as a possible mechanism of the hydrolysis and two highly conserved residues, His-129 and Glu-122, as an acid-base catalytic dyad. Structural differences between EF1143 apo and holo forms revealed mobility of the α3 helix that can regulate the size of the active site binding pocket and could be stabilized in the open conformation upon formation of the tetramer and dGTP effector binding.
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Affiliation(s)
- Ivan I Vorontsov
- Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
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22
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Abstract
Molecular dynamics simulations employing a combined quantum mechanical and molecular mechanical potential have been carried out to elucidate the reaction mechanism of the hydrolysis of a cyclic nucleotide cAMP substrate by phosphodiesterase 4B (PDE4B). PDE4B is a member of the PDE superfamily of enzymes that play crucial roles in cellular signal transduction. We have determined a two-dimensional potential of mean force (PMF) for the coupled phosphoryl bond cleavage and proton transfer through a general acid catalysis mechanism in PDE4B. The results indicate that the ring-opening process takes place through an S(N)2 reaction mechanism, followed by a proton transfer to stabilize the leaving group. The computed free energy of activation for the PDE4B-catalyzed cAMP hydrolysis is about 13 kcal·mol(-1) and an overall reaction free energy is about -17 kcal·mol(-1), both in accord with experimental results. In comparison with the uncatalyzed reaction in water, the enzyme PDE4B provides a strong stabilization of the transition state, lowering the free energy barrier by 14 kcal·mol(-1). We found that the proton transfer from the general acid residue His234 to the O3' oxyanion of the ribosyl leaving group lags behind the nucleophilic attack, resulting in a shallow minimum on the free energy surface. A key contributing factor to transition state stabilization is the elongation of the distance between the divalent metal ions Zn(2+) and Mg(2+) in the active site as the reaction proceeds from the Michaelis complex to the transition state.
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Affiliation(s)
- Kin-Yiu Wong
- Department of Chemistry, Digital Technology Center, University of Minnesota, Minneapolis, MN 55455, USA.
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23
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Francis SH, Blount MA, Corbin JD. Mammalian Cyclic Nucleotide Phosphodiesterases: Molecular Mechanisms and Physiological Functions. Physiol Rev 2011; 91:651-90. [DOI: 10.1152/physrev.00030.2010] [Citation(s) in RCA: 451] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The superfamily of cyclic nucleotide (cN) phosphodiesterases (PDEs) is comprised of 11 families of enzymes. PDEs break down cAMP and/or cGMP and are major determinants of cellular cN levels and, consequently, the actions of cN-signaling pathways. PDEs exhibit a range of catalytic efficiencies for breakdown of cAMP and/or cGMP and are regulated by myriad processes including phosphorylation, cN binding to allosteric GAF domains, changes in expression levels, interaction with regulatory or anchoring proteins, and reversible translocation among subcellular compartments. Selective PDE inhibitors are currently in clinical use for treatment of erectile dysfunction, pulmonary hypertension, intermittent claudication, and chronic pulmonary obstructive disease; many new inhibitors are being developed for treatment of these and other maladies. Recently reported x-ray crystallographic structures have defined features that provide for specificity for cAMP or cGMP in PDE catalytic sites or their GAF domains, as well as mechanisms involved in catalysis, oligomerization, autoinhibition, and interactions with inhibitors. In addition, major advances have been made in understanding the physiological impact and the biochemical basis for selective localization and/or recruitment of specific PDE isoenzymes to particular subcellular compartments. The many recent advances in understanding PDE structures, functions, and physiological actions are discussed in this review.
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Affiliation(s)
- Sharron H. Francis
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee; and Department of Medicine-Renal Division, Emory University School of Medicine, Atlanta, Georgia
| | - Mitsi A. Blount
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee; and Department of Medicine-Renal Division, Emory University School of Medicine, Atlanta, Georgia
| | - Jackie D. Corbin
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee; and Department of Medicine-Renal Division, Emory University School of Medicine, Atlanta, Georgia
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24
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Yang B, Hamza A, Chen G, Wang Y, Zhan CG. Computational determination of binding structures and free energies of phosphodiesterase-2 with benzo[1,4]diazepin-2-one derivatives. J Phys Chem B 2010; 114:16020-8. [PMID: 21077589 PMCID: PMC3072033 DOI: 10.1021/jp1086416] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Phosphodiesterase-2 (PDE2) is a key enzyme catalyzing hydrolysis of both cyclic adenosine monophosphate (cAMP) and cyclic guanosine monophosphate (cGMP) that serve as intracellular second messengers. PDE2 has been recognized as an attractive drug target, and selective inhibitors of PDE2 are expected to be promising candidates for the memory enhancer, antidepressant, and anxiolytic agent. In the present study, we examined the detailed binding structures and free energies for PDE2 interacting with a promising series of inhibitors, i.e., benzo[1,4]diazepin-2-one derivatives, by carrying out molecular docking, molecular dynamics (MD) simulations, binding free energy calculations, and binding energy decompositions. The computational results provide valuable insights into the detailed enzyme-inhibitor binding modes including important intermolecular interactions, e.g., the π-π stacking interactions with the common benzo[1,4]diazepin-2-one scaffold of the inhibitors, hydrogen bonding and hydrophobic interactions with the substituents on the benzo[1,4]diazepin-2-one scaffold. Future rational design of new, more potent inhibitors of PDE2 should carefully account for all of these favorable intermolecular interactions. By use of the MD-simulated binding structures, the calculated binding free energies are in good agreement with the experimental activity data for all of the examined benzo[1,4]diazepin-2-one derivatives. The enzyme-inhibitor binding modes determined and the agreement between the calculated and experimental results are expected to be valuable for future rational design of more potent inhibitors of PDE2.
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Affiliation(s)
- Bo Yang
- Department of Chemistry, College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536
| | - Adel Hamza
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536
| | - Guangju Chen
- Department of Chemistry, College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Yan Wang
- Department of Chemistry, College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Chang-Guo Zhan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536
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25
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Tchigvintsev A, Xu X, Singer A, Chang C, Brown G, Proudfoot M, Cui H, Flick R, Anderson WF, Joachimiak A, Galperin MY, Savchenko A, Yakunin AF. Structural insight into the mechanism of c-di-GMP hydrolysis by EAL domain phosphodiesterases. J Mol Biol 2010; 402:524-38. [PMID: 20691189 DOI: 10.1016/j.jmb.2010.07.050] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Revised: 07/22/2010] [Accepted: 07/25/2010] [Indexed: 11/19/2022]
Abstract
Cyclic diguanylate (or bis-(3'-5') cyclic dimeric guanosine monophosphate; c-di-GMP) is a ubiquitous second messenger that regulates diverse cellular functions, including motility, biofilm formation, cell cycle progression, and virulence in bacteria. In the cell, degradation of c-di-GMP is catalyzed by highly specific EAL domain phosphodiesterases whose catalytic mechanism is still unclear. Here, we purified 13 EAL domain proteins from various organisms and demonstrated that their catalytic activity is associated with the presence of 10 conserved EAL domain residues. The crystal structure of the TBD1265 EAL domain was determined in free state (1.8 Å) and in complex with c-di-GMP (2.35 A), and unveiled the role of conserved residues in substrate binding and catalysis. The structure revealed the presence of two metal ions directly coordinated by six conserved residues, two oxygens of c-di-GMP phosphate, and potential catalytic water molecule. Our results support a two-metal-ion catalytic mechanism of c-di-GMP hydrolysis by EAL domain phosphodiesterases.
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Affiliation(s)
- Anatoli Tchigvintsev
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
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26
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Lau JKC, Li XB, Cheng YK. A substrate selectivity and inhibitor design lesson from the PDE10-cAMP crystal structure: a computational study. J Phys Chem B 2010; 114:5154-60. [PMID: 20349929 DOI: 10.1021/jp911156g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Phosphodiesterases (PDEs) catalyze the hydrolysis of second messengers cAMP and cGMP in regulating many important cellular signals and have been recognized as important drug targets. Experimentally, a range of specificity/selectivity toward cAMP and cGMP is well-known for the individual PDE families. The study reported here reveals that PDEs might also exhibit selectivity toward conformations of the endogenous substrates cAMP and cGMP. Molecular dynamics simulations and free energy study have been applied to study the binding of the cAMP torsional conformers about the glycosyl bond in PDE10A2. The computational results elucidated that PDE10A2 is energetically more favorable in complex with the syn cAMP conformer (as reported in the crystal structure) and the binding of anti cAMP to PDE10A2 would lead to either a nonreactive configuration or significant perturbation on the catalytic pocket of the enzyme. This experimentally inaccessible information provides important molecular insights for the development of effective PDE10 ligands.
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Affiliation(s)
- Justin Kai-Chi Lau
- Department of Chemistry, The Hong Kong Baptist University, Waterloo Road, Kowloon Tong, Kowloon, Hong Kong, China.
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27
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Barends TRM, Hartmann E, Griese JJ, Beitlich T, Kirienko NV, Ryjenkov DA, Reinstein J, Shoeman RL, Gomelsky M, Schlichting I. Structure and mechanism of a bacterial light-regulated cyclic nucleotide phosphodiesterase. Nature 2009; 459:1015-8. [PMID: 19536266 DOI: 10.1038/nature07966] [Citation(s) in RCA: 221] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2008] [Accepted: 03/05/2009] [Indexed: 11/10/2022]
Abstract
The ability to respond to light is crucial for most organisms. BLUF is a recently identified photoreceptor protein domain that senses blue light using a FAD chromophore. BLUF domains are present in various proteins from the Bacteria, Euglenozoa and Fungi. Although structures of single-domain BLUF proteins have been determined, none are available for a BLUF protein containing a functional output domain; the mechanism of light activation in this new class of photoreceptors has thus remained poorly understood. Here we report the biochemical, structural and mechanistic characterization of a full-length, active photoreceptor, BlrP1 (also known as KPN_01598), from Klebsiella pneumoniae. BlrP1 consists of a BLUF sensor domain and a phosphodiesterase EAL output domain which hydrolyses cyclic dimeric GMP (c-di-GMP). This ubiquitous second messenger controls motility, biofilm formation, virulence and antibiotic resistance in the Bacteria. Crystal structures of BlrP1 complexed with its substrate and metal ions involved in catalysis or in enzyme inhibition provide a detailed understanding of the mechanism of the EAL-domain c-di-GMP phosphodiesterases. These structures also sketch out a path of light activation of the phosphodiesterase output activity. Photon absorption by the BLUF domain of one subunit of the antiparallel BlrP1 homodimer activates the EAL domain of the second subunit through allosteric communication transmitted through conserved domain-domain interfaces.
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Affiliation(s)
- Thomas R M Barends
- Max Planck Institute for Medical Research, Department of Biomolecular Mechanisms, Jahnstrasse 29, 69120 Heidelberg, Germany
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28
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Liu S, Mansour MN, Dillman KS, Perez JR, Danley DE, Aeed PA, Simons SP, Lemotte PK, Menniti FS. Structural basis for the catalytic mechanism of human phosphodiesterase 9. Proc Natl Acad Sci U S A 2008; 105:13309-14. [PMID: 18757755 PMCID: PMC2533186 DOI: 10.1073/pnas.0708850105] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2007] [Indexed: 11/18/2022] Open
Abstract
The phosphodiesterases (PDEs) are metal ion-dependent enzymes that regulate cellular signaling by metabolic inactivation of the ubiquitous second messengers cAMP and cGMP. In this role, the PDEs are involved in many biological and metabolic processes and are proven targets of successful drugs for the treatments of a wide range of diseases. However, because of the rapidity of the hydrolysis reaction, an experimental knowledge of the enzymatic mechanisms of the PDEs at the atomic level is still lacking. Here, we report the structures of reaction intermediates accumulated at the reaction steady state in PDE9/crystal and preserved by freeze-trapping. These structures reveal the catalytic process of a PDE and explain the substrate specificity of PDE9 in an actual reaction and the cation requirements of PDEs in general.
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Affiliation(s)
- Shenping Liu
- Pfizer Global Research and Development, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA.
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