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Redzicka A, Wiatrak B, Jęśkowiak-Kossakowska I, Kochel A, Płaczek R, Czyżnikowska Ż. Design, Synthesis, Biological Evaluation, and Molecular Docking Study of 4,6-Dimethyl-5-aryl/alkyl-2-[2-hydroxy-3-(4-substituted-1-piperazinyl)propyl]pyrrolo[3,4- c]pyrrole-1,3(2 H,5 H)-diones as Anti-Inflammatory Agents with Dual Inhibition of COX and LOX. Pharmaceuticals (Basel) 2023; 16:804. [PMID: 37375750 DOI: 10.3390/ph16060804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/11/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
In the present study, we characterize the biological activity of a newly designed and synthesized series of 15 compounds 2-[2-hydroxy-3-(4-substituted-1-piperazinyl)propyl] derivatives of pyrrolo[3,4-c]pyrrole 3a-3o. The compounds were obtained with good yields of pyrrolo[3,4-c]pyrrole scaffold 2a-2c with secondary amines in C2H5OH. The chemical structures of the compounds were characterized by 1H-NMR, 13C-NMR, FT-IR, and MS. All the new compounds were investigated for their potencies to inhibit the activity of three enzymes, i.e., COX-1, COX-2, and LOX, by a colorimetric inhibitor screening assay. In order to analyze the structural basis of interactions between the ligands and cyclooxygenase/lipooxygenase, experimental data were supported by the results of molecular docking simulations. The data indicate that all of the tested compounds influence the activity of COX-1, COX-2, and LOX.
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Affiliation(s)
- Aleksandra Redzicka
- Department of Medicinal Chemistry, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211, 50-556 Wroclaw, Poland
| | - Benita Wiatrak
- Department of Pharmacology, Wroclaw Medical University, Mikulicza-Radeckiego 2, 50-345 Wroclaw, Poland
| | | | - Andrzej Kochel
- Faculty of Chemistry, University of Wroclaw, ul. F.J oliot-Curie 14, 50-383 Wroclaw, Poland
| | - Remigiusz Płaczek
- Faculty of Pharmacy, Wroclaw Medical University, Borowska 211a, 50-556 Wroclaw, Poland
| | - Żaneta Czyżnikowska
- Department of Basic Chemical Sciences, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211a, 50-556 Wroclaw, Poland
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2
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Thiour-Mauprivez C, Dayan FE, Terol H, Devers M, Calvayrac C, Martin-Laurent F, Barthelmebs L. Assessing the effects of β-triketone herbicides on HPPD from environmental bacteria using a combination of in silico and microbiological approaches. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:9932-9944. [PMID: 36068455 DOI: 10.1007/s11356-022-22801-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 08/26/2022] [Indexed: 06/15/2023]
Abstract
4-hydroxyphenylpyruvate dioxygenase (HPPD) is the molecular target of β-triketone herbicides in plants. This enzyme, involved in the tyrosine pathway, is also present in a wide range of living organisms, including microorganisms. Previous studies, focusing on a few strains and using high herbicide concentrations, showed that β-triketones are able to inhibit microbial HPPD. Here, we measured the effect of agronomical doses of β-triketone herbicides on soil bacterial strains. The HPPD activity of six bacterial strains was tested with 1× or 10× the recommended field dose of the herbicide sulcotrione. The selected strains were tested with 0.01× to 15× the recommended field dose of sulcotrione, mesotrione, and tembotrione. Molecular docking was also used to measure and model the binding mode of the three herbicides with the different bacterial HPPD. Our results show that responses to herbicides are strain-dependent with Pseudomonas fluorescens F113 HPPD activity not inhibited by any of the herbicide tested, when all three β-triketone herbicides inhibited HPPD in Bacillus cereus ATCC14579 and Shewanella oneidensis MR-1. These responses are also molecule-dependent with tembotrione harboring the strongest inhibitory effect. Molecular docking also reveals different binding potentials. This is the first time that the inhibitory effect of β-triketone herbicides is tested on environmental strains at agronomical doses, showing a potential effect of these molecules on the HPPD enzymatic activity of non-target microorganisms. The whole-cell assay developed in this study, coupled with molecular docking analysis, appears as an interesting way to have a first idea of the effect of herbicides on microbial communities, prior to setting up microcosm or even field experiments. This methodology could then largely be applied to other family of pesticides also targeting an enzyme present in microorganisms.
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Affiliation(s)
- Clémence Thiour-Mauprivez
- University Perpignan Via Domitia, Biocapteurs-Analyses-Environnement, 66860 Perpignan, France; Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR 3579 Sorbonne Universités (UPMC) Paris 6 et CNRS Observatoire Océanologique, 66650, Banyuls-sur-Mer, France
- Agroécologie, INRAE, Institut Agro, Unv. Bourgogne, University Bourgogne Franche-Comté, F-21000, Dijon, France
| | - Franck Emmanuel Dayan
- Agricultural Biology Department, Colorado State University, Fort Collins, CO, 80523, USA
| | - Hugo Terol
- University Perpignan Via Domitia, Biocapteurs-Analyses-Environnement, 66860 Perpignan, France; Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR 3579 Sorbonne Universités (UPMC) Paris 6 et CNRS Observatoire Océanologique, 66650, Banyuls-sur-Mer, France
| | - Marion Devers
- Agroécologie, INRAE, Institut Agro, Unv. Bourgogne, University Bourgogne Franche-Comté, F-21000, Dijon, France
| | - Christophe Calvayrac
- University Perpignan Via Domitia, Biocapteurs-Analyses-Environnement, 66860 Perpignan, France; Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR 3579 Sorbonne Universités (UPMC) Paris 6 et CNRS Observatoire Océanologique, 66650, Banyuls-sur-Mer, France
| | - Fabrice Martin-Laurent
- Agroécologie, INRAE, Institut Agro, Unv. Bourgogne, University Bourgogne Franche-Comté, F-21000, Dijon, France
| | - Lise Barthelmebs
- University Perpignan Via Domitia, Biocapteurs-Analyses-Environnement, 66860 Perpignan, France; Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR 3579 Sorbonne Universités (UPMC) Paris 6 et CNRS Observatoire Océanologique, 66650, Banyuls-sur-Mer, France.
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3
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Hoang LG, Goßen J, Capelli R, Nguyen TT, Sun Z, Zuo K, Schulz JB, Rossetti G, Carloni P. Multiple Poses and Thermodynamics of Ligands Targeting Protein Surfaces: The Case of Furosemide Binding to mitoNEET in Aqueous Solution. Front Cell Dev Biol 2022; 10:886568. [PMID: 35557955 PMCID: PMC9086288 DOI: 10.3389/fcell.2022.886568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/04/2022] [Indexed: 11/25/2022] Open
Abstract
Human NEET proteins, such as NAF-1 and mitoNEET, are homodimeric, redox iron-sulfur proteins characterized by triple cysteine and one histidine-coordinated [2Fe-2S] cluster. They exist in an oxidized and reduced state. Abnormal release of the cluster is implicated in a variety of diseases, including cancer and neurodegeneration. The computer-aided and structure-based design of ligands affecting cluster release is of paramount importance from a pharmaceutical perspective. Unfortunately, experimental structural information so far is limited to only one ligand/protein complex. This is the X-ray structure of furosemide bound to oxidized mitoNEET. Here we employ an enhanced sampling approach, Localized Volume-based Metadynamics, developed by some of us, to identify binding poses of furosemide to human mitoNEET protein in solution. The binding modes show a high variability within the same shallow binding pocket on the protein surface identified in the X-ray structure. Among the different binding conformations, one of them is in agreement with the crystal structure’s one. This conformation might have been overstabilized in the latter because of the presence of crystal packing interactions, absent in solution. The calculated binding affinity is compatible with experimental data. Our protocol can be used in a straightforward manner in drug design campaigns targeting this pharmaceutically important family of proteins.
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Affiliation(s)
- Linh Gia Hoang
- INM-11, Forschungszentrum, Jülich, Germany.,Key Laboratory for Multiscale Simulations of Complex Systems, VNU University of Science, Vietnam National University, Hanoi, Vietnam
| | - Jonas Goßen
- IAS-5/INM-9, Forschungszentrum, Jülich, Germany.,Faculty of Mathematics, Computer Science and Natural Sciences, RWTH Aachen University, Aachen, Germany
| | - Riccardo Capelli
- Department of Applied Science and Technology (DISAT), Politecnico di Torino, Torino, Italy
| | - Toan T Nguyen
- Key Laboratory for Multiscale Simulations of Complex Systems, VNU University of Science, Vietnam National University, Hanoi, Vietnam
| | - Zhaoxi Sun
- College of Chemistry and Molecular Engineering, Institute of Theoretical and Computational Chemistry, Peking University, Beijing, China
| | - Ke Zuo
- IAS-5/INM-9, Forschungszentrum, Jülich, Germany.,The Alexander Silberman Institute of Life Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem, Israel.,Department of Physics, RWTH Aachen University, Aachen, Germany
| | - Jörg B Schulz
- INM-11, Forschungszentrum, Jülich, Germany.,Department of Neurology, University Hospital Aachen (UKA), RWTH Aachen University, Aachen, Germany
| | - Giulia Rossetti
- IAS-5/INM-9, Forschungszentrum, Jülich, Germany.,Department of Neurology, University Hospital Aachen (UKA), RWTH Aachen University, Aachen, Germany.,Jülich Supercomputing Centre (JSC), Forschungszentrum, Jülich, Germany
| | - Paolo Carloni
- INM-11, Forschungszentrum, Jülich, Germany.,Key Laboratory for Multiscale Simulations of Complex Systems, VNU University of Science, Vietnam National University, Hanoi, Vietnam.,IAS-5/INM-9, Forschungszentrum, Jülich, Germany
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4
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Mandal SK, Kanaujia SP. Role of an orphan substrate-binding protein MhuP in transient heme transfer in Mycobacterium tuberculosis. Int J Biol Macromol 2022; 211:342-356. [PMID: 35569676 DOI: 10.1016/j.ijbiomac.2022.05.059] [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: 02/27/2022] [Revised: 04/25/2022] [Accepted: 05/08/2022] [Indexed: 11/25/2022]
Abstract
The redox property of iron makes it an essential cofactor for numerous enzymes involved in various metabolic processes. In vertebrates, iron is attached to either heme molecules or with other circulatory proteins, making its accessibility restricted for bacterial pathogens residing inside the host. Due to this importance, there is always an ongoing battle between the host system and pathogens, known as nutritional immunity. To capture the bound iron from the human hosts, intracellular pathogens like Mycobacterium tuberculosis secrete siderophore molecules which are ultimately uptaken by versatile transport machinery such as ATP-binding cassette (ABC) transporters. Earlier reports have suggested the presence of a heme uptake protein MhuP (ORF id: Rv0265c) in M. tuberculosis, which transiently transfers the bound iron to the protein DppA for further heme transport by utilizing its cognate transport machinery (DppBCD). In the present study, we report the crystal structure of MhuP. The binding experiments of heme with MhuP suggest its specific nature. Molecular docking studies confirm the binding of the protein MhuP with heme as well as to the protein DppA. Thus, the results indicate the binding of heme to MhuP and its probable transient transport via the DppABCD transport system in M. tuberculosis.
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Affiliation(s)
- Suraj Kumar Mandal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Shankar Prasad Kanaujia
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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5
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Characterization of acetolactate decarboxylase of Streptococcus thermophilus and its stereoselectivity in decarboxylation of α-hydroxy-β-ketoacids. Bioorg Chem 2022; 122:105719. [DOI: 10.1016/j.bioorg.2022.105719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 01/29/2022] [Accepted: 03/02/2022] [Indexed: 11/22/2022]
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6
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DeLaney C, Sheng Y, Pectol DC, Vantansever E, Zhang H, Bhuvanesh N, Salas I, Liu WR, Fierke CF, Darensbourg MY. Zinc thiotropolone combinations as inhibitors of the SARS-CoV-2 main protease. Dalton Trans 2021; 50:12226-12233. [PMID: 34396374 DOI: 10.1039/d1dt02499j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Numerous organic molecules are known to inhibit the main protease of SARS-CoV-2, (SC2Mpro), a key component in viral replication of the 2019 novel coronavirus. We explore the hypothesis that zinc ions, long used as a medicinal supplement and known to support immune function, bind to the SC2Mpro enzyme in combination with lipophilic tropolone and thiotropolone ligands, L, block substrate docking, and inhibit function. This study combines synthetic inorganic chemistry, in vitro protease activity assays, and computational modeling. While the ligands themselves have half maximal inhibition concentrations, IC50, for SC2Mpro in the 8-34 μM range, the IC50 values are ca. 100 nM for Zn(NO3)2 which are further enhanced in Zn-L combinations (59-97 nM). Isolation of the Zn(L)2 binary complexes and characterization of their ability to undergo ligand displacement is the basis for computational modeling of the chemical features of the enzyme inhibition. Blind docking onto the SC2Mpro enzyme surface using a modified Autodock4 protocol found preferential binding into the active site pocket. Such Zn-L combinations orient so as to permit dative bonding of Zn(L)+ to basic active site residues.
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Affiliation(s)
| | - Yan Sheng
- 3255 TAMU, College Station, TX, 77843, USA.
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7
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Peregrym K, Szczukowski Ł, Wiatrak B, Potyrak K, Czyżnikowska Ż, Świątek P. In Vitro and In Silico Evaluation of New 1,3,4-Oxadiazole Derivatives of Pyrrolo[3,4- d]pyridazinone as Promising Cyclooxygenase Inhibitors. Int J Mol Sci 2021; 22:ijms22179130. [PMID: 34502040 PMCID: PMC8431030 DOI: 10.3390/ijms22179130] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/20/2021] [Accepted: 08/21/2021] [Indexed: 12/24/2022] Open
Abstract
Since long-term use of classic NSAIDs can cause severe side effects related mainly to the gastroduodenal tract, discovery of novel cyclooxygenase inhibitors with a safe gastric profile still remains a crucial challenge. Based on the most recent literature data and previous own studies, we decided to modify the structure of already reported 1,3,4-oxadiazole based derivatives of pyrrolo[3,4-d]pyridazinone in order to obtain effective COX inhibitors. Herein we present the synthesis, biological evaluation and molecular docking studies of 12 novel compounds with disubstituted arylpiperazine pharmacophore linked in a different way with 1,3,4-oxadiazole ring. None of the obtained molecules show cytotoxicity on NHDF and THP-1 cell lines and, therefore, all were qualified for further investigation. In vitro cyclooxygenase inhibition assay revealed almost equal activity of new derivatives towards both COX-1 and COX-2 isoenzymes. Moreover, all compounds inhibit COX-2 isoform better than Meloxicam which was used as reference. Anti-inflammatory activity was confirmed in biological assays according to which title molecules are able to reduce induced inflammation within cells. Molecular docking studies were performed to describe the binding mode of new structures to cyclooxygenase. Investigated derivatives take place in the active site of COX, very similar to Meloxicam. For some compounds, promising druglikeness was calculated using in silico predictions.
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Affiliation(s)
- Krzysztof Peregrym
- Department of Medicinal Chemistry, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211, 50-556 Wroclaw, Poland;
| | - Łukasz Szczukowski
- Department of Medicinal Chemistry, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211, 50-556 Wroclaw, Poland;
- Correspondence: (Ł.S.); (P.Ś.); Tel.: +48-71-784-03-91 (P.Ś.)
| | - Benita Wiatrak
- Department of Pharmacology, Faculty of Medicine, Wroclaw Medical University, Mikulicza-Radeckiego 2, 50-345 Wroclaw, Poland; (B.W.); (K.P.)
| | - Katarzyna Potyrak
- Department of Pharmacology, Faculty of Medicine, Wroclaw Medical University, Mikulicza-Radeckiego 2, 50-345 Wroclaw, Poland; (B.W.); (K.P.)
| | - Żaneta Czyżnikowska
- Department of Inorganic Chemistry, Wroclaw Medical University, Borowska 211, 50-556 Wroclaw, Poland;
| | - Piotr Świątek
- Department of Medicinal Chemistry, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211, 50-556 Wroclaw, Poland;
- Correspondence: (Ł.S.); (P.Ś.); Tel.: +48-71-784-03-91 (P.Ś.)
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8
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Tylińska B, Dobosz A, Spychała J, Cwynar-Zając Ł, Czyżnikowska Ż, Kuźniarski A, Gębarowski T. Evaluation of Interactions of Selected Olivacine Derivatives with DNA and Topoisomerase II. Int J Mol Sci 2021; 22:ijms22168492. [PMID: 34445198 PMCID: PMC8395211 DOI: 10.3390/ijms22168492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/02/2021] [Accepted: 08/04/2021] [Indexed: 11/16/2022] Open
Abstract
Olivacine and ellipticine are model anticancer drugs acting as topoisomerase II inhibitors. Here, we present investigations performed on four olivacine derivatives in light of their antitumor activity. The aim of this study was to identify the best antitumor compound among the four tested olivacine derivatives. The study was performed using CCRF/CEM and MCF-7 cell lines. Comet assay, polarography, inhibition of topoisomerase II activity, histone acetylation, and molecular docking studies were performed. Each tested compound displayed interaction with DNA and topoisomerase II, but did not cause histone acetylation. Compound 2 (9-methoxy-5,6-dimethyl-1-({[1-hydroxy-2-(hydroxymethyl)butan-2-yl]amino}methyl)-6H-pyrido[4,3-b]carbazole) was found to be the best candidate as an anticancer drug because it had the highest affinity for topoisomerase II and caused the least genotoxic damage in cells.
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Affiliation(s)
- Beata Tylińska
- Department of Organic Chemistry, Wroclaw Medical University, 50-556 Wroclaw, Poland;
| | - Agnieszka Dobosz
- Department of Basic Medical Sciences, Wroclaw Medical University, 50-556 Wroclaw, Poland; (J.S.); (Ł.C.-Z.); (T.G.)
- Correspondence: ; Tel.: +48-717-840-482
| | - Jan Spychała
- Department of Basic Medical Sciences, Wroclaw Medical University, 50-556 Wroclaw, Poland; (J.S.); (Ł.C.-Z.); (T.G.)
| | - Łucja Cwynar-Zając
- Department of Basic Medical Sciences, Wroclaw Medical University, 50-556 Wroclaw, Poland; (J.S.); (Ł.C.-Z.); (T.G.)
| | - Żaneta Czyżnikowska
- Department of Inorganic Chemistry, Wroclaw Medical University, 50-556 Wroclaw, Poland;
| | - Amadeusz Kuźniarski
- Department of Prosthetic Dentistry, Wroclaw Medical University, 50-425 Wroclaw, Poland;
| | - Tomasz Gębarowski
- Department of Basic Medical Sciences, Wroclaw Medical University, 50-556 Wroclaw, Poland; (J.S.); (Ł.C.-Z.); (T.G.)
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9
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Pectol DC, DeLaney CR, Zhu J, Mellott DM, Katzfuss A, Taylor ZW, Meek TD, Darensbourg MY. Dinitrosyl iron complexes (DNICs) as inhibitors of the SARS-CoV-2 main protease. Chem Commun (Camb) 2021; 57:8352-8355. [PMID: 34337637 DOI: 10.1039/d1cc03103a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
By repurposing DNICs designed for other medicinal purposes, the possibility of protease inhibition was investigated in silico using AutoDock 4.2.6 (AD4) and in vitro via a FRET protease assay. AD4 was validated as a predictive computational tool for coordinatively unsaturated DNIC binding using the only known crystal structure of a protein-bound DNIC, PDB- (calculation RMSD = 1.77). From the in silico data the dimeric DNICs TGTA-RRE, [(μ-S-TGTA)Fe(NO)2]2 (TGTA = 1-thio-β-d-glucose tetraacetate) and TG-RRE, [(μ-S-TG)Fe(NO)2]2 (TG = 1-thio-β-d-glucose) were identified as promising leads for inhibition via coordinative inhibition at Cys-145 of the SARS-CoV-2 Main Protease (SC2Mpro). In vitro studies indicate inhibition of protease activity upon DNIC treatment, with an IC50 of 38 ± 2 μM for TGTA-RRE and 33 ± 2 μM for TG-RRE. This study presents a simple computational method for predicting DNIC-protein interactions; the in vitro study is consistent with in silico leads.
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Affiliation(s)
- D Chase Pectol
- Department of Chemistry, Texas A&M University, College Station, Texas 77842-3012, USA.
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10
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Tylińska B, Wiatrak B, Czyżnikowska Ż, Cieśla-Niechwiadowicz A, Gębarowska E, Janicka-Kłos A. Novel Pyrimidine Derivatives as Potential Anticancer Agents: Synthesis, Biological Evaluation and Molecular Docking Study. Int J Mol Sci 2021; 22:ijms22083825. [PMID: 33917090 PMCID: PMC8067809 DOI: 10.3390/ijms22083825] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 01/06/2023] Open
Abstract
In the present paper, new pyrimidine derivatives were designed, synthesized and analyzed in terms of their anticancer properties. The tested compounds were evaluated in vitro for their antitumor activity. The cytotoxic effect on normal human dermal fibroblasts (NHDF) was also determined. According to the results, all the tested compounds exhibited inhibitory activity on the proliferation of all lines of cancer cells (colon adenocarcinoma (LoVo), resistant colon adenocarcinoma (LoVo/DX), breast cancer (MCF-7), lung cancer (A549), cervical cancer (HeLa), human leukemic lymphoblasts (CCRF-CEM) and human monocytic (THP-1)). In particular, their feature stronger influence on the activity of P-glycoprotein of cell cultures resistant to doxorubicin than doxorubicin. Tested compounds have more lipophilic character than doxorubicin, which determines their affinity for the molecular target and passive transport through biological membranes. Moreover, the inhibitory potential against topoisomerase II and DNA intercalating properties of synthesized compounds were analyzed via molecular docking.
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Affiliation(s)
- Beata Tylińska
- Department of Organic Chemistry, Wroclaw Medical University, Borowska 211A, 50-556 Wroclaw, Poland
- Correspondence: (B.T.); (B.W.)
| | - Benita Wiatrak
- Department of Pharmacology, Wroclaw Medical University, Mikulicza-Radeckiego 2, 50-345 Wrocław, Poland
- Correspondence: (B.T.); (B.W.)
| | - Żaneta Czyżnikowska
- Department of Inorganic Chemistry, Wroclaw Medical University, Borowska 211A, Borowska 211A, 50-556 Wroclaw, Poland; (Ż.C.); (A.J.-K.)
| | | | - Elżbieta Gębarowska
- Agricultural Microbiology Lab, Department of Plant Protection, Wrocław University of Environmental and Life Sciences, Grunwaldzka 53, 50-375 Wrocław, Poland;
| | - Anna Janicka-Kłos
- Department of Inorganic Chemistry, Wroclaw Medical University, Borowska 211A, Borowska 211A, 50-556 Wroclaw, Poland; (Ż.C.); (A.J.-K.)
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11
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Kurt B, Temel H, Atlan M, Kaya S. Synthesis, characterization, DNA interaction and docking studies of novel Schiff base ligand derived from 2,6-diaminopyridine and its complexes. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.127928] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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12
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Zueva IV, Lushchekina SV, Daudé D, Chabrière E, Masson P. Steady-State Kinetics of Enzyme-Catalyzed Hydrolysis of Echothiophate, a P-S Bonded Organophosphorus as Monitored by Spectrofluorimetry. Molecules 2020; 25:molecules25061371. [PMID: 32192230 PMCID: PMC7144395 DOI: 10.3390/molecules25061371] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 03/14/2020] [Accepted: 03/16/2020] [Indexed: 02/02/2023] Open
Abstract
Enzyme-catalyzed hydrolysis of echothiophate, a P–S bonded organophosphorus (OP) model, was spectrofluorimetrically monitored, using Calbiochem Probe IV as the thiol reagent. OP hydrolases were: the G117H mutant of human butyrylcholinesterase capable of hydrolyzing OPs, and a multiple mutant of Brevundimonas diminuta phosphotriesterase, GG1, designed to hydrolyze a large spectrum of OPs at high rate, including V agents. Molecular modeling of interaction between Probe IV and OP hydrolases (G117H butyrylcholinesterase, GG1, wild types of Brevundimonas diminuta and Sulfolobus solfataricus phosphotriesterases, and human paraoxonase-1) was performed. The high sensitivity of the method allowed steady-state kinetic analysis of echothiophate hydrolysis by highly purified G117H butyrylcholinesterase concentration as low as 0.85 nM. Hydrolysis was michaelian with Km = 0.20 ± 0.03 mM and kcat = 5.4 ± 1.6 min−1. The GG1 phosphotriesterase hydrolyzed echothiophate with a high efficiency (Km = 2.6 ± 0.2 mM; kcat = 53400 min−1). With a kcat/Km = (2.6 ± 1.6) × 107 M−1min−1, GG1 fulfills the required condition of potential catalytic bioscavengers. quantum mechanics/molecular mechanics (QM/MM) and molecular docking indicate that Probe IV does not interact significantly with the selected phosphotriesterases. Moreover, results on G117H mutant show that Probe IV does not inhibit butyrylcholinesterase. Therefore, Probe IV can be recommended for monitoring hydrolysis of P–S bonded OPs by thiol-free OP hydrolases.
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Affiliation(s)
- Irina V. Zueva
- Arbuzov Institute of Organic and Physical Chemistry, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, Arbuzov str. 8, 420088 Kazan, Russia;
| | - Sofya V. Lushchekina
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygin str 4, 119334 Moscow, Russia;
| | - David Daudé
- Gene&GreenTK, HU Méditerranée Infection, Jean Moulin Blvd 19–21, 13005 Marseille, France;
| | - Eric Chabrière
- Aix-Marseille University, IRD, APHM, MEPHI, IHU-Méditerranée Infection, 15005 Marseille, France;
| | - Patrick Masson
- Kazan Federal University, Neuropharmacology Laboratory, Kremlevskaya str 18, 480002 Kazan, Russia
- Correspondence: ; Tel.: +7-96-5581-0473
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13
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Ercan S, Şenses Y. Design and molecular docking studies of new inhibitor candidates for EBNA1 DNA binding site: a computational study. MOLECULAR SIMULATION 2020. [DOI: 10.1080/08927022.2019.1709638] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Selami Ercan
- Department of Nursing, School of Health Sciences, Batman University, Batman, Turkey
| | - Yusuf Şenses
- Institute of Science, Batman University, Batman, Turkey
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14
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Ercan S, Şenyiğit B, Şenses Y. Dual inhibitor design for HIV-1 reverse transcriptase and integrase enzymes: a molecular docking study. J Biomol Struct Dyn 2019; 38:573-580. [DOI: 10.1080/07391102.2019.1700166] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Selami Ercan
- School of Health Sciences, Department of Nursing, Batman University, Batman, Turkey
| | | | - Yusuf Şenses
- Institute of Science, Batman University, Batman, Turkey
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15
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Valera-Vera EA, Sayé M, Reigada C, Miranda MR, Pereira CA. In silico repositioning of etidronate as a potential inhibitor of the Trypanosoma cruzi enolase. J Mol Graph Model 2019; 95:107506. [PMID: 31821935 DOI: 10.1016/j.jmgm.2019.107506] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 11/27/2019] [Accepted: 12/01/2019] [Indexed: 10/25/2022]
Abstract
Enolase is a glycolytic enzyme that catalyzes the interconversion between 2-phosphoglycerate and phosphoenolpyruvate. In trypanosomatids, enolase was proposed as a key enzyme after in silico and in vivo analysis and it was validated as a protein essential for the survival of the parasite. Therefore, enolase constitutes an interesting enzyme target for the identification of drugs against Chagas disease. In this work, a combined virtual screening strategy was implemented, employing similarity virtual screening, molecular docking, and molecular dynamics. First, two known enolase inhibitors and the enzyme substrates were used as queries for the similarity screening on the Sweetlead database using five different algorithms. Compounds retrieved in the top 10 of at least three search algorithms were selected for further analysis, resulting in six compounds of medical use (etidronate, pamidronate, fosfomycin, acetohydroxamate, triclofos, and aminohydroxybutyrate). Molecular docking simulations and pose re-scoring predicted that binding with acetohydroxamate and triclofos would be weak, while fosfomycin and aminohydroxybutyrate predicted binding is experimentally implausible. Docking poses obtained for etidronate, pamidronate, and PEP were used for molecular dynamics calculations to describe their mode of binding. From the obtained results, we propose etidronate as a potential TcENO inhibitor and describe molecular motifs to be taken into account in the repurposing or design of drugs targeting this enzyme active site.
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Affiliation(s)
- Edward A Valera-Vera
- Universidad de Buenos Aires, Facultad de Medicina, Instituto de Investigaciones Médicas A. Lanari, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad de Buenos Aires, Instituto de Investigaciones Médicas (IDIM), Laboratorio de Parasitología Molecular, Buenos Aires, Argentina
| | - Melisa Sayé
- Universidad de Buenos Aires, Facultad de Medicina, Instituto de Investigaciones Médicas A. Lanari, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad de Buenos Aires, Instituto de Investigaciones Médicas (IDIM), Laboratorio de Parasitología Molecular, Buenos Aires, Argentina
| | - Chantal Reigada
- Universidad de Buenos Aires, Facultad de Medicina, Instituto de Investigaciones Médicas A. Lanari, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad de Buenos Aires, Instituto de Investigaciones Médicas (IDIM), Laboratorio de Parasitología Molecular, Buenos Aires, Argentina
| | - Mariana R Miranda
- Universidad de Buenos Aires, Facultad de Medicina, Instituto de Investigaciones Médicas A. Lanari, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad de Buenos Aires, Instituto de Investigaciones Médicas (IDIM), Laboratorio de Parasitología Molecular, Buenos Aires, Argentina
| | - Claudio A Pereira
- Universidad de Buenos Aires, Facultad de Medicina, Instituto de Investigaciones Médicas A. Lanari, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad de Buenos Aires, Instituto de Investigaciones Médicas (IDIM), Laboratorio de Parasitología Molecular, Buenos Aires, Argentina.
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16
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A computational study of the molecular basis of antibiotic resistance in a DXR mutant. J Comput Aided Mol Des 2019; 33:927-940. [DOI: 10.1007/s10822-019-00229-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 09/28/2019] [Indexed: 10/25/2022]
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17
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Ji F, Feng Y, Li M, Long F, Yang Y, Wang T, Wang J, Bao Y, Xue S. Structure and catalytic mechanistic insight into Enterobacter aerogenes acetolactate decarboxylase. Enzyme Microb Technol 2019; 126:9-17. [PMID: 31000168 DOI: 10.1016/j.enzmictec.2019.03.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 02/20/2019] [Accepted: 03/04/2019] [Indexed: 11/25/2022]
Abstract
α-Acetolactate decarboxylase (ALDC) catalyses α-acetolactate into acetoin (3-hydroxy-2-butanone, AC) and is considered to be the rate-limiting enzyme in the synthesis of 2,3-butanediol. In this work, the enzymatic activity of ALDC from Enterobacter aerogenes ALDC (E.a.-ALDC) was fully characterized with enzyme kinetics, indicating a Km of 14.83 ± 0.87 mM and a kcat of 0.81 ± 0.09 s-1. However, compared with the activities of ALDCs reported from other bacteria, the activity of E.a.-ALDC was determined to present a relatively lower value of 849.08 ± 35.21 U/mg. The enzyme showed maximum activity at pH 5.5. In addition, the activity of E.a.-ALDC was promoted by Mg2+. The crystal structure of E.a.-ALDC firstly solved by X-ray crystallography at resolution of 2.4 Å revealed a chelated zinc ion with conserved His199, His201, His212, Glu70 and Glu259. In the active center, the conservative Arg150 was particularly proven to deviate from the zinc ion of the active centre, by adopting a flexible conformational change, resulting in a weak interaction network of the enzyme and the substrate. Further in silico docking of E.a.-ALDC with two enantiomers, (R)-acetolactate and (S)-acetolactate, unaltered the interaction network of E.a.-ALDC from the apo structure, which confirmed the weakened role of Arg150 in the catalytic properties of E.a.-ALDC. Our results reveal a unique structure-function relationship of acetolactate decarboxylase and provide a fundamental basis for the enzymatic synthesis of acetoin.
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Affiliation(s)
- Fangling Ji
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, Liaoning, 116024, PR China.
| | - Yanbin Feng
- Marine Bioengineering Group, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, PR China
| | - Mingyang Li
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, Liaoning, 116024, PR China
| | - Feida Long
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, Liaoning, 116024, PR China
| | - Yongliang Yang
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, Liaoning, 116024, PR China
| | - Tianqi Wang
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, Liaoning, 116024, PR China
| | - Jingyun Wang
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, Liaoning, 116024, PR China
| | - Yongming Bao
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, Liaoning, 116024, PR China; School of Food and Environment Science and Engineering, Dalian University of Technology, Panjin, Liaoning, 12422, PR China
| | - Song Xue
- Marine Bioengineering Group, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, 116023, PR China.
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18
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Mandal SK, Adhikari R, Sharma A, Chandravanshi M, Gogoi P, Kanaujia SP. Designating ligand specificities to metal uptake ABC transporters in Thermus thermophilus HB8. Metallomics 2019; 11:597-612. [DOI: 10.1039/c8mt00374b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Acquisition of different metal ions by metal uptake ABC transporters of Thermus thermophilus HB8 for accomplishing its various cellular functions.
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Affiliation(s)
- Suraj Kumar Mandal
- Department of Biosciences and Bioengineering
- Indian Institute of Technology Guwahati
- Guwahati – 781039
- India
| | - Rahi Adhikari
- Department of Biosciences and Bioengineering
- Indian Institute of Technology Guwahati
- Guwahati – 781039
- India
| | - Anjaney Sharma
- Department of Biosciences and Bioengineering
- Indian Institute of Technology Guwahati
- Guwahati – 781039
- India
| | - Monika Chandravanshi
- Department of Biosciences and Bioengineering
- Indian Institute of Technology Guwahati
- Guwahati – 781039
- India
| | - Prerana Gogoi
- Department of Biosciences and Bioengineering
- Indian Institute of Technology Guwahati
- Guwahati – 781039
- India
| | - Shankar Prasad Kanaujia
- Department of Biosciences and Bioengineering
- Indian Institute of Technology Guwahati
- Guwahati – 781039
- India
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Yuan Y, Hu Z, Bao M, Sun R, Long X, Long L, Li J, Wu C, Bao J. Screening of novel histone deacetylase 7 inhibitors through molecular docking followed by a combination of molecular dynamics simulations and ligand-based approach. J Biomol Struct Dyn 2018; 37:4092-4103. [PMID: 30417746 DOI: 10.1080/07391102.2018.1541141] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Histone acetylation/deacetylation is a key mechanism for transcription regulation which plays an important role in control of gene expression, tissue growth, and development. In particular, histone deacetylase 7 (HDAC7), a member of class IIa HDACs, is crucial to maintain cell homeostasis, and HDAC7 has emerged as a new target for cancer therapy. In this study, molecular docking was applied to screen candidate inhibitors and 21 compounds were found. Following the 50 ns molecular dynamics simulations and binding free energy calculation, ZINC00156160, ZINC01703144, ZINC04293665, and ZINC13900201 were identified as potential HDAC7 inhibitors, which would provide a sound starting point for further studies involving molecular modeling coupled with biochemical experiments. Meanwhile, similarity computation and substructure search were combined, and then we found that compounds sharing common backbone "CC(=O)N[C@@H](CSc1ccccc1)C(=O)O" could be efficient to inhibit the bioactivity of HDAC7. Then comparative molecular similarity indices analysis (CoMSIA) techniques were implemented to investigate the relationship between properties of the substituent group and bioactivities of small molecules. The CoMSIA model exhibited powerful predictivity, with satisfactory statistical parameters such as q2 of 0.659, R2 of 0.952, and F of 268.448. Contour maps of the CoMSIA model gave insight into the feature requirements of the common backbone for the HDAC7 inhibitory activity. Finally, details of designing novel HDAC7 inhibitors were confirmed by a combination of receptor-based docking and ligand-based structure-activity relationship. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yuan Yuan
- a Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University , Chengdu , Sichuan , P.R. China
| | - Zongyue Hu
- a Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University , Chengdu , Sichuan , P.R. China
| | - Minyue Bao
- b State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University , Chengdu , Sichuan , China
| | - Rong Sun
- a Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University , Chengdu , Sichuan , P.R. China
| | - Xin Long
- a Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University , Chengdu , Sichuan , P.R. China
| | - Li Long
- a Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University , Chengdu , Sichuan , P.R. China
| | - Jianzong Li
- a Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University , Chengdu , Sichuan , P.R. China
| | - Chuanfang Wu
- a Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University , Chengdu , Sichuan , P.R. China
| | - Jinku Bao
- a Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University , Chengdu , Sichuan , P.R. China.,b State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University , Chengdu , Sichuan , China
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20
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Ren L, Yu D, Wang Y, Shen L, Zhang J, Wang Y, Fang X. Inhibiting effects of common trivalent metal ions on transmembrane-type 2 matrix metalloproteinase. Int J Biol Macromol 2018; 119:683-691. [PMID: 30048727 DOI: 10.1016/j.ijbiomac.2018.07.145] [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: 06/12/2018] [Revised: 07/14/2018] [Accepted: 07/23/2018] [Indexed: 11/29/2022]
Abstract
Transmembrane-type 2 matrix metalloproteinase (MT2-MMP) degrades connective extracellular matrix between cells and enables tumor cells to migrate and metastasize, making this substance a potential therapeutic target in various diseases. In this work, the interactions between MT2-MMP and common trivalent metal ions, including aluminum (Al3+) and ferrum (Fe3+) ions, were investigated. Enzymatic detection revealed that Al3+ and Fe3+ strongly inhibited the MT2-MMP. Fluorescence spectrography elucidated a static quenching interaction between the negatively charged amino acids on MT2-MMP and the inhibitory trivalent metal ions, indicating that a stable complex was formed between MT2-MMP and metal ions. In addition, fluorescence data and molecular modeling analysis of the binding characteristics revealed that one trivalent metal ion bound with a protein in the stable complex formation process. The potential inhibitory effect of Al3+ on MT2-MMP was further examined in an MT2-MMP-overexpressed cell line, HT1080, by using flow cytometry. As a result, Al3+ can promote HT1080 cell apoptosis in a micromolar concentration-dependent manner. This work illustrated that common trivalent metal ions can potentially inhibit MT2-MMP-related tumors.
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Affiliation(s)
- Li Ren
- College of Food Science and Engineering, Jilin University, 5333 Xi'an Street, Changchun, Jilin 130062, PR China; State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, PR China
| | - Dahai Yu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, College of Life Science, Jilin University, 2699 Qianjin Street, Changchun 130012, PR China
| | - Yanyan Wang
- School of Biological Engineering, Dalian Polytechnic University, Dalian 116034, PR China
| | - Liqiao Shen
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, College of Life Science, Jilin University, 2699 Qianjin Street, Changchun 130012, PR China
| | - Jinrui Zhang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, College of Life Science, Jilin University, 2699 Qianjin Street, Changchun 130012, PR China
| | - Ye Wang
- School of Life Science, Jilin University, 2699 Qianjin Street, Changchun, Jilin 130012, PR China.
| | - Xuexun Fang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, College of Life Science, Jilin University, 2699 Qianjin Street, Changchun 130012, PR China.
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21
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Šebera J, Dubankova A, Sychrovský V, Ruzek D, Boura E, Nencka R. The structural model of Zika virus RNA-dependent RNA polymerase in complex with RNA for rational design of novel nucleotide inhibitors. Sci Rep 2018; 8:11132. [PMID: 30042483 PMCID: PMC6057956 DOI: 10.1038/s41598-018-29459-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 07/09/2018] [Indexed: 12/30/2022] Open
Abstract
Zika virus is a global health threat due to significantly elevated risk of fetus malformations in infected pregnant women. Currently, neither an effective therapy nor a prophylactic vaccination is available for clinical use, desperately necessitating novel therapeutics and approaches to obtain them. Here, we present a structural model of the Zika virus RNA-dependent RNA polymerase (ZIKV RdRp) in complex with template and nascent RNAs, Mg2+ ions and accessing nucleoside triphosphate. The model allowed for docking studies aimed at effective pre-screening of potential inhibitors of ZIKV RdRp. Applicability of the structural model for docking studies was illustrated with the NITD008 artificial nucleotide that is known to effectively inhibit the function of the ZIKV RdRp. The ZIKV RdRp – RNA structural model is provided for all possible variations of the nascent RNA bases pairs to enhance its general utility in docking and modelling experiments. The developed model makes the rational design of novel nucleosides and nucleotide analogues feasible and thus provides a solid platform for the development of advanced antiviral therapy.
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Affiliation(s)
- Jakub Šebera
- Gilead Sciences Research Centre at IOCB Prague, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Praha, Czech Republic
| | - Anna Dubankova
- Gilead Sciences Research Centre at IOCB Prague, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Praha, Czech Republic
| | - Vladimír Sychrovský
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Praha, Czech Republic
| | - Daniel Ruzek
- Veterinary Research Institute, Hudcova 70, CZ-62100, Brno, Czech Republic.,Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, CZ-37005, Ceske Budejovice, Czech Republic
| | - Evzen Boura
- Gilead Sciences Research Centre at IOCB Prague, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Praha, Czech Republic.
| | - Radim Nencka
- Gilead Sciences Research Centre at IOCB Prague, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Praha, Czech Republic.
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23
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Khanppnavar B, Datta S. Crystal structure and substrate specificity of ExoY, a unique T3SS mediated secreted nucleotidyl cyclase toxin from Pseudomonas aeruginosa. Biochim Biophys Acta Gen Subj 2018; 1862:2090-2103. [PMID: 29859257 DOI: 10.1016/j.bbagen.2018.05.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 05/15/2018] [Accepted: 05/25/2018] [Indexed: 01/03/2023]
Abstract
BACKGROUND The nucleotidyl cyclase toxin ExoY is an important virulence determinant of Pseudomonas aeruginosa that causes severe acute and chronic infections in immune-compromised individuals. Additionally, this unique T3SS effector shows a striking preference for cUMP, a newly identified non-canonical secondary messenger. Thereby, ExoY is also considered as a potential tool to study unexplored cUMP signaling pathways. METHODS The crystal structure of ExoY was determined at 2.2 Å resolutions by in-situ proteolysis assisted crystallization and Rosetta-molecular replacement method. Additionally, isothermal calorimetric (ITC) and molecular dynamic (MD) simulation studies were also carried out to gain molecular insights into its substrate specificity and catalysis. RESULTS AND CONCLUSION ExoY is a partially unfolded protein with higher propensity to form soluble higher-order oligomers. However, with meticulous attempts of removing of disordered regions by proteases, the recalcitrant ExoY could be successfully crystallized. The crystal structure of ExoY revealed similar overall structural fold present in other anthrax toxA family of nucleotidyl cyclases, with two-to-three distinctly conserved regions conferring specificity to eukaryotic binding partner. The in-vitro catalytic preference of ExoY is in the following order: cGMP > cUMP > cAMP > cCMP. The substrate specificity of ExoY mainly depends on its ability to bind NTP in proper geometrical orientations. ExoY also seems to prefer one-metal-ion dependent catalysis than two-metal-ion dependent catalysis. GENERAL SIGNIFICANCE Our results provide much needed structural insight on ExoY, an important virulence determinant of Pseudomonas aeruginosa and an exciting tool to study non-canonical cNMP signaling pathways. ACCESSION NUMBERS The structure factors and coordinate files have been deposited in the Protein Data Bank with accession number 5XNW.
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Affiliation(s)
- Basavraj Khanppnavar
- Department of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology (CSIR-IICB), Kolkata, India; Academy of Scientific and Innovative Research (AcSIR), India
| | - Saumen Datta
- Department of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology (CSIR-IICB), Kolkata, India; Academy of Scientific and Innovative Research (AcSIR), India.
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24
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Ji F, Li M, Feng Y, Wu S, Wang T, Pu Z, Wang J, Yang Y, Xue S, Bao Y. Structural and enzymatic characterization of acetolactate decarboxylase from Bacillus subtilis. Appl Microbiol Biotechnol 2018; 102:6479-6491. [DOI: 10.1007/s00253-018-9049-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 04/20/2018] [Accepted: 04/24/2018] [Indexed: 11/25/2022]
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25
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Garba L, Mohamad Yussoff MA, Abd Halim KB, Ishak SNH, Mohamad Ali MS, Oslan SN, Raja Abd Rahman RNZ. Homology modeling and docking studies of a Δ9-fatty acid desaturase from a Cold-tolerant Pseudomonas sp. AMS8. PeerJ 2018; 6:e4347. [PMID: 29576935 PMCID: PMC5863719 DOI: 10.7717/peerj.4347] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 01/19/2018] [Indexed: 01/02/2023] Open
Abstract
Membrane-bound fatty acid desaturases perform oxygenated desaturation reactions to insert double bonds within fatty acyl chains in regioselective and stereoselective manners. The Δ9-fatty acid desaturase strictly creates the first double bond between C9 and 10 positions of most saturated substrates. As the three-dimensional structures of the bacterial membrane fatty acid desaturases are not available, relevant information about the enzymes are derived from their amino acid sequences, site-directed mutagenesis and domain swapping in similar membrane-bound desaturases. The cold-tolerant Pseudomonas sp. AMS8 was found to produce high amount of monounsaturated fatty acids at low temperature. Subsequently, an active Δ9-fatty acid desaturase was isolated and functionally expressed in Escherichia coli. In this paper we report homology modeling and docking studies of a Δ9-fatty acid desaturase from a Cold-tolerant Pseudomonas sp. AMS8 for the first time to the best of our knowledge. Three dimensional structure of the enzyme was built using MODELLER version 9.18 using a suitable template. The protein model contained the three conserved-histidine residues typical for all membrane-bound desaturase catalytic activity. The structure was subjected to energy minimization and checked for correctness using Ramachandran plots and ERRAT, which showed a good quality model of 91.6 and 65.0%, respectively. The protein model was used to preform MD simulation and docking of palmitic acid using CHARMM36 force field in GROMACS Version 5 and Autodock tool Version 4.2, respectively. The docking simulation with the lowest binding energy, -6.8 kcal/mol had a number of residues in close contact with the docked palmitic acid namely, Ile26, Tyr95, Val179, Gly180, Pro64, Glu203, His34, His206, His71, Arg182, Thr85, Lys98 and His177. Interestingly, among the binding residues are His34, His71 and His206 from the first, second, and third conserved histidine motif, respectively, which constitute the active site of the enzyme. The results obtained are in compliance with the in vivo activity of the Δ9-fatty acid desaturase on the membrane phospholipids.
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Affiliation(s)
- Lawal Garba
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.,Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.,Department of Microbiology, Faculty of Science, Gombe State University, Gombe, Gombe State, Nigeria
| | - Mohamad Ariff Mohamad Yussoff
- Department of Biotechnology, Kulliyyah of Science, International Islamic University Malaysia, Kuantan, Pahang Darul Makmur, Malaysia
| | - Khairul Bariyyah Abd Halim
- Department of Biotechnology, Kulliyyah of Science, International Islamic University Malaysia, Kuantan, Pahang Darul Makmur, Malaysia
| | - Siti Nor Hasmah Ishak
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.,Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Siti Nurbaya Oslan
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.,Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.,Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
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26
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Huang Y, Yang Z, Xu H, Zhang P, Gao Z, Li H. Insulin enhances the peroxidase activity of heme by forming heme-insulin complex: Relevance to type 2 diabetes mellitus. Int J Biol Macromol 2017; 102:1009-1015. [DOI: 10.1016/j.ijbiomac.2017.04.113] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 04/26/2017] [Accepted: 04/28/2017] [Indexed: 12/12/2022]
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Dong LH, Cao XR. Studies of the Interaction of Influenza Virus RNA Polymerase PA N with Endonuclease Inhibitors. Interdiscip Sci 2017. [PMID: 28631174 DOI: 10.1007/s12539-017-0239-2] [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] [Indexed: 11/29/2022]
Abstract
Influenza virus is a major causative agent of respiratory viral infections, and RNA polymerase catalyzes its replication and transcription activities in infected cell nuclei. Since it is highly conserved in all virus strains, RNA polymerase becomes a key target of anti-influenza virus agents. Although experimental studies have revealed the good inhibitory activity of endonuclease inhibitors to RNA polymerase, the mechanism is still unclear. In this study, the docking and molecular dynamics simulations have been performed to explore the interaction of three kinds of endonuclease inhibitors with the subunit (PAN) of RNA polymerase. Our calculations indicate that all these endonuclease inhibitors can bind to the binding pocket of PAN, in which the electronegative oxygen atoms of the inhibitors form a chelated structure with the two Mn2+ cations of the active center. The most important interaction between these inhibitors and PAN is electrostatic interaction. The electron density of the chelate oxygen atoms determines the magnitude of the electrostatic energy, and the chelated structure and orientation of inhibitors depend largely on the distance between the chelate oxygen atoms.
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Affiliation(s)
- Li-Hua Dong
- School of Chemistry and Chemical Engineering, Qilu Normal University, Jinan, 250200, China.
| | - Xiao-Rong Cao
- School of Chemistry and Chemical Engineering, Qilu Normal University, Jinan, 250200, China
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28
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Nawaz H, Waseem A, Zia‐ur‐Rehman, Nafees M, Arshad MN, Rashid U. Synthesis, characterization, cytotoxicity and computational studies of new phosphine‐ and carbodithioate‐based palladium(II) complexes. Appl Organomet Chem 2017. [DOI: 10.1002/aoc.3771] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Hamid Nawaz
- Department of ChemistryQuaid‐i‐Azam University Islamabad 45320 Pakistan
| | - Amir Waseem
- Department of ChemistryQuaid‐i‐Azam University Islamabad 45320 Pakistan
| | - Zia‐ur‐Rehman
- Department of ChemistryQuaid‐i‐Azam University Islamabad 45320 Pakistan
| | - Muhammad Nafees
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical EngineeringNanjing University Nanjing 210093 China
| | | | - Umer Rashid
- Department of ChemistryCOMSATS Institute of Information Technology Abbottabad 22060 Pakistan
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29
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Wang Y, Jiang Y, Yin Y, Liu J, Ding L, Liu J, Zhang T. Identification and Inhibitory Mechanism of Angiotensin I-Converting Enzyme Inhibitory Peptides Derived from Bovine Hemoglobin. Protein J 2017; 36:166-173. [DOI: 10.1007/s10930-017-9708-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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30
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Captopril/enalapril inhibit promiscuous esterase activity of carbonic anhydrase at micromolar concentrations: An in vitro study. Chem Biol Interact 2017; 265:24-35. [PMID: 28126276 DOI: 10.1016/j.cbi.2017.01.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 12/30/2016] [Accepted: 01/19/2017] [Indexed: 11/23/2022]
Abstract
The inhibitory activity of captopril, a thiol-containing competitive inhibitor of the angiotensin-converting enzyme, ACE, against esterase activity of carbonic anhydrase, CA was investigated. This small molecule, as well as enalapril, was selected in order to represents both thiol and carboxylate, as two well-known metal binding functional groups of metalloprotein inhibitors. Since captopril, has also been observed to inhibit other metalloenzymes such as tyrosinase and metallo-beta lactamase through binding to the catalytic metal ions and regarding CA as a zinc-containing metallo-enzyme, in the current study, we set out to determine whether captopril/enalapril inhibit CA esterase activity of the purified human CA II or not? Then, we revealed the inhibitors' potencies (IC50, Ki and Kdiss values) and also mode of inhibition. Our results also showed that enalapril is more potent CA inhibitor than captopril. Since enalapril represents no sulfhydryl moiety, thus carboxylate group may have a determinant role in inhibiting of CA esterase activity, the conclusion confirmed by molecular docking studies. Additionally, since CA inhibitory potencies of captopril/enalapril were much lower than those of classic sulfonamide drugs, the findings of the current study may explain why these drugs exhibit no effective CA inhibition at the concentrations reached in vivo and also may shed light on the way of generating new class of inhibitors that will discriminately inhibit various CA isoforms.
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Degradation products of the artificial azo dye, Allura red, inhibit esterase activity of carbonic anhydrase II: A basic in vitro study on the food safety of the colorant in terms of enzyme inhibition. Food Chem 2016; 213:494-504. [DOI: 10.1016/j.foodchem.2016.06.078] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 06/07/2016] [Accepted: 06/23/2016] [Indexed: 11/18/2022]
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32
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Kravchuk VO, Savytskyi OV, Odynets KO, Mykuliak VV, Kornelyuk AI. Computational modeling and molecular dynamics simulations of mammalian cytoplasmic tyrosyl-tRNA synthetase and its complexes with substrates. J Biomol Struct Dyn 2016; 35:2772-2788. [PMID: 27615678 DOI: 10.1080/07391102.2016.1235512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Cytoplasmic tyrosyl-tRNA synthetase (TyrRS) is one of the key enzymes of protein biosynthesis. TyrRSs of pathogenic organisms have gained attention as potential targets for drug development. Identifying structural differences between various TyrRSs will facilitate the development of specific inhibitors for the TyrRSs of pathogenic organisms. However, there is a deficiency in structural data for mammalian cytoplasmic TyrRS in complexes with substrates. In this work, we constructed spatial structure of full-length Bos taurus TyrRS (BtTyrRS) and its complexes with substrates using the set of computational modeling techniques. Special attention was paid to BtTyrRS complexes with substrates [L-tyrosine, K+ and ATP:Mg2+] and intermediate products [tyrosyl-adenylate (Tyr-AMP), K+ and PPi:Mg2+] with the different catalytic loop conformations. In order to analyze their dynamical properties, we performed 100 ns of molecular dynamics (MD) simulations. MD simulations revealed new structural data concerning the tyrosine activation reaction in mammalian TyrRS. Formation of strong interaction between Lys154 and γ-phosphate suggests the additional role of CP1 insertion as an important factor for ATP binding. The presence of a potassium-binding pocket within the active site of mammalian TyrRS compensates the absence of the second lysine in the KMSKS motif. Our data provide new details concerning a role of K+ ions at different stages of the first step of the tyrosylation reaction, including the coordination of substrates and involvement in the PPi releasing. The results of this work suggest that differences between ATP-binding sites of mammalian and bacterial TyrRSs are meaningful and could be exploited in the drug design.
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Affiliation(s)
- Vladyslav O Kravchuk
- a Department of Protein Engineering and Bioinformatics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150, Akademika Zabolotnogo Str., Kyiv , 03143 , Ukraine.,b Department of Biotechnology , National Aviation University , 1, Kosmonavta Komarova Str., Kyiv , 03058 , Ukraine
| | - Oleksandr V Savytskyi
- a Department of Protein Engineering and Bioinformatics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150, Akademika Zabolotnogo Str., Kyiv , 03143 , Ukraine
| | - Konstantin O Odynets
- a Department of Protein Engineering and Bioinformatics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150, Akademika Zabolotnogo Str., Kyiv , 03143 , Ukraine
| | - Vasyl V Mykuliak
- a Department of Protein Engineering and Bioinformatics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150, Akademika Zabolotnogo Str., Kyiv , 03143 , Ukraine.,c Institute of High Technologies , Taras Shevchenko National University of Kyiv , 64, Volodymyrs'ka Str., Kyiv , 01601 , Ukraine
| | - Alexander I Kornelyuk
- a Department of Protein Engineering and Bioinformatics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150, Akademika Zabolotnogo Str., Kyiv , 03143 , Ukraine.,c Institute of High Technologies , Taras Shevchenko National University of Kyiv , 64, Volodymyrs'ka Str., Kyiv , 01601 , Ukraine
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33
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Kumar R, Gupta D. Identification of CYP1B1-specific candidate inhibitors using combination ofin silicoscreening, integrated knowledge-based filtering, and molecular dynamics simulations. Chem Biol Drug Des 2016; 88:730-739. [DOI: 10.1111/cbdd.12803] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 06/09/2016] [Accepted: 06/12/2016] [Indexed: 01/03/2023]
Affiliation(s)
- Rakesh Kumar
- Translational Bioinformatics Group; International Centre for Genetic Engineering and Biotechnology (ICGEB); New Delhi Delhi India
| | - Dinesh Gupta
- Translational Bioinformatics Group; International Centre for Genetic Engineering and Biotechnology (ICGEB); New Delhi Delhi India
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34
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Schein CH, Rowold D, Choi KH. Allosteric inhibitors of Coxsackie virus A24 RNA polymerase. Bioorg Med Chem 2016; 24:570-7. [PMID: 26762834 PMCID: PMC4743507 DOI: 10.1016/j.bmc.2015.12.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 12/04/2015] [Accepted: 12/14/2015] [Indexed: 10/22/2022]
Abstract
Coxsackie virus A24 (CVA24), a causative agent of acute hemorrhagic conjunctivitis, is a prototype of enterovirus (EV) species C. The RNA polymerase (3D(pol)) of CVA24 can uridylylate the viral peptide linked to the genome (VPg) from distantly related EV and is thus, a good model for studying this reaction. Once UMP is bound, VPgpU primes RNA elongation. Structural and mutation data have identified a conserved binding surface for VPg on the RNA polymerase (3D(pol)), located about 20Å from the active site. Here, computational docking of over 60,000 small compounds was used to select those with the lowest (best) specific binding energies (BE) for this allosteric site. Compounds with varying structures and low BE were assayed for their effect on formation of VPgU by CVA24-3D(pol). Two compounds with the lowest specific BE for the site inhibited both uridylylation and formation of VPgpolyU at 10-20μM. These small molecules can be used to probe the role of this allosteric site in polymerase function, and may be the basis for novel antiviral compounds.
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Affiliation(s)
- Catherine H Schein
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd, Box 7, Alachua, FL 32616, United States; Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, United States.
| | - Diane Rowold
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd, Box 7, Alachua, FL 32616, United States
| | - Kyung H Choi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, United States; Sealy Center for Structural Biology and Molecular Biophysics, UTMB, United States
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35
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Gupta S, Jadaun A, Kumar H, Raj U, Varadwaj PK, Rao A. Exploration of new drug-like inhibitors for serine/threonine protein phosphatase 5 ofPlasmodium falciparum: a docking and simulation study. J Biomol Struct Dyn 2015; 33:2421-41. [DOI: 10.1080/07391102.2015.1051114] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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36
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Kolomytseva M, Ferraroni M, Chernykh A, Golovleva L, Scozzafava A. Structural basis for the substrate specificity and the absence of dehalogenation activity in 2-chloromuconate cycloisomerase from Rhodococcus opacus 1CP. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1541-9. [DOI: 10.1016/j.bbapap.2014.04.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 04/09/2014] [Accepted: 04/13/2014] [Indexed: 11/26/2022]
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37
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Lindstad RI, Teigen K, Skjeldal L. Inhibition of sorbitol dehydrogenase by nucleosides and nucleotides. Biochem Biophys Res Commun 2013; 435:202-8. [PMID: 23665021 DOI: 10.1016/j.bbrc.2013.04.081] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 04/16/2013] [Indexed: 11/19/2022]
Abstract
Sorbitol dehydrogenase inhibitors have been found to prevent, or alleviate, various secondary complications of diabetes mellitus. In the present study, the effects of nucleosides and nucleotides on the rate of sorbitol oxidation catalyzed by the sheep liver enzyme were studied by steady-state kinetics at pH 7.4. Various such compounds, including ATP and the 2'-deoxy-analogues of ATP, ADP and AMP, reversibly inhibit enzyme activity by formation of enzyme-coenzyme-inhibitor ternary complexes. In each case, no deviations from linearity were seen in the double-reciprocal plots using sorbitol or NAD(+) as the varied substrate and there was a linear relationship between inhibitor concentration and the observed inhibitory effects. Sorbitol was docked into a model of the sheep SDH-NAD(+) complex based upon the structure of the human SDH-NAD(+) holoenzyme. The resulting structure of the ternary complex of sheep SDH, NAD(+) and sorbitol (PMDB ID code PM 0078068) shows that the reactive C-2 hydroxyl group of sorbitol is oriented toward the 4'-position of the nicotinamide moiety of the coenzyme, and that the adjacent primary hydroxyl group of sorbitol interacts with the catalytic zinc. The results indicate that the ribose moiety of the inhibitor structures is an important determinant for the observed effects. Specifically, the 2'-position of the ribose ring exerts an effect with respect to inhibitor potency.
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Affiliation(s)
- Rune I Lindstad
- Institute of Chemistry, Biotechnology and Food Science (IKBM), Norwegian University of Life Sciences,Ås, Norway
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38
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Wang H, Liu P, Xie H. An empirical molecular docking study of a di-iron binding protein with iron ions. ACTA ACUST UNITED AC 2013. [DOI: 10.1631/jzus.c1200072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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39
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Abstract
Antibiotic treatment may fail to protect individuals, if not started early enough, after infection with Bacillus anthracis, due to the continuing activity of toxins that the bacterium produces. Stable and easily stored inhibitors of the edema factor toxin (EF), an adenylyl cyclase, could save lives in the event of an outbreak, due to natural causes or a bioweapon attack. The toxin’s basic activity is to convert ATP to cAMP, and it is thus in principle a simple phosphatase, which means that many mammalian enzymes, including intracellular adenylcyclases, may have a similar activity. While nucleotide based inhibitors, similar to its natural substrate, ATP, were identified early, these compounds had low activity and specificity for EF. We used a combined structural and computational approach to choose small organic molecules in large, web-based compound libraries that would, based on docking scores, bind to residues within the substrate binding pocket of EF. A family of fluorenone-based inhibitors was identified that inhibited the release of cAMP from cells treated with EF. The lead inhibitor was also shown to inhibit the diarrhea caused by enterotoxigenic E. coli (ETEC) in a murine model, perhaps by serving as a quorum sensor. These inhibitors are now being tested for their ability to inhibit Anthrax infection in animal models and may have use against other pathogens that produce toxins similar to EF, such as Bordetella pertussis or Vibrio cholera.
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40
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Liu Y, Zhao L, Li W, Zhao D, Song M, Yang Y. FIPSDock: A new molecular docking technique driven by fully informed swarm optimization algorithm. J Comput Chem 2012; 34:67-75. [DOI: 10.1002/jcc.23108] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Revised: 07/22/2012] [Accepted: 08/05/2012] [Indexed: 11/12/2022]
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41
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Chen D, Ma L, Kanalas JJ, Gao J, Pawlik J, Jimenez ME, Walter MA, Peterson JW, Gilbertson SR, Schein CH. Structure-based redesign of an edema toxin inhibitor. Bioorg Med Chem 2012; 20:368-76. [PMID: 22154558 PMCID: PMC3251925 DOI: 10.1016/j.bmc.2011.10.091] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 10/17/2011] [Accepted: 10/25/2011] [Indexed: 11/17/2022]
Abstract
Edema factor (EF) toxin of Bacillus anthracis (NIAID category A), and several other toxins from NIAID category B Biodefense target bacteria are adenylyl cyclases or adenylyl cyclase agonists that catalyze the conversion of ATP to 3',5'-cyclic adenosine monophosphate (cAMP). We previously identified compound 1 (3-[(9-oxo-9H-fluorene-1-carbonyl)-amino]-benzoic acid), that inhibits EF activity in cultured mammalian cells, and reduces diarrhea caused by enterotoxigenic Escherichia coli (ETEC) at an oral dosage of 15μg/mouse. Here, molecular docking was used to predict improvements in potency and solubility of new derivatives of compound 1 in inhibiting edema toxin (ET)-catalyzed stimulation of cyclic AMP production in murine monocyte-macrophage cells (RAW 264.7). Structure-activity relationship (SAR) analysis of the bioassay results for 22 compounds indicated positions important for activity. Several derivatives demonstrated superior pharmacological properties compared to our initial lead compound, and are promising candidates to treat anthrax infections and diarrheal diseases induced by toxin-producing bacteria.
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Affiliation(s)
- Deliang Chen
- Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, UTMB, Galveston, TX 77555-0857, USA
| | - Lili Ma
- Department of Chemistry, University of Houston. Houston, TX 77004, USA
| | | | - Jian Gao
- Mission Pharmacal Company, San Antonio, TX USA
| | - Jennifer Pawlik
- Sealy Center for Vaccine Development, Center for Biodefense and Emerging Infections, UTMB, Galveston, TX 77555, USA
- Department of Microbiology and Immunology, UTMB, Galveston, TX 77555-1070, USA
| | | | | | - Johnny W. Peterson
- Sealy Center for Vaccine Development, Center for Biodefense and Emerging Infections, UTMB, Galveston, TX 77555, USA
- Department of Microbiology and Immunology, UTMB, Galveston, TX 77555-1070, USA
| | | | - Catherine H. Schein
- Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, UTMB, Galveston, TX 77555-0857, USA
- Sealy Center for Vaccine Development, Center for Biodefense and Emerging Infections, UTMB, Galveston, TX 77555, USA
- Department of Microbiology and Immunology, UTMB, Galveston, TX 77555-1070, USA
- Member, Institute for Translational Studies, UTMB
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42
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Inhibition of melanogenesis by 5,7-dihydroxyflavone (chrysin) via blocking adenylyl cyclase activity. Biochem Biophys Res Commun 2011; 411:121-5. [DOI: 10.1016/j.bbrc.2011.06.108] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Accepted: 06/16/2011] [Indexed: 01/17/2023]
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43
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Bruce NJ, Chen D, Dastidar SG, Marks GE, Schein CH, Bryce RA. Molecular dynamics simulations of Aβ fibril interactions with β-sheet breaker peptides. Peptides 2010; 31:2100-8. [PMID: 20691234 DOI: 10.1016/j.peptides.2010.07.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Revised: 07/26/2010] [Accepted: 07/26/2010] [Indexed: 01/21/2023]
Abstract
Accumulation and aggregation of the 42-residue amyloid-β (Aβ) protein fragment, which originates from the cleavage of amyloid precursor protein by β and γ secretase, correlates with the pathology of Alzheimer's disease (AD). Possible therapies for AD include peptides based on the Aβ sequence, and recently identified small molecular weight compounds designed to mimic these, that interfere with the aggregation of Aβ and prevent its toxic effects on neuronal cells in culture. Here, we use molecular dynamics simulations to compare the mode of interaction of an active (LPFFD) and inactive (LHFFD) β-sheet breaker peptide with an Aβ fibril structure from solid-state NMR studies. We found that LHFFD had a weaker interaction with the fibril than the active peptide, LPFFD, from geometric and energetic considerations, as estimated by the MM/PBSA approach. Cluster analysis and computational alanine scanning identified important ligand-fibril contacts, including a possible difference in the effect of histidine on ligand-fibril π-stacking interactions, and the role of the proline residue in establishing contacts that compete with those essential for maintenance of the inter-monomer β-sheet structure of the fibril. Our results show that molecular dynamics simulations can be a useful way to classify the stability of docking sites. These mechanistic insights into the ability of LPFFD to reverse aggregation of toxic Aβ will guide the redesign of lead compounds, and aid in developing realistic therapies for AD and other diseases of protein aggregation.
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Affiliation(s)
- Neil J Bruce
- School of Pharmacy and Pharmaceutical Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK.
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44
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Ling B, Zhang R, Wang Z, Dong L, Liu Y, Zhang C, Liu C. Theoretical studies on the interaction of guanine riboswitch with guanine and its closest analogues. MOLECULAR SIMULATION 2010. [DOI: 10.1080/08927022.2010.492833] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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45
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Bouzianas DG. Current and future medical approaches to combat the anthrax threat. J Med Chem 2010; 53:4305-31. [PMID: 20102155 DOI: 10.1021/jm901024b] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Dimitrios G Bouzianas
- Laboratory of Molecular Endocrinology, Division of Endocrinology and Metabolism, AHEPA University Hospital, 1 S. Kyriakidi Street, P.C. 54636, Thessaloniki, Macedonia, Greece.
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46
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Martínez L, Laine E, Malliavin TE, Nilges M, Blondel A. ATP conformations and ion binding modes in the active site of anthrax edema factor: a computational analysis. Proteins 2010; 77:971-83. [PMID: 19705488 DOI: 10.1002/prot.22523] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The Edema Factor (EF), one of the virulence factors of anthrax, is an adenylyl cyclase that promotes the overproduction of cyclic-AMP (cAMP) from ATP, and therefore perturbs cell signaling. Crystallographic structures of EF bound to ATP analogs and reaction products, cyclic-AMP, and Pyrophosphate (PPi), revealed different substrate conformations and catalytic-cation binding modes, one or two cations being observed in the active site. To shed light into the biological significance of these crystallographic structures, the energetics, geometry, and dynamics of the active site are analyzed using molecular dynamics simulations. The ATP conformation observed in the one-metal-ion structure allows stronger interactions with the catalytic ion, and ATP is more restrained than in the structure containing two Mg(2+) ions. Therefore, we propose that the conformation observed in the one-ion crystal structure is a more probable starting point for the reaction. The simulations also suggest that a C3'-endo sugar pucker facilitates nucleophilic attack. Additionally, the two-cation binding mode restrains the mobility of the reaction products, and thus their tendency to dissociate.
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Affiliation(s)
- Leandro Martínez
- Unité de Bioinformatique Structurale, URA CNRS 2185, Institut Pasteur, Paris, France
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47
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Testing the efficacy and toxicity of adenylyl cyclase inhibitors against enteric pathogens using in vitro and in vivo models of infection. Infect Immun 2010; 78:1740-9. [PMID: 20123712 DOI: 10.1128/iai.01114-09] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Enterotoxigenic Escherichia coli (ETEC) produces the ADP-ribosyltransferase toxin known as heat-labile enterotoxin (LT). In addition to the toxic effect of LT resulting in increases of cyclic AMP (cAMP) and disturbance of cellular metabolic processes, this toxin promotes bacterial adherence to intestinal epithelial cells (A. M. Johnson, R. S. Kaushik, D. H. Francis, J. M. Fleckenstein, and P. R. Hardwidge, J. Bacteriol. 191:178-186, 2009). Therefore, we hypothesized that the identification of a compound that inhibits the activity of the toxin would have a suppressive effect on the ETEC colonization capabilities. Using in vivo and in vitro approaches, we present evidence demonstrating that a fluorenone-based compound, DC5, which inhibits the accumulation of cAMP in intoxicated cultured cells, significantly decreases the colonization abilities of adenylyl cyclase toxin-producing bacteria, such as ETEC. These findings established that DC5 is a potent inhibitor both of toxin-induced cAMP accumulation and of ETEC adherence to epithelial cells. Thus, DC5 may be a promising compound for treatment of diarrhea caused by ETEC and other adenylyl cyclase toxin-producing bacteria.
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48
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Zhang G. Design andin silicoscreening of inhibitors of the cholera toxin. Expert Opin Drug Discov 2009; 4:923-38. [DOI: 10.1517/17460440903186118] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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49
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Chen D, Martin ZS, Soto C, Schein CH. Computational selection of inhibitors of Abeta aggregation and neuronal toxicity. Bioorg Med Chem 2009; 17:5189-97. [PMID: 19540126 PMCID: PMC2743868 DOI: 10.1016/j.bmc.2009.05.047] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2009] [Revised: 05/13/2009] [Accepted: 05/18/2009] [Indexed: 11/18/2022]
Abstract
Alzheimer's disease (AD) is characterized by the cerebral accumulation of misfolded and aggregated amyloid-beta protein (Abeta). Disease symptoms can be alleviated, in vitro and in vivo, by 'beta-sheet breaker' pentapeptides that reduce plaque load. However the peptide nature of these compounds, made them biologically unstable and unable to penetrate membranes with high efficiency. The main goal of this study was to use computational methods to identify small molecule mimetics with better drug-like properties. For this purpose, the docked conformations of the active peptides were used to identify compounds with similar activities. A series of related beta-sheet breaker peptides were docked to solid state NMR structures of a fibrillar form of Abeta. The lowest energy conformations of the active peptides were used to design three dimensional (3D)-pharmacophores, suitable for screening the NCI database with Unity. Small molecular weight compounds with physicochemical features and a conformation similar to the active peptides were selected, ranked by docking and biochemical parameters. Of 16 diverse compounds selected for experimental screening, 2 prevented and reversed Abeta aggregation at 2-3microM concentration, as measured by Thioflavin T (ThT) fluorescence and ELISA assays. They also prevented the toxic effects of aggregated Abeta on neuroblastoma cells. Their low molecular weight and aqueous solubility makes them promising lead compounds for treating AD.
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Affiliation(s)
- Deliang Chen
- Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, UTMB, Galveston, TX 77555-0857, USA
| | - Zane S. Martin
- George and Cynthia Mitchell Center for Neurodegenerative diseases, Department of Neurology, Neurosciences & Cell Biology UTMB, Galveston TX 77555-1045, USA
| | - Claudio Soto
- George and Cynthia Mitchell Center for Neurodegenerative diseases, Department of Neurology, Neurosciences & Cell Biology UTMB, Galveston TX 77555-1045, USA
- Department of Neurology, University of Texas Medical School at Houston. Houston, TX 77030, USA
| | - Catherine H. Schein
- Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, UTMB, Galveston, TX 77555-0857, USA
- Department of Microbiology and Immunology, and Sealy Center for Vaccine Development, UTMB, Galveston, TX 77555-0857, USA
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Familiar O, Munier‐Lehmann H, Negri A, Gago F, Douguet D, Rigouts L, Hernández A, Camarasa M, Pérez‐Pérez M. Exploring Acyclic Nucleoside Analogues as Inhibitors ofMycobacterium tuberculosisThymidylate Kinase. ChemMedChem 2008; 3:1083-93. [DOI: 10.1002/cmdc.200800060] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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