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Bhardwaj T, Haque S, Somvanshi P. Comparative assessment of the therapeutic drug targets of C. botulinum ATCC 3502 and C. difficile str. 630 using in silico subtractive proteomics approach. J Cell Biochem 2019; 120:16160-16184. [PMID: 31081164 DOI: 10.1002/jcb.28897] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 02/11/2019] [Accepted: 02/14/2019] [Indexed: 12/13/2022]
Abstract
Growing antimicrobial resistance of the pathogens against multiple drugs posed a serious threat to the human health worldwide. This fueled the need of identifying the novel therapeutic targets that can be used for developing new class of the drugs. Recently, there is a substantial rise in the rate of Clostridium infections as well as in the emergence of virulent and antibiotic resistant strains. Hence, there is an urgent need for the identification of potential therapeutic targets and the development of new drugs for the treatment and prevention of Clostridium infections. In the present study, a combinatorial approach involving systems biology and comparative genomics strategy was tested against Clostridium botulinum ATCC 3502 and Clostridium difficile str. 630 pathogens, to render potential therapeutic target at qualitative and quantitative level. This resulted in the identification of five common (present in both the pathogens, 34 in C. botulinum ATCC 3502 and 42 in C. difficile str. 630) drug targets followed by virtual screening-based identification of potential inhibitors employing molecular docking and molecular dynamics simulations. The identified targets will provide a solid platform for the designing of novel wide-spectrum lead compounds capable of inhibiting their catalytic activities against multidrug-resistant Clostridium in the near future.
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Affiliation(s)
- Tulika Bhardwaj
- Department of Biotechnology, TERI School of Advanced Studies, Vasant Kunj, India
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Pallavi Somvanshi
- Department of Biotechnology, TERI School of Advanced Studies, Vasant Kunj, India
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2
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Manhas A, Patel D, Lone MY, Jha PC. Identification of natural compound inhibitors against PfDXR: A hybrid structure-based molecular modeling approach and molecular dynamics simulation studies. J Cell Biochem 2019; 120:14531-14543. [PMID: 30994966 DOI: 10.1002/jcb.28714] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 01/18/2019] [Accepted: 01/24/2019] [Indexed: 12/30/2022]
Abstract
In the present contribution, multicomplex-based pharmacophore studies were carried out on the structural proteome of Plasmodium falciparum 1-deoxy-D-xylulose-5-phosphate reductoisomerase. Among the constructed models, a representative model with complementary features, accountable for the inhibition was used as a primary filter for the screening of database molecules. Auxiliary evaluations of the screened molecules were performed via drug-likeness and molecular docking studies. Subsequently, the stability of the docked inhibitors was envisioned by molecular dynamics simulations, principle component analysis, and molecular mechanics-Poisson-Boltzmann surface area-based free binding energy calculations. The stability assessment of the hits was done by comparing with the reference (beta-substituted fosmidomycin analog, LC5) to prioritize more potent candidates. All the complexes showed stable dynamic behavior while three of them displayed higher binding free energy compared with the reference. The work resulted in the identification of the compounds with diverse scaffolds, which could be used as initial leads for the design of novel PfDXR inhibitors.
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Affiliation(s)
- Anu Manhas
- School of Chemical Sciences, Central University of Gujarat, Gandhinagar, Gujarat, India
| | - Dhaval Patel
- Department of Bioinformatics and Stśructural Biology, Indian Institute of Advanced Research, Gujarat, India
| | - Mohsin Y Lone
- School of Chemical Sciences, Central University of Gujarat, Gandhinagar, Gujarat, India.,Department of Chemistry, Indian Institute of Technology, Gandhinagar, Gujarat, India
| | - Prakash C Jha
- Centre for Applied Chemistry, Central University of Gujarat, Gandhinagar, Gujarat, India
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3
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Ussin NK, Bagnell AM, Offermann LR, Abdulsalam R, Perdue ML, Magee P, Chruszcz M. Structural characterization of 1-deoxy-D-xylulose 5-phosphate Reductoisomerase from Vibrio vulnificus. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:1209-1215. [PMID: 30278288 DOI: 10.1016/j.bbapap.2018.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 09/20/2018] [Accepted: 09/25/2018] [Indexed: 10/28/2022]
Abstract
Vibrio vulnificus, a gram-negative bacterium, is the leading cause of seafood-borne illnesses and mortality in the United States. Previous studies have identified metabolites 2-C-methylerythritol 4-phosphate (MEP) as being essential for V. vulnificus growth and function. It was shown that 1-deoxy-D-xylulose-5-phosphate reductoisomerase (Dxr) is a critical enzyme in the viability of V. vulnificus, and many other bacteria, as it catalyzes the rearrangement of 1-deoxy-D-xylulose-5-phosphate (Dxp) to 2-C-methylerythritol 4-phosphate (MEP) within the MEP pathway, found in plants and bacteria. The MEP pathway produces the isoprenoids, isopentenyl diphosphate and dimethylallyl pyrophosphate. In this study, we produced and structurally characterized V. vulnificus Dxr. The enzyme forms a dimeric assembly and contains a metal ion in the active site. Protein produced in Escherichia coli co-purifies with Mg2+ ions, however the Mg2+ cations may be substituted with Mn2+, as both of these metals may be utilized by Dxrs. These findings will provide a basis for the design of Dxr inhibitors that may find application as antimicrobial compounds.
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Affiliation(s)
- Nikita K Ussin
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States
| | - Anna M Bagnell
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States
| | - Lesa R Offermann
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States; Department of Chemistry, Davidson College, Davidson, NC 28035, United States
| | - Rawan Abdulsalam
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States
| | - Makenzie L Perdue
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States
| | - Patrick Magee
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States
| | - Maksymilian Chruszcz
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States.
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4
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Mechanism and inhibition of 1-deoxy-d-xylulose-5-phosphate reductoisomerase. Bioorg Chem 2014; 57:171-185. [DOI: 10.1016/j.bioorg.2014.06.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 06/06/2014] [Accepted: 06/09/2014] [Indexed: 12/23/2022]
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5
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Zinglé C, Tritsch D, Grosdemange-Billiard C, Rohmer M. Catechol–rhodanine derivatives: Specific and promiscuous inhibitors of Escherichia coli deoxyxylulose phosphate reductoisomerase (DXR). Bioorg Med Chem 2014; 22:3713-9. [DOI: 10.1016/j.bmc.2014.05.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 04/29/2014] [Accepted: 05/05/2014] [Indexed: 11/27/2022]
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6
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Chaudhary KK, Prasad CVSS. Virtual Screening of compounds to 1-deoxy-Dxylulose 5-phosphate reductoisomerase (DXR) from Plasmodium falciparum. Bioinformation 2014; 10:358-64. [PMID: 25097379 PMCID: PMC4110427 DOI: 10.6026/97320630010358] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 05/28/2014] [Accepted: 05/29/2014] [Indexed: 12/02/2022] Open
Abstract
The 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) protein (Gen Bank ID AAN37254.1) from Plasmodium falciparum is a
potential drug target. Therefore, it is of interest to screen DXR against a virtual library of compounds (at the ZINC database) for
potential binders as possible inhibitors. This exercise helped to choose 10 top ranking molecules with ZINC00200163 [N-(2,2di
methoxy ethyl)-6-methyl-2, 3, 4, 9-tetrahydro-1H-carbazol-1-amine] a having good fit (-6.43 KJ/mol binding energy) with the target
protein. Thus, ZINC00200163 is identified as a potential molecule for further comprehensive characterization and in-depth
analysis.
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Affiliation(s)
- Kamal Kumar Chaudhary
- Division of Applied Sciences & IRCB, Systems Biology lab, Indian Institute of Information Technology Allahabad, Deoghat, Jhalwa, Allahabad 211012, India
| | - C V S Siva Prasad
- Division of Applied Sciences & IRCB, Systems Biology lab, Indian Institute of Information Technology Allahabad, Deoghat, Jhalwa, Allahabad 211012, India
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Affiliation(s)
| | - Salim Al-Babili
- BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Eleanore T. Wurtzel
- The Graduate School and University Center, The City University of New York, New York, New York, USA
- Department of Biological Sciences, Lehman College, The City University of New York, Bronx, New York, USA
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8
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Hartmann M, Hemmerlin A, Gas-Pascual E, Gerber E, Tritsch D, Rohmer M, Bach TJ. The effect of MEP pathway and other inhibitors on the intracellular localization of a plasma membrane-targeted, isoprenylable GFP reporter protein in tobacco BY-2 cells. F1000Res 2013; 2:170. [PMID: 24555083 DOI: 10.12688/f1000research.2-170.v1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/01/2013] [Indexed: 11/20/2022] Open
Abstract
We have established anin vivovisualization system for the geranylgeranylation of proteins in a stably transformed tobacco BY-2 cell line, based on the expression of a dexamethasone-inducible GFP fused to the carboxy-terminal basic domain of the rice calmodulin CaM61, which naturally bears a CaaL geranylgeranylation motif (GFP-BD-CVIL). By using pathway-specific inhibitors it was demonstrated that inhibition of the methylerythritol phosphate (MEP) pathway with known inhibitors like oxoclomazone and fosmidomycin, as well as inhibition of the protein geranylgeranyltransferase type 1 (PGGT-1), shifted the localization of the GFP-BD-CVIL protein from the membrane to the nucleus. In contrast, the inhibition of the mevalonate (MVA) pathway with mevinolin did not affect the localization. During the present work, this test system has been used to examine the effect of newly designed inhibitors of the MEP pathway and inhibitors of sterol biosynthesis such as squalestatin, terbinafine and Ro48-8071. In addition, we also studied the impact of different post-prenylation inhibitors or those suspected to affect the transport of proteins to the plasma membrane on the localization of the geranylgeranylable fusion protein GFP-BD-CVIL.
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Affiliation(s)
- Michael Hartmann
- Département Réseaux Métaboliques, Institut de Biologie Moléculaire des Plantes, CNRS UPR 2357, Université de Strasbourg, F-67083 Strasbourg, France ; Current address: Institute of Biological Chemistry, Washington State University, Pullman WA, 99164-6340, USA
| | - Andrea Hemmerlin
- Département Réseaux Métaboliques, Institut de Biologie Moléculaire des Plantes, CNRS UPR 2357, Université de Strasbourg, F-67083 Strasbourg, France
| | - Elisabet Gas-Pascual
- Département Réseaux Métaboliques, Institut de Biologie Moléculaire des Plantes, CNRS UPR 2357, Université de Strasbourg, F-67083 Strasbourg, France ; Current address: Department of Horticulture and Crop Science, Ohio State University, Wooster OH, 44691, USA
| | - Esther Gerber
- Département Réseaux Métaboliques, Institut de Biologie Moléculaire des Plantes, CNRS UPR 2357, Université de Strasbourg, F-67083 Strasbourg, France ; Current address: Deinove SA, F-34830 Clapiers, France
| | - Denis Tritsch
- UMR 7177 CNRS, Laboratoire de Chimie et Biochimie des Microorganismes, Institut de Chimie de Strasbourg, Université de Strasbourg, F-67008 Strasbourg, France
| | - Michel Rohmer
- UMR 7177 CNRS, Laboratoire de Chimie et Biochimie des Microorganismes, Institut de Chimie de Strasbourg, Université de Strasbourg, F-67008 Strasbourg, France
| | - Thomas J Bach
- Département Réseaux Métaboliques, Institut de Biologie Moléculaire des Plantes, CNRS UPR 2357, Université de Strasbourg, F-67083 Strasbourg, France
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9
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Hartmann M, Hemmerlin A, Gas-Pascual E, Gerber E, Tritsch D, Rohmer M, Bach TJ. The effect of MEP pathway and other inhibitors on the intracellular localization of a plasma membrane-targeted, isoprenylable GFP reporter protein in tobacco BY-2 cells. F1000Res 2013; 2:170. [PMID: 24555083 PMCID: PMC3886798 DOI: 10.12688/f1000research.2-170.v2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/12/2013] [Indexed: 11/20/2022] Open
Abstract
We have established an
in vivo visualization system for the geranylgeranylation of proteins in a stably transformed tobacco BY-2 cell line, based on the expression of a dexamethasone-inducible GFP fused to the carboxy-terminal basic domain of the rice calmodulin CaM61, which naturally bears a CaaL geranylgeranylation motif (GFP-BD-CVIL). By using pathway-specific inhibitors it was demonstrated that inhibition of the methylerythritol phosphate (MEP) pathway with known inhibitors like oxoclomazone and fosmidomycin, as well as inhibition of the protein geranylgeranyltransferase type 1 (PGGT-1), shifted the localization of the GFP-BD-CVIL protein from the membrane to the nucleus. In contrast, the inhibition of the mevalonate (MVA) pathway with mevinolin did not affect the localization. During the present work, this test system has been used to examine the effect of newly designed inhibitors of the MEP pathway and inhibitors of sterol biosynthesis such as squalestatin, terbinafine and Ro48-8071. In addition, we also studied the impact of different post-prenylation inhibitors or those suspected to affect the transport of proteins to the plasma membrane on the localization of the geranylgeranylable fusion protein GFP-BD-CVIL.
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Affiliation(s)
- Michael Hartmann
- Département Réseaux Métaboliques, Institut de Biologie Moléculaire des Plantes, CNRS UPR 2357, Université de Strasbourg, F-67083 Strasbourg, France ; Current address: Institute of Biological Chemistry, Washington State University, Pullman WA, 99164-6340, USA
| | - Andrea Hemmerlin
- Département Réseaux Métaboliques, Institut de Biologie Moléculaire des Plantes, CNRS UPR 2357, Université de Strasbourg, F-67083 Strasbourg, France
| | - Elisabet Gas-Pascual
- Département Réseaux Métaboliques, Institut de Biologie Moléculaire des Plantes, CNRS UPR 2357, Université de Strasbourg, F-67083 Strasbourg, France ; Current address: Department of Horticulture and Crop Science, Ohio State University, Wooster OH, 44691, USA
| | - Esther Gerber
- Département Réseaux Métaboliques, Institut de Biologie Moléculaire des Plantes, CNRS UPR 2357, Université de Strasbourg, F-67083 Strasbourg, France ; Current address: Deinove SA, F-34830 Clapiers, France
| | - Denis Tritsch
- UMR 7177 CNRS, Laboratoire de Chimie et Biochimie des Microorganismes, Institut de Chimie de Strasbourg, Université de Strasbourg, F-67008 Strasbourg, France
| | - Michel Rohmer
- UMR 7177 CNRS, Laboratoire de Chimie et Biochimie des Microorganismes, Institut de Chimie de Strasbourg, Université de Strasbourg, F-67008 Strasbourg, France
| | - Thomas J Bach
- Département Réseaux Métaboliques, Institut de Biologie Moléculaire des Plantes, CNRS UPR 2357, Université de Strasbourg, F-67083 Strasbourg, France
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Awwad K, Desai A, Smith C, Sommerhalter M. Structural and functional characterization of a noncanonical nucleoside triphosphate pyrophosphatase from Thermotoga maritima. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:184-93. [PMID: 23385455 PMCID: PMC3565439 DOI: 10.1107/s0907444912044630] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 10/29/2012] [Indexed: 11/11/2022]
Abstract
The hyperthermophilic bacterium Thermotoga maritima has a noncanonical nucleoside triphosphatase that catalyzes the conversion of inosine triphosphate (ITP), deoxyinosine triphosphate (dITP) and xanthosine triphosphate (XTP) into inosine monophosphate (IMP), deoxyinosine monophosphate (IMP) and xanthosine monophosphate (XMP), respectively. The k(cat)/K(m) values determined at 323 and 353 K fall between 1.31 × 10(4) and 7.80 × 10(4) M(-1) s(-1). ITP and dITP are slightly preferred over XTP. Activity towards canonical nucleoside triphosphates (ATP and GTP) was not detected. The enzyme has an absolute requirement for Mg(2+) as a cofactor and has a preference for alkaline conditions. A protein X-ray structure of the enzyme with bound IMP was obtained at 2.15 Å resolution. The active site houses a well conserved network of residues that are critical for substrate recognition and catalysis. The crystal structure shows a tetramer with two possible dimer interfaces. One of these interfaces strongly resembles the dimer interface that is found in the structures of other noncanonical nucleoside pyrophosphatases from human (human ITPase) and archaea (Mj0226 and PhNTPase).
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Affiliation(s)
- Khaldeyah Awwad
- Chemistry and Biochemistry, California State University East Bay, 25800 Carlos Bee Boulevard, Hayward, CA 94542, USA
| | - Anna Desai
- Chemistry and Biochemistry, California State University East Bay, 25800 Carlos Bee Boulevard, Hayward, CA 94542, USA
| | - Clyde Smith
- Stanford Synchrotron Radiation Lightsource, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Monika Sommerhalter
- Chemistry and Biochemistry, California State University East Bay, 25800 Carlos Bee Boulevard, Hayward, CA 94542, USA
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11
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Tanaka N, Umeda T, Kusakabe Y, Nakanishi M, Kitade Y, T. Nakamura K. Structural Biology for Developing Antimalarial Compounds. YAKUGAKU ZASSHI 2013; 133:527-37. [DOI: 10.1248/yakushi.13-00001-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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12
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Katsuyama Y, Harmrolfs K, Pistorius D, Li Y, Müller R. Eine Semipinakol-Umlagerung - katalysiert durch ein Enzymsystem mit difunktioneller FAD-abhängiger Monooxygenase. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201204138] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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13
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Katsuyama Y, Harmrolfs K, Pistorius D, Li Y, Müller R. A Semipinacol Rearrangement Directed by an Enzymatic System Featuring Dual-Function FAD-Dependent Monooxygenase. Angew Chem Int Ed Engl 2012; 51:9437-40. [DOI: 10.1002/anie.201204138] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Indexed: 11/08/2022]
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He QF, Li D, Xu QY, Zheng S. Predicted essential proteins of Plasmodium falciparum for potential drug targets. ASIAN PAC J TROP MED 2012; 5:352-4. [PMID: 22546649 DOI: 10.1016/s1995-7645(12)60057-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2012] [Revised: 03/15/2012] [Accepted: 04/15/2012] [Indexed: 11/16/2022] Open
Abstract
OBJECTIVE To identify novel drug targets for treatment of Plasmodium falciparum. METHODS Local BLASTP were used to find the proteins non-homologous to human essential proteins as novel drug targets. Functional domains of novel drug targets were identified by InterPro and Pfam, 3D structures of potential drug targets were predicated by the SWISS-MODEL workspace. Ligands and ligand-binding sites of the proteins were searched by Ef-seek. RESULTS Three essential proteins were identified that might be considered as potential drug targets. AAN37254.1 belonged to 1-deoxy-D-xylulose 5-phosphate reductoisomerase, CAD50499.1 belonged to chorismate synthase, CAD51220.1 belonged to FAD binging 3 family, but the function of CAD51220.1 was unknown. The 3D structures, ligands and ligand-binding sites of AAN37254.1 and CAD50499.1 were successfully predicated. CONCLUSIONS Two of these potential drug targets are key enzymes in 2-C-methyl-d-erythritol 4-phosphate pathway and shikimate pathway, which are absent in humans, so these two essential proteins are good potential drug targets. The function and 3D structures of CAD50499.1 is still unknown, it still need further study.
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Affiliation(s)
- Qing-Feng He
- Department of Parasitology, Guangdong Medical College, Dongguan, Guangdong, China.
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15
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Pérez-Gil J, Calisto BM, Behrendt C, Kurz T, Fita I, Rodríguez-Concepción M. Crystal structure of Brucella abortus deoxyxylulose-5-phosphate reductoisomerase-like (DRL) enzyme involved in isoprenoid biosynthesis. J Biol Chem 2012; 287:15803-9. [PMID: 22442144 DOI: 10.1074/jbc.m112.354811] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Most bacteria use the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway for the synthesis of their essential isoprenoid precursors. The absence of the MEP pathway in humans makes it a promising new target for the development of much needed new and safe antimicrobial drugs. However, bacteria show a remarkable metabolic plasticity for isoprenoid production. For example, the NADPH-dependent production of MEP from 1-deoxy-D-xylulose 5-phosphate in the first committed step of the MEP pathway is catalyzed by 1-deoxy-D-xylulose-5-phosphate reductoisomerase (DXR) in most bacteria, whereas an unrelated DXR-like (DRL) protein was recently found to catalyze the same reaction in some organisms, including the emerging human and animal pathogens Bartonella and Brucella. Here, we report the x-ray crystal structures of the Brucella abortus DRL enzyme in its apo form and in complex with the broad-spectrum antibiotic fosmidomycin solved to 1.5 and 1.8 Å resolution, respectively. DRL is a dimer, with each polypeptide folding into three distinct domains starting with the NADPH-binding domain, in resemblance to the structure of bacterial DXR enzymes. Other than that, DRL and DXR show a low structural relationship, with a different disposition of the domains and a topologically unrelated C-terminal domain. In particular, the active site of DRL presents a unique arrangement, suggesting that the design of drugs that would selectively inhibit DRL-harboring pathogens without affecting beneficial or innocuous bacteria harboring DXR should be feasible. As a proof of concept, we identified two strong DXR inhibitors that have virtually no effect on DRL activity.
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Affiliation(s)
- Jordi Pérez-Gil
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG), Consejo Superior de Investigaciones Científicas (CSIC)-Institut de Recerca i Tecnologia Agroalimentàries (IRTA)-Universitat Autònoma de Barcelona (UAB), 08193 Barcelona, Spain
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16
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Björkelid C, Bergfors T, Unge T, Mowbray SL, Jones TA. Structural studies on Mycobacterium tuberculosis DXR in complex with the antibiotic FR-900098. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:134-43. [PMID: 22281742 DOI: 10.1107/s0907444911052231] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Accepted: 12/03/2011] [Indexed: 11/10/2022]
Abstract
A number of pathogens, including the causative agents of tuberculosis and malaria, synthesize the essential isoprenoid precursor isopentenyl diphosphate via the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway rather than the classical mevalonate pathway that is found in humans. As part of a structure-based drug-discovery program against tuberculosis, DXR, the enzyme that carries out the second step in the MEP pathway, has been investigated. This enzyme is the target for the antibiotic fosmidomycin and its active acetyl derivative FR-900098. The structure of DXR from Mycobacterium tuberculosis in complex with FR-900098, manganese and the NADPH cofactor has been solved and refined. This is a new crystal form that diffracts to a higher resolution than any other DXR complex reported to date. Comparisons with other ternary complexes show that the conformation is that of the enzyme in an active state: the active-site flap is well defined and the cofactor-binding domain has a conformation that brings the NADPH into the active site in a manner suitable for catalysis. The substrate-binding site is highly conserved in a number of pathogens that use this pathway, so any new inhibitor that is designed for the M. tuberculosis enzyme is likely to exhibit broad-spectrum activity.
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Affiliation(s)
- Christofer Björkelid
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
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Gräwert T, Groll M, Rohdich F, Bacher A, Eisenreich W. Biochemistry of the non-mevalonate isoprenoid pathway. Cell Mol Life Sci 2011; 68:3797-814. [PMID: 21744068 PMCID: PMC11114746 DOI: 10.1007/s00018-011-0753-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Revised: 05/26/2011] [Accepted: 06/14/2011] [Indexed: 02/08/2023]
Abstract
The non-mevalonate pathway of isoprenoid (terpenoid) biosynthesis is essential in many eubacteria including the major human pathogen, Mycobacterium tuberculosis, in apicomplexan protozoa including the Plasmodium spp. causing malaria, and in the plastids of plants. The metabolic route is absent in humans and is therefore qualified as a promising target for new anti-infective drugs and herbicides. Biochemical and structural knowledge about all enzymes involved in the pathway established the basis for discovery and development of inhibitors by high-throughput screening of compound libraries and/or structure-based rational design.
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Affiliation(s)
- Tobias Gräwert
- Department Chemie, Lehrstuhl für Biochemie, Center for Integrated Protein Science München, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Michael Groll
- Department Chemie, Lehrstuhl für Biochemie, Center for Integrated Protein Science München, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | | | - Adelbert Bacher
- Department Chemie, Lehrstuhl für Biochemie, Center for Integrated Protein Science München, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Wolfgang Eisenreich
- Department Chemie, Lehrstuhl für Biochemie, Center for Integrated Protein Science München, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
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de Ruyck J, Wouters J, Poulter CD. Inhibition Studies on Enzymes Involved in Isoprenoid Biosynthesis: Focus on Two Potential Drug Targets: DXR and IDI-2 Enzymes. ACTA ACUST UNITED AC 2011; 7. [PMID: 24339799 DOI: 10.2174/157340811796575317] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Isoprenoid compounds constitute an immensely diverse group of acyclic, monocyclic and polycyclic compounds that play important roles in all living organisms. Despite the diversity of their structures, this plethora of natural products arises from only two 5-carbon precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). This review will discuss the enzymes in the mevalonate (MVA) and methylerythritol phosphate (MEP) biosynthetic pathways leading to IPP and DMAPP with a particular focus on MEP synthase (DXR) and IPP isomerase (IDI), which are potential targets for the development of antibiotic compounds. DXR is the second enzyme in the MEP pathway and the only one for which inhibitors with antimicrobial activity at pharmaceutically relevant concentrations are known. All of the published DXR inhibitors are fosmidomycin analogues, except for a few bisphosphonates with moderate inhibitory activity. These far, there are no other candidates that target DXR. IDI was first identified and characterised over 40 years ago (IDI-1) and a second convergently evolved isoform (IDI-2) was discovered in 2001. IDI-1 is a metalloprotein found in Eukarya and many species of Bacteria. Its mechanism has been extensively studied. In contrast, IDI-2 requires reduced flavin mononucleotide as a cofactor. The mechanism of action for IDI-2 is less well defined. This review will describe how lead inhibitors are being improved by structure-based drug design and enzymatic assays against DXR to lead to new drug families and how mechanistic probes are being used to address questions about the mechanisms of the isomerases.
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Affiliation(s)
- Jérôme de Ruyck
- Department of Chemistry, University of Utah, 315 South 1400 East RM 2020, Salt Lake City, UT 84112, USA
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Umeda T, Tanaka N, Kusakabe Y, Nakanishi M, Kitade Y, Nakamura KT. Molecular basis of fosmidomycin's action on the human malaria parasite Plasmodium falciparum. Sci Rep 2011; 1:9. [PMID: 22355528 PMCID: PMC3216497 DOI: 10.1038/srep00009] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Revised: 04/05/2011] [Accepted: 04/05/2011] [Indexed: 11/30/2022] Open
Abstract
The human malaria parasite Plasmodium falciparum is responsible for the deaths of more than a million people each year. Fosmidomycin has been proven to be efficient in the treatment of P. falciparum malaria by inhibiting 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR), an enzyme of the non-mevalonate pathway, which is absent in humans. However, the structural details of DXR inhibition by fosmidomycin in P. falciparum are unknown. Here, we report the crystal structures of fosmidomycin-bound complete quaternary complexes of PfDXR. Our study revealed that (i) an intrinsic flexibility of the PfDXR molecule accounts for an induced-fit movement to accommodate the bound inhibitor in the active site and (ii) a cis arrangement of the oxygen atoms of the hydroxamate group of the bound inhibitor is essential for tight binding of the inhibitor to the active site metal. We expect the present structures to be useful guides for the design of more effective antimalarial compounds.
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Affiliation(s)
- Tomonobu Umeda
- School of Pharmacy, Showa University, Tokyo 142-8555, Japan
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