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Black WB, Zhang L, Mak WS, Maxel S, Cui Y, King E, Fong B, Sanchez Martinez A, Siegel JB, Li H. Engineering a nicotinamide mononucleotide redox cofactor system for biocatalysis. Nat Chem Biol 2020; 16:87-94. [PMID: 31768035 PMCID: PMC7546441 DOI: 10.1038/s41589-019-0402-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 10/07/2019] [Indexed: 01/29/2023]
Abstract
Biological production of chemicals often requires the use of cellular cofactors, such as nicotinamide adenine dinucleotide phosphate (NADP+). These cofactors are expensive to use in vitro and difficult to control in vivo. We demonstrate the development of a noncanonical redox cofactor system based on nicotinamide mononucleotide (NMN+). The key enzyme in the system is a computationally designed glucose dehydrogenase with a 107-fold cofactor specificity switch toward NMN+ over NADP+ based on apparent enzymatic activity. We demonstrate that this system can be used to support diverse redox chemistries in vitro with high total turnover number (~39,000), to channel reducing power in Escherichia coli whole cells specifically from glucose to a pharmaceutical intermediate, levodione, and to sustain the high metabolic flux required for the central carbon metabolism to support growth. Overall, this work demonstrates efficient use of a noncanonical cofactor in biocatalysis and metabolic pathway design.
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Affiliation(s)
- William B Black
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA, USA
| | - Linyue Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA, USA
| | - Wai Shun Mak
- Department of Chemistry, University of California, Davis, Davis, CA, USA
- Genome Center, University of California, Davis, Davis, CA, USA
| | - Sarah Maxel
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA, USA
| | - Youtian Cui
- Department of Chemistry, University of California, Davis, Davis, CA, USA
- Genome Center, University of California, Davis, Davis, CA, USA
| | - Edward King
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Bonnie Fong
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA, USA
| | - Alicia Sanchez Martinez
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA, USA
| | - Justin B Siegel
- Department of Chemistry, University of California, Davis, Davis, CA, USA.
- Genome Center, University of California, Davis, Davis, CA, USA.
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, USA.
| | - Han Li
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA, USA.
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Reductive Activity and Mechanism of Hypoxia- Targeted AGT Inhibitors: An Experimental and Theoretical Investigation. Int J Mol Sci 2019; 20:ijms20246308. [PMID: 31847200 PMCID: PMC6941096 DOI: 10.3390/ijms20246308] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 12/05/2019] [Accepted: 12/10/2019] [Indexed: 11/16/2022] Open
Abstract
O6-alkylguanine-DNA alkyltransferase (AGT) is the main cause of tumor cell resistance to DNA-alkylating agents, so it is valuable to design tumor-targeted AGT inhibitors with hypoxia activation. Based on the existing benchmark inhibitor O6-benzylguanine (O6-BG), four derivatives with hypoxia-reduced potential and their corresponding reduction products were synthesized. A reductase system consisting of glucose/glucose oxidase, xanthine/xanthine oxidase, and catalase were constructed, and the reduction products of the hypoxia-activated prodrugs under normoxic and hypoxic conditions were determined by high-performance liquid chromatography electrospray ionization tandem mass spectrometry (HPLC-ESI-MS/MS). The results showed that the reduction products produced under hypoxic conditions were significantly higher than that under normoxic condition. The amount of the reduction product yielded from ANBP (2-nitro-6-(3-amino) benzyloxypurine) under hypoxic conditions was the highest, followed by AMNBP (2-nitro-6-(3-aminomethyl)benzyloxypurine), 2-NBP (2-nitro-6-benzyloxypurine), and 3-NBG (O6-(3-nitro)benzylguanine). It should be noted that although the levels of the reduction products of 2-NBP and 3-NBG were lower than those of ANBP and AMNBP, their maximal hypoxic/normoxic ratios were higher than those of the other two prodrugs. Meanwhile, we also investigated the single electron reduction mechanism of the hypoxia-activated prodrugs using density functional theory (DFT) calculations. As a result, the reduction of the nitro group to the nitroso was proven to be a rate-limiting step. Moreover, the 2-nitro group of purine ring was more ready to be reduced than the 3-nitro group of benzyl. The energy barriers of the rate-limiting steps were 34–37 kcal/mol. The interactions between these prodrugs and nitroreductase were explored via molecular docking study, and ANBP was observed to have the highest affinity to nitroreductase, followed by AMNBP, 2-NBP, and 3-NBG. Interestingly, the theoretical results were generally in a good agreement with the experimental results. Finally, molecular docking and molecular dynamics simulations were performed to predict the AGT-inhibitory activity of the four prodrugs and their reduction products. In summary, simultaneous consideration of reduction potential and hypoxic selectivity is necessary to ensure that such prodrugs have good hypoxic tumor targeting. This study provides insights into the hypoxia-activated mechanism of nitro-substituted prodrugs as AGT inhibitors, which may contribute to reasonable design and development of novel tumor-targeted AGT inhibitors.
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Yan Y, Chen J, Galván AE, Garbinski LD, Zhu YG, Rosen BP, Yoshinaga M. Reduction of Organoarsenical Herbicides and Antimicrobial Growth Promoters by the Legume Symbiont Sinorhizobium meliloti. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:13648-13656. [PMID: 31682413 DOI: 10.1021/acs.est.9b04026] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Massive amounts of methyl [e.g., methylarsenate, MAs(V)] and aromatic arsenicals [e.g., roxarsone (4-hydroxy-3-nitrophenylarsonate, Rox(V)] have been utilized as herbicides for weed control and growth promotors for poultry and swine, respectively. The majority of these organoarsenicals degrade into more toxic inorganic species. Here, we demonstrate that the legume symbiont Sinorhizobium meliloti both reduces MAs(V) to MAs(III) and catalyzes sequential two-step reduction of nitro and arsenate groups in Rox(V), producing the highly toxic trivalent amino aromatic derivative 4-hydroxy-3-aminophenylarsenite (HAPA(III)). The existence of this process suggests that S. meliloti possesses the ability to transform pentavalent methyl and aromatic arsenicals into antibiotics to provide a competitive advantage over other microbes, which would be a critical process for the synthetic aromatic arsenicals to function as antimicrobial growth promoters. The activated trivalent aromatic arsenicals are degraded into less-toxic inorganic species by an MAs(III)-demethylating aerobe, suggesting that environmental aromatic arsenicals also undergo a multiple-step degradation pathway, in analogy with the previously reported demethylation pathway of the methylarsenate herbicide. We further show that an FAD-NADPH-dependent nitroreductase encoded by mdaB gene catalyzes nitroreduction of roxarsone both in vivo and in vitro. Our results demonstrate that environmental organoarsenicals trigger competition between members of microbial communities, resulting in gradual degradation of organoarsenicals and contamination by inorganic arsenic.
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Affiliation(s)
- Yu Yan
- Department of Environmental Science and Engineering , Huaqiao University , Xiamen 361021 , Fujian , China
- Department of Cellular Biology and Pharmacology, Herbert Wertheim College of Medicine , Florida International University , Miami 33199 , Florida , United States
| | - Jian Chen
- Department of Cellular Biology and Pharmacology, Herbert Wertheim College of Medicine , Florida International University , Miami 33199 , Florida , United States
| | - Adriana E Galván
- Department of Cellular Biology and Pharmacology, Herbert Wertheim College of Medicine , Florida International University , Miami 33199 , Florida , United States
| | - Luis D Garbinski
- Department of Cellular Biology and Pharmacology, Herbert Wertheim College of Medicine , Florida International University , Miami 33199 , Florida , United States
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment , Chinese Academy of Sciences , Xiamen 361021 , Fujian , China
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environ-mental Sciences , Chinese Academy of Sciences , Beijing 100085 , Hebei , China
| | - Barry P Rosen
- Department of Cellular Biology and Pharmacology, Herbert Wertheim College of Medicine , Florida International University , Miami 33199 , Florida , United States
| | - Masafumi Yoshinaga
- Department of Cellular Biology and Pharmacology, Herbert Wertheim College of Medicine , Florida International University , Miami 33199 , Florida , United States
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Hibbard HA, Reynolds MM. Synthesis of novel nitroreductase enzyme-activated nitric oxide prodrugs to site-specifically kill bacteria. Bioorg Chem 2019; 93:103318. [DOI: 10.1016/j.bioorg.2019.103318] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 09/18/2019] [Accepted: 09/26/2019] [Indexed: 02/06/2023]
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Degradation of High Energy Materials Using Biological Reduction: A Rational Way to Reach Bioremediation. Int J Mol Sci 2019; 20:ijms20225556. [PMID: 31703334 PMCID: PMC6888211 DOI: 10.3390/ijms20225556] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/22/2019] [Accepted: 11/04/2019] [Indexed: 02/07/2023] Open
Abstract
Explosives molecules have been widely used since World War II, leading to considerable contamination of soil and groundwater. Recently, bioremediation has emerged as an environmentally friendly approach to solve such contamination issues. However, the 1,3,5,7-tetranitro-1,3,5,7-tetrazocane (HMX) explosive, which has very low solubility in water, does not provide satisfying results with this approach. In this study, we used a rational design strategy for improving the specificity of the nitroreductase from E. Cloacae (PDB ID 5J8G) toward HMX. We used the Coupled Moves algorithm from Rosetta to redesign the active site around HMX. Molecular Dynamics (MD) simulations and affinity calculations allowed us to study the newly designed protein. Five mutations were performed. The designed nitroreductase has a better fit with HMX. We observed more H-bonds, which productively stabilized the HMX molecule for the mutant than for the wild type enzyme. Thus, HMX’s nitro groups are close enough to the reductive cofactor to enable a hydride transfer. Also, the HMX affinity for the designed enzyme is better than for the wild type. These results are encouraging. However, the total reduction reaction implies numerous HMX derivatives, and each of them has to be tested to check how far the reaction can’ go.
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Novel 5-Nitrofuran-Activating Reductase in Escherichia coli. Antimicrob Agents Chemother 2019; 63:AAC.00868-19. [PMID: 31481448 DOI: 10.1128/aac.00868-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 08/28/2019] [Indexed: 02/07/2023] Open
Abstract
The global spread of multidrug-resistant enterobacteria warrants new strategies to combat these pathogens. One possible approach is the reconsideration of "old" antimicrobials, which remain effective after decades of use. Synthetic 5-nitrofurans such as furazolidone, nitrofurantoin, and nitrofurazone are such a class of antimicrobial drugs. Recent epidemiological data showed a very low prevalence of resistance to this antimicrobial class among clinical Escherichia coli isolates in various parts of the world, forecasting the increasing importance of its uses to battle antibiotic-resistant enterobacteria. However, although they have had a long history of clinical use, a detailed understanding of the 5-nitrofurans' mechanisms of action remains limited. Nitrofurans are known as prodrugs that are activated in E. coli by reduction catalyzed by two redundant nitroreductases, NfsA and NfsB. Furazolidone, nevertheless, retains relatively significant antibacterial activity in the nitroreductase-deficient ΔnfsA ΔnfsB E. coli strain, indicating the presence of additional activating enzymes and/or antibacterial activity of the unreduced form. Using genome sequencing, genetic, biochemical, and bioinformatic approaches, we discovered a novel 5-nitrofuran-activating enzyme, AhpF, in E. coli The discovery of a new nitrofuran-reducing enzyme opens new avenues for overcoming 5-nitrofuran resistance, such as designing nitrofuran analogues with higher affinity for AhpF or screening for adjuvants that enhance AhpF expression.
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57
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Zuo R, Ding Y. Direct Aromatic Nitration System for Synthesis of Nitrotryptophans in Escherichia coli. ACS Synth Biol 2019; 8:857-865. [PMID: 30865826 DOI: 10.1021/acssynbio.8b00534] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Nitrotryptophan and its analogues are useful building blocks for synthesizing bioactive and biotechnologically relevant chemicals, materials, and proteins. However, synthetic routes to enantiopure nitro-containing tryptophan derivatives are either complex and polluting or even unestablished yet. Herein, we describe microbial production of 4-NO2-l-tryptophan (Nitrotrp) and its analogues by designing and expressing the biosynthetic pathway in Escherichia coli. The biosynthetic pathway comprised one engineered self-sufficient P450 TB14 of Streptomyces origin for direct nitration of the C-4 of l-Trp indole and one nitric oxide synthase from Bacillus subtilis (BsNOS) for the production of nitric oxide (NO) from l-Arg to support the direct aromatic nitration. As both TB14 and BsNOS require reducing agent NADPH for their reactions, we also included one glucose dehydrogenase (GDH) from B. subtilis for in situ NADPH regeneration. The initially designed pathway led to 16.2 ± 2.3 mg/L of Nitrotrp by the engineered E. coli fermented in the M9 minimal medium for 3 days. A combination of the design and screening of three additional pathways, fermentation optimization and the knockout of competitive metabolic pathways together improved the Nitrotrp titer to around 192 mg/L within 20 h. Finally, the whole-cell biotransformation system produced eight Nitrotrp analogues with their titers varying from 2.5 to 61.5 mg/L. This work provides the first microbial direct aromatic nitration processes and sets the stage for the development of biocatalytic routes to other useful nitroaromatics in the future.
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Affiliation(s)
- Ran Zuo
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
| | - Yousong Ding
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
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58
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Crofts TS, Sontha P, King AO, Wang B, Biddy BA, Zanolli N, Gaumnitz J, Dantas G. Discovery and Characterization of a Nitroreductase Capable of Conferring Bacterial Resistance to Chloramphenicol. Cell Chem Biol 2019; 26:559-570.e6. [PMID: 30799223 PMCID: PMC6474809 DOI: 10.1016/j.chembiol.2019.01.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 11/06/2018] [Accepted: 01/14/2019] [Indexed: 12/13/2022]
Abstract
Widespread antibiotic resistance has led to the reappraisal of abandoned antibiotics including chloramphenicol. However, enzyme(s) underlying one form of chloramphenicol resistance, nitroreduction, have eluded identification. Here we demonstrate that expression of the Haemophilus influenzae nitroreductase gene nfsB confers chloramphenicol resistance in Escherichia coli. We characterized the enzymatic product of H. influenzae NfsB acting on chloramphenicol and found it to be amino-chloramphenicol. Kinetic analysis revealed reduction of diverse substrates including the incomplete reduction of 5-nitro antibiotics metronidazole and nitrofurantoin, likely resulting in activation of these antibiotic pro-drugs to their cytotoxic forms. We observed that expression of the H. influenzae nfsB gene in E. coli results in significantly increased susceptibility to metronidazole. Finally, we found that in this strain metronidazole attenuates chloramphenicol resistance synergistically, and in vitro metronidazole weakly inhibits chloramphenicol reduction by NfsB. Our findings reveal the underpinnings of a chloramphenicol resistance mechanism nearly 70 years after its description.
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Affiliation(s)
- Terence S Crofts
- Department of Pathology and Immunology, Washington University in St Louis School of Medicine, Saint Louis, MO 63110, USA; The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, Saint Louis, MO 63110, USA.
| | - Pratyush Sontha
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, Saint Louis, MO 63110, USA
| | - Amber O King
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, Saint Louis, MO 63110, USA
| | - Bin Wang
- Department of Pathology and Immunology, Washington University in St Louis School of Medicine, Saint Louis, MO 63110, USA; The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, Saint Louis, MO 63110, USA
| | - Brent A Biddy
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, Saint Louis, MO 63110, USA
| | - Nicole Zanolli
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, Saint Louis, MO 63110, USA
| | - John Gaumnitz
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, Saint Louis, MO 63110, USA
| | - Gautam Dantas
- Department of Pathology and Immunology, Washington University in St Louis School of Medicine, Saint Louis, MO 63110, USA; The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, Saint Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University in St Louis School of Medicine, Saint Louis, MO 63110, USA; Department of Biomedical Engineering, Washington University in St Louis, Saint Louis, MO 63110, USA.
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59
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Ball P, Thompson E, Anderson S, Gwenin V, Gwenin C. Time dependent HPLC analysis of the product ratio of enzymatically reduced prodrug CB1954 by a modified and immobilised nitroreductase. Eur J Pharm Sci 2018; 127:217-224. [PMID: 30414836 DOI: 10.1016/j.ejps.2018.11.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/25/2018] [Accepted: 11/01/2018] [Indexed: 02/01/2023]
Abstract
Directed enzyme prodrug therapy is a chemotherapy strategy that utilises prodrug-activating enzymes to activate prodrugs at the tumour location, thus reducing off-target effects. The most commonly investigated enzyme for use with the CB1954 prodrug is the NfnB nitroreductase from E. coli. Literature states that CB1954 is reduced by NfnB at the 2- or 4-position at a 1:1 ratio; deviation from this ratio has been observed in the literature, but not further investigated. The kinetic parameters for the genetically-modified enzymes; NfnB-his, NfnB-cys and AuNP-NfnB-cys were assessed and HPLC analysis was used to determine the hydroxylamine product ratios formed when reacted with CB1954. Time-dependent HPLC studies were carried out to assess how this ratio changes over time. It was shown that the hydroxylamine ratio formed by the reduction of CB1954 by a nitroreductase changes over time and that this change in ratio relates directly to the kinetics of the reaction. Thus, the hydroxylamine ratio measured using HPLC at a given time point was not a true indication of the preference of the nitroreductase enzymes during catalysis. These results question how nitroreductases are evaluated in terms of the hydroxylamine ratio and it is suspected that this phenomenon may also apply to other enzyme/prodrug combinations.
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Affiliation(s)
- Patrick Ball
- College of Environmental Sciences and Engineering, School of Natural Sciences, Chemistry Bangor University, LL57 2DG, United Kingdom of Great Britain and Northern Ireland
| | - Emma Thompson
- College of Environmental Sciences and Engineering, School of Natural Sciences, Chemistry Bangor University, LL57 2DG, United Kingdom of Great Britain and Northern Ireland
| | - Simon Anderson
- College of Environmental Sciences and Engineering, School of Natural Sciences, Chemistry Bangor University, LL57 2DG, United Kingdom of Great Britain and Northern Ireland
| | - Vanessa Gwenin
- College of Environmental Sciences and Engineering, School of Natural Sciences, Chemistry Bangor University, LL57 2DG, United Kingdom of Great Britain and Northern Ireland
| | - Chris Gwenin
- College of Environmental Sciences and Engineering, School of Natural Sciences, Chemistry Bangor University, LL57 2DG, United Kingdom of Great Britain and Northern Ireland.
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60
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Gruber TD, Krishnamurthy C, Grimm JB, Tadross MR, Wysocki LM, Gartner ZJ, Lavis LD. Cell-Specific Chemical Delivery Using a Selective Nitroreductase-Nitroaryl Pair. ACS Chem Biol 2018; 13:2888-2896. [PMID: 30111097 DOI: 10.1021/acschembio.8b00524] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The utility of small molecules to probe or perturb biological systems is limited by the lack of cell-specificity. "Masking" the activity of small molecules using a general chemical modification and "unmasking" it only within target cells overcomes this limitation. To this end, we have developed a selective enzyme-substrate pair consisting of engineered variants of E. coli nitroreductase (NTR) and a 2-nitro- N-methylimidazolyl (NM) masking group. To discover and optimize this NTR-NM system, we synthesized a series of fluorogenic substrates containing different nitroaromatic masking groups, confirmed their stability in cells, and identified the best substrate for NTR. We then engineered the enzyme for improved activity in mammalian cells, ultimately yielding an enzyme variant (enhanced NTR, or eNTR) that possesses up to 100-fold increased activity over wild-type NTR. These improved NTR enzymes combined with the optimal NM masking group enable rapid, selective unmasking of dyes, indicators, and drugs to genetically defined populations of cells.
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Affiliation(s)
- Todd D Gruber
- Janelia Research Campus , Howard Hughes Medical Institute , Ashburn , Virginia 20147 , United States
| | - Chithra Krishnamurthy
- Janelia Research Campus , Howard Hughes Medical Institute , Ashburn , Virginia 20147 , United States
- Department of Pharmaceutical Chemistry , University of California , San Francisco , California 94158 , United States
| | - Jonathan B Grimm
- Janelia Research Campus , Howard Hughes Medical Institute , Ashburn , Virginia 20147 , United States
| | - Michael R Tadross
- Janelia Research Campus , Howard Hughes Medical Institute , Ashburn , Virginia 20147 , United States
| | - Laura M Wysocki
- Janelia Research Campus , Howard Hughes Medical Institute , Ashburn , Virginia 20147 , United States
| | - Zev J Gartner
- Department of Pharmaceutical Chemistry , University of California , San Francisco , California 94158 , United States
| | - Luke D Lavis
- Janelia Research Campus , Howard Hughes Medical Institute , Ashburn , Virginia 20147 , United States
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Yang J, Bai J, Qu M, Xie B, Yang Q. Biochemical characteristics of a nitroreductase with diverse substrate specificity from Streptomyces mirabilis DUT001. Biotechnol Appl Biochem 2018; 66:33-42. [PMID: 30231196 DOI: 10.1002/bab.1692] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 09/11/2018] [Indexed: 11/09/2022]
Abstract
A nitroreductase-encoded gene from an efficient nitro-reducing bacterium Streptomyces mirabilis DUT001, named snr, was cloned and heterogeneously expressed in Escherichia coli. The purified Streptomyces nitroreductase SNR was a homodimer with an apparent subunit molecular weight of 24 kDa and preferred NADH to NADPH as a cofactor. By enzyme incubation and isothermal calorimetry experiments, flavin mononucleotide (FMN) was found to be the preferred flavin cofactor; the binding process was exothermic and primarily enthalpy driven. The enzyme can reduce multiple nitro compounds and flavins, including antibacterial drug nitrofurazone, priority pollutants 2,4-dinitrotoluene and 2,4,6-trinitrotoluene, as well as key chemical intermediates 3-nitrophthalimide, 4-nitrophthalimide, and 4-nitro-1,8-naphthalic anhydride. Among the substrates tested, the highest activity of kcat(app) /Km(app) (0.234 μM-1 Sec-1 ) was observed for the reduction of FMN. Multiple sequence alignment revealed that the high FMN reduction activity of SNR may be due to the absence of a helix, constituting the entrance to the substrate pocket in other nitroreductases.
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Affiliation(s)
- Jun Yang
- State Key Laboratory of Fine Chemical Engineering and School of Life Science and Biotechnology, Dalian University of Technology, Dalian, People's Republic of China
| | - Jing Bai
- College of Bioscience and Bioengineering, Hebei University of Science & Technology, Hebei, People's Republic of China
| | - Mingbo Qu
- State Key Laboratory of Fine Chemical Engineering and School of Life Science and Biotechnology, Dalian University of Technology, Dalian, People's Republic of China
| | - Bo Xie
- State Key Laboratory of Fine Chemical Engineering and School of Life Science and Biotechnology, Dalian University of Technology, Dalian, People's Republic of China
| | - Qing Yang
- State Key Laboratory of Fine Chemical Engineering and School of Life Science and Biotechnology, Dalian University of Technology, Dalian, People's Republic of China
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Kienle DF, Falatach RM, Kaar JL, Schwartz DK. Correlating Structural and Functional Heterogeneity of Immobilized Enzymes. ACS NANO 2018; 12:8091-8103. [PMID: 30067333 DOI: 10.1021/acsnano.8b02956] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Many nanobiotechnology applications rely on stable and efficient integration of functional biomacromolecules with synthetic nanomaterials. Unfortunately, the reasons for the ubiquitous loss of activity of immobilized enzymes remain poorly understood due to the difficulty in distinguishing between distinct molecular-level mechanisms. Here, we employ complementary single-molecule fluorescence methods that independently measure the impact of immobilization on the structure and function ( i. e., substrate binding kinetics) of nitroreductase (NfsB). Stochastic statistical modeling methods were used to unambiguously quantify the effects of immobilized NfsB structural dynamics on function, allowing us to explicitly separate effects due to conformation and accessibility. Interestingly, we found that nonspecifically tethered NfsB exhibited enhanced stability compared to site-specifically tethered NfsB; however, the folded state of site-specifically tethered NfsB had faster substrate binding rates, suggesting improved active site accessibility. This demonstrated an unexpected intrinsic trade-off associated with competing bioconjugation methods, suggesting that it may be necessary to balance conformational stability versus active site accessibility. This nuanced view of the impact of immobilization will facilitate a rational approach to the integration of enzymes with synthetic nanomaterials.
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Affiliation(s)
- Daniel F Kienle
- Department of Chemical and Biological Engineering , University of Colorado , Boulder , Colorado 80309 , United States
| | - Rebecca M Falatach
- Department of Chemical and Biological Engineering , University of Colorado , Boulder , Colorado 80309 , United States
| | - Joel L Kaar
- Department of Chemical and Biological Engineering , University of Colorado , Boulder , Colorado 80309 , United States
| | - Daniel K Schwartz
- Department of Chemical and Biological Engineering , University of Colorado , Boulder , Colorado 80309 , United States
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Sadlowski C, Park B, Araújo C, Das S, Kerr DL, He M, Han H, Riley L, Murthy N. Nitro Sulfonyl Fluorides are a new pharmacophore for the development of antibiotics. MOLECULAR SYSTEMS DESIGN & ENGINEERING 2018; 3:599-603. [PMID: 30740245 PMCID: PMC6366622 DOI: 10.1039/c8me00011e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The development of antibiotics against Gram-negative bacteria is a central problem in drug discovery. In this report, we demonstrate that aromatic sulfonyl fluorides with a nitro group in their ortho position have remarkable antibacterial activity and are active against drug-resistant pathogens, such as methicillin-resistant Staphylococcus aureus (MRSA), multidrug resistant Acinetobacter baumannii, and Pseudomonas aeruginosa.
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Affiliation(s)
- Corinne Sadlowski
- Department of Bioengineering, University of California, Berkeley, California, 94720, USA
- These authors contributed equally to this work
| | - Bora Park
- Department of Bioengineering, University of California, Berkeley, California, 94720, USA
- These authors contributed equally to this work
| | - Clarissa Araújo
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, 94720, USA
| | - Subhamoy Das
- Department of Bioengineering, University of California, Berkeley, California, 94720, USA
| | - D Lucas Kerr
- Department of Bioengineering, University of California, Berkeley, California, 94720, USA
| | - Maomao He
- Department of Bioengineering, University of California, Berkeley, California, 94720, USA
| | - Hesong Han
- Department of Bioengineering, University of California, Berkeley, California, 94720, USA
| | - Lee Riley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, 94720, USA
| | - Niren Murthy
- Department of Bioengineering, University of California, Berkeley, California, 94720, USA
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Mechanism of Two-/Four-Electron Reduction of Nitroaromatics by Oxygen-Insensitive Nitroreductases: The Role of a Non-Enzymatic Reduction Step. Molecules 2018; 23:molecules23071672. [PMID: 29987261 PMCID: PMC6100041 DOI: 10.3390/molecules23071672] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 07/02/2018] [Accepted: 07/05/2018] [Indexed: 11/21/2022] Open
Abstract
Oxygen-insensitive NAD(P)H:nitroreductases (NR) reduce nitroaromatics (Ar-NO2) into hydroxylamines (Ar-NHOH) through nitroso (Ar-NO) intermediates. Ar-NO may be reduced both enzymatically and directly by reduced nicotinamide adenine dinucleotide or its phosphate NAD(P)H, however, it is unclear which process is predominant in catalysis of NRs. We found that E. coli NR-A (NfsA) oxidizes 2 mol of NADPH per mol of 2,4,6-trinitrotoluene (TNT) and 4 mol of NADPH per mol of tetryl. Addition of ascorbate, which reduces Ar-NO into Ar-NHOH, changes the stoichiometry NADPH/Ar-NO2 into 1:1 (TNT) and 2:1 (tetryl), and decreases the rate of NADPH oxidation. Ascorbate does not interfere with the oxidation of NADPH during reduction of quinones by NfsA. Our analysis of ascorbate inhibition patterns and both enzymatic and non-enzymatic reduction of nitrosobenzene suggests that direct reduction of Ar-NO by NADPH rather than enzymatic reduction is the predominant mechanism during nitroaromatic reduction.
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66
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Gao X, Sun JZ, Tang BZ. Reaction-based AIE-active Fluorescent Probes for Selective Detection and Imaging. Isr J Chem 2018. [DOI: 10.1002/ijch.201800035] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Xiaoying Gao
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering; Zhejiang University; Hangzhou 310027 China
| | - Jing Zhi Sun
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering; Zhejiang University; Hangzhou 310027 China
| | - Ben Zhong Tang
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering; Zhejiang University; Hangzhou 310027 China
- Department of Chemistry, Division of Biomedical Engineering, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, State Key Laboratory of Molecular Neuroscience, Institute of Molecular Functional Materials, Division of Life Science; Hong Kong University of Science and Technology; Clear Water Bay Kowloon, Hong Kong China
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67
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Nitrothiophene carboxamides, a novel narrow spectrum antibacterial series: Mechanism of action and Efficacy. Sci Rep 2018; 8:7263. [PMID: 29740005 PMCID: PMC5940854 DOI: 10.1038/s41598-018-25407-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 04/20/2018] [Indexed: 12/24/2022] Open
Abstract
The mechanism of efflux is a tour-de-force in the bacterial armoury that has thwarted the development of novel antibiotics. We report the discovery of a novel chemical series with potent antibacterial properties that was engineered to overcome efflux liability. Compounds liable to efflux specifically via the Resistance Nodulation and cell Division (RND) pump, AcrAB-TolC were chosen for a hit to lead progression. Using structure-based design, the compounds were optimised to lose their binding to the efflux pump, thereby making them potent on wild-type bacteria. We discovered these compounds to be pro-drugs that require activation in E. coli by specific bacterial nitroreductases NfsA and NfsB. Hit to lead chemistry led to the generation of compounds that were potent on wild-type and multi-drug resistant clinical isolates of E. coli, Shigella spp., and Salmonella spp. These compounds are bactericidal and efficacious in a mouse thigh infection model.
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68
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Aerobic Transformation of 2,4-Dinitrotoluene by Escherichia coli and Its Implications for the Detection of Trace Explosives. Appl Environ Microbiol 2018; 84:AEM.01729-17. [PMID: 29222096 DOI: 10.1128/aem.01729-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 11/25/2017] [Indexed: 11/20/2022] Open
Abstract
DNT (2,4-dinitrotoluene), a volatile impurity in military-grade 2,4,6-trinitrotoluene (TNT)-based explosives, is a potential tracer for the detection of buried landmines and other explosive devices. We have previously described an Escherichia coli bioreporter strain engineered to detect traces of DNT and have demonstrated that the yqjF gene promoter, the sensing element of this bioreporter, is induced not by DNT but by at least one of its transformation products. In the present study, we have characterized the initial stages of DNT biotransformation in E. coli, have identified the key metabolic products in this reductive pathway, and demonstrate that the main DNT metabolite that induces yqjF is 2,4,5-trihydroxytoluene. We further show that E. coli cannot utilize DNT as a sole carbon or nitrogen source and propose that this compound is metabolized in order to neutralize its toxicity to the cells.IMPORTANCE The information provided in this article sheds new light both on the microbial biodegradability of nitroaromatic compounds and on the metabolic capabilities of E. coli By doing so, it also clarifies the pathway leading to the previously unexplained induction of the E. coli yqjF gene by 2,4-dinitrotoluene, an impurity that accompanies 2,4,6-trinitrotoluene (TNT)-based explosives. Our improved understanding of these processes will serve to molecularly enhance the performance of a previously described microbial bioreporter of buried landmines and other explosive devices, in which the yqjF gene promoter serves as the sensing element.
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Miller AF, Park JT, Ferguson KL, Pitsawong W, Bommarius AS. Informing Efforts to Develop Nitroreductase for Amine Production. Molecules 2018; 23:molecules23020211. [PMID: 29364838 PMCID: PMC6017928 DOI: 10.3390/molecules23020211] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 01/03/2018] [Accepted: 01/12/2018] [Indexed: 12/19/2022] Open
Abstract
Nitroreductases (NRs) hold promise for converting nitroaromatics to aromatic amines. Nitroaromatic reduction rate increases with Hammett substituent constant for NRs from two different subgroups, confirming substrate identity as a key determinant of reactivity. Amine yields were low, but compounds yielding amines tend to have a large π system and electron withdrawing substituents. Therefore, we also assessed the prospects of varying the enzyme. Several different subgroups of NRs include members able to produce aromatic amines. Comparison of four NR subgroups shows that they provide contrasting substrate binding cavities with distinct constraints on substrate position relative to the flavin. The unique architecture of the NR dimer produces an enormous contact area which we propose provides the stabilization needed to offset the costs of insertion of the active sites between the monomers. Thus, we propose that the functional diversity included in the NR superfamily stems from the chemical versatility of the flavin cofactor in conjunction with a structure that permits tremendous active site variability. These complementary properties make NRs exceptionally promising enzymes for development for biocatalysis in prodrug activation and conversion of nitroaromatics to valuable aromatic amines. We provide a framework for identifying NRs and substrates with the greatest potential to advance.
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Affiliation(s)
- Anne-Frances Miller
- Department of Chemistry, University of Kentucky, Lexington, KY 40506-0055, USA.
| | - Jonathan T Park
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332-0100, USA.
| | - Kyle L Ferguson
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0100, USA.
| | - Warintra Pitsawong
- Department of Chemistry, University of Kentucky, Lexington, KY 40506-0055, USA.
| | - Andreas S Bommarius
- School of Chemical and Biomolecular Engineering, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0100, USA.
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Biošić M, Škorić I, Beganović J, Babić S. Nitrofurantoin hydrolytic degradation in the environment. CHEMOSPHERE 2017; 186:660-668. [PMID: 28818593 DOI: 10.1016/j.chemosphere.2017.08.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 07/29/2017] [Accepted: 08/03/2017] [Indexed: 06/07/2023]
Abstract
Occurrence of pharmaceuticals, especially antibiotics in the environment increased attention to their environmental fate. Hydrolysis is one of two abiotic processes by which compounds are degraded in the environment. According to authors knowledge this is the first study investigating hydrolytic degradation of nitrofurantoin at pH-values normally found in the environment. Nitrofurantoin hydrolytic degradation appeared to be much slower at acidic (pH 4) solution compared to neutral (pH 7) and alkaline (pH 9) solutions at all three investigated temperatures (20 °C, 40 °C and 60 °C). In all cases nitrofurantoin hydrolysis followed the first-order kinetics with half-lives ranged from 0.5 days at pH 9 and 60 °C to 3.9 years at pH 4 and 20 °C. Temperature dependence of the hydrolysis rate constant was quantified by Arrhenius equation; obtained Ea values were as follows: 100.7 kJ mol-1 at pH 4, 111.2 kJ mol-1 at pH 7 and 102.3 kJ mol-1 at pH 9. Increase in hydrolysis rate constants for each 10 °C increase in temperature were 3.4, 3.9 and 3.5 at pH 4, pH 7 and pH 9, respectively. The structures of hydrolytic degradation products were determined and degradation pathways were suggested. Three main processes occurred depending on pH-values: protonation of the nitrofurantoin followed by cleavage of the NN single bond, heterocyclic non-aromatic ring cleavage, and reduction of the non-aromatic heterocyclic ring.
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Affiliation(s)
- Martina Biošić
- Department of Analytical Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 19, 10000 Zagreb, Croatia.
| | - Irena Škorić
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 19, 10000 Zagreb, Croatia
| | - Jasmina Beganović
- Department of Analytical Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 19, 10000 Zagreb, Croatia
| | - Sandra Babić
- Department of Analytical Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 19, 10000 Zagreb, Croatia
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Whang CH, Kim KS, Bae J, Chen J, Jun HW, Jo S. Novel Biodegradable Polymer with Redox-Triggered Backbone Cleavage Through Sequential 1,6-Elimination and 1,5-Cyclization Reactions. Macromol Rapid Commun 2017; 38. [PMID: 28833950 DOI: 10.1002/marc.201700395] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 07/20/2017] [Indexed: 01/10/2023]
Abstract
In the past decade, the self-immolative biodegradable polymer arose as a novel paradigm for its efficient degradation mechanism and vast potential for advanced biomedical applications. This study reports successful synthesis of a novel biodegradable polymer capable of self-immolative backbone cleavage. The monomer is designed by covalent conjugations of both pendant redox-trigger (p-nitrobenzyl alcohol) and self-immolative linker (p-hydroxybenzyl alcohol) to the cyclization spacer (n-2-(hydroxyethyl)ethylene diamine), which serves as the structural backbone. The polymerization of the monomer with hexamethylene diisocyanate yields a linear redox-sensitive polymer that can systemically degrade via sequential 1,6-elimination and 1,5-cyclization reactions within an effective timeframe. Ultimately, the polymer's potential for biomedical application is simulated through in vitro redox-triggered release of paclitaxel from polymeric nanoparticles.
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Affiliation(s)
- Chang-Hee Whang
- Department of Pharmaceutics and Drug Delivery, School of Pharmacy, The University of Mississippi, University, MS, 38677, USA
| | - Kyeong Soo Kim
- Department of Pharmaceutics and Drug Delivery, School of Pharmacy, The University of Mississippi, University, MS, 38677, USA
| | - Jungeun Bae
- Department of Pharmaceutics and Drug Delivery, School of Pharmacy, The University of Mississippi, University, MS, 38677, USA
| | - Jun Chen
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Ho-Wook Jun
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Seongbong Jo
- Department of Pharmaceutics and Drug Delivery, School of Pharmacy, The University of Mississippi, University, MS, 38677, USA
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72
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Sun Z, Su Q, Rokita SE. The distribution and mechanism of iodotyrosine deiodinase defied expectations. Arch Biochem Biophys 2017; 632:77-87. [PMID: 28774660 DOI: 10.1016/j.abb.2017.07.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 07/24/2017] [Accepted: 07/30/2017] [Indexed: 12/19/2022]
Abstract
Iodotyrosine deiodinase (IYD) is unusual for its reliance on flavin to promote reductive dehalogenation under aerobic conditions. As implied by the name, this enzyme was first discovered to catalyze iodide elimination from iodotyrosine for recycling iodide during synthesis of tetra- and triiodothyronine collectively known as thyroid hormone. However, IYD likely supports many more functions and has been shown to debrominate and dechlorinate bromo- and chlorotyrosines. A specificity for halotyrosines versus halophenols is well preserved from humans to bacteria. In all examples to date, the substrate zwitterion establishes polar contacts with both the protein and the isoalloxazine ring of flavin. Mechanistic data suggest dehalogenation is catalyzed by sequential one electron transfer steps from reduced flavin to substrate despite the initial expectations for a single two electron transfer mechanism. A purported flavin semiquinone intermediate is stabilized by hydrogen bonding between its N5 position and the side chain of a Thr. Mutation of this residue to Ala suppresses dehalogenation and enhances a nitroreductase activity that is reminiscent of other enzymes within the same structural superfamily.
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Affiliation(s)
- Zuodong Sun
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Qi Su
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Steven E Rokita
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA.
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73
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Ramakrishnan G, Chandra N, Srinivasan N. Exploring anti-malarial potential of FDA approved drugs: an in silico approach. Malar J 2017; 16:290. [PMID: 28720135 PMCID: PMC5516367 DOI: 10.1186/s12936-017-1937-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 07/13/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The critically important issue on emergence of drug-resistant malarial parasites is compounded by cross resistance, where resistance to one drug confers resistance to other chemically similar drugs or those that share mode of action. This aspect requires discovery of new anti-malarial compounds or formulation of new combination therapy. The current study attempts to contribute towards accelerating anti-malarial drug development efforts, by exploring the potential of existing FDA-approved drugs to target proteins of Plasmodium falciparum. METHODS Using comparative sequence and structure analyses, FDA-approved drugs, originally developed against other pathogens, were identified as potential repurpose-able candidates against P. falciparum. The rationale behind the undertaken approach is the likeliness of small molecules to bind to homologous targets. Such a study of evolutionary relationships between established targets and P. falciparum proteins aided in identification of approved drug candidates that can be explored for their anti-malarial potential. RESULTS Seventy-one FDA-approved drugs were identified that could be repurposed against P. falciparum. A total of 89 potential targets were recognized, of which about 70 are known to participate in parasite housekeeping machinery, protein biosynthesis, metabolic pathways and cell growth and differentiation, which can be prioritized for chemotherapeutic interventions. An additional aspect of prioritization of predicted repurpose-able drugs has been explored on the basis of ability of the drugs to permeate cell membranes, i.e., lipophilicity, since the parasite resides within a parasitophorous vacuole, within the erythrocyte, during the blood stages of infection. Based on this consideration, 46 of 71 FDA-approved drugs have been identified as feasible repurpose-able candidates against P. falciparum, and form a first-line for laboratory investigations. At least five of the drugs identified in the current analysis correspond to existing antibacterial agents already under use as repurposed anti-malarial agents. CONCLUSIONS The drug-target associations predicted, primarily by taking advantage of evolutionary information, provide a valuable resource of attractive and feasible candidate drugs that can be readily taken through further stages of anti-malarial drug development pipeline.
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Affiliation(s)
- Gayatri Ramakrishnan
- Indian Institute of Science Mathematics Initiative, Indian Institute of Science, Bangalore, 560012, India.,Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Nagasuma Chandra
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
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Werther T, Wahlefeld S, Salewski J, Kuhlmann U, Zebger I, Hildebrandt P, Dobbek H. Redox-dependent substrate-cofactor interactions in the Michaelis-complex of a flavin-dependent oxidoreductase. Nat Commun 2017. [PMCID: PMC5519977 DOI: 10.1038/ncomms16084] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
How an enzyme activates its substrate for turnover is fundamental for catalysis but incompletely understood on a structural level. With redox enzymes one typically analyses structures of enzyme–substrate complexes in the unreactive oxidation state of the cofactor, assuming that the interaction between enzyme and substrate is independent of the cofactors oxidation state. Here, we investigate the Michaelis complex of the flavoenzyme xenobiotic reductase A with the reactive reduced cofactor bound to its substrates by X-ray crystallography and resonance Raman spectroscopy and compare it to the non-reactive oxidized Michaelis complex mimics. We find that substrates bind in different orientations to the oxidized and reduced flavin, in both cases flattening its structure. But only authentic Michaelis complexes display an unexpected rich vibrational band pattern uncovering a strong donor–acceptor complex between reduced flavin and substrate. This interaction likely activates the catalytic ground state of the reduced flavin, accelerating the reaction within a compressed cofactor–substrate complex. Due to their transient nature, enzyme-substrate complexes are difficult to characterize structurally. Here, the authors capture the reactive reduced form of xenobiotic reductase A bound to its substrate and show that the oxidation state of the flavin cofactor affects the interaction of the substrate with the enzyme.
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75
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Shukla P, Khodade VS, SharathChandra M, Chauhan P, Mishra S, Siddaramappa S, Pradeep BE, Singh A, Chakrapani H. "On demand" redox buffering by H 2S contributes to antibiotic resistance revealed by a bacteria-specific H 2S donor. Chem Sci 2017; 8:4967-4972. [PMID: 28959420 PMCID: PMC5607856 DOI: 10.1039/c7sc00873b] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 04/20/2017] [Indexed: 12/15/2022] Open
Abstract
Understanding the mechanisms of antimicrobial resistance (AMR) will help launch a counter-offensive against human pathogens that threaten our ability to effectively treat common infections. Herein, we report bis(4-nitrobenzyl)sulfanes, which are activated by a bacterial enzyme to produce hydrogen sulfide (H2S) gas. We found that H2S helps maintain redox homeostasis and protects bacteria against antibiotic-triggered oxidative stress "on demand", through activation of alternate respiratory oxidases and cellular antioxidants. We discovered, a hitherto unknown role for this gas, that chemical inhibition of H2S biosynthesis reversed antibiotic resistance in multidrug-resistant (MDR) uropathogenic Escherichia coli strains of clinical origin, whereas exposure to the H2S donor restored drug tolerance. Together, our study provides a greater insight into the dynamic defence mechanisms of this gas, modes of antibiotic action as well as resistance while progressing towards new pharmacological targets to address AMR.
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Affiliation(s)
- Prashant Shukla
- Department of Microbiology and Cell Biology , Centre for Infectious Disease and Research , Indian Institute of Science , Bangalore 5600012 , Karnataka , India .
- International Centre for Genetic Engineering and Biotechnology , New Delhi , India
| | - Vinayak S Khodade
- Department of Chemistry , Indian Institute of Science Education and Research Pune , Dr Homi Bhabha Road, Pashan , Pune 411 008 , Maharashtra , India .
| | - Mallojjala SharathChandra
- Department of Chemistry , Indian Institute of Science Education and Research Pune , Dr Homi Bhabha Road, Pashan , Pune 411 008 , Maharashtra , India .
| | - Preeti Chauhan
- Department of Chemistry , Indian Institute of Science Education and Research Pune , Dr Homi Bhabha Road, Pashan , Pune 411 008 , Maharashtra , India .
| | - Saurabh Mishra
- Department of Microbiology and Cell Biology , Centre for Infectious Disease and Research , Indian Institute of Science , Bangalore 5600012 , Karnataka , India .
| | | | | | - Amit Singh
- Department of Microbiology and Cell Biology , Centre for Infectious Disease and Research , Indian Institute of Science , Bangalore 5600012 , Karnataka , India .
| | - Harinath Chakrapani
- Department of Chemistry , Indian Institute of Science Education and Research Pune , Dr Homi Bhabha Road, Pashan , Pune 411 008 , Maharashtra , India .
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76
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Humayun MZ, Zhang Z, Butcher AM, Moshayedi A, Saier MH. Hopping into a hot seat: Role of DNA structural features on IS5-mediated gene activation and inactivation under stress. PLoS One 2017; 12:e0180156. [PMID: 28666002 PMCID: PMC5493358 DOI: 10.1371/journal.pone.0180156] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 06/09/2017] [Indexed: 11/30/2022] Open
Abstract
Insertion sequence elements (IS elements) are proposed to play major roles in shaping the genetic and phenotypic landscapes of prokaryotic cells. Recent evidence has raised the possibility that environmental stress conditions increase IS hopping into new sites, and often such hopping has the phenotypic effect of relieving the stress. Although stress-induced targeted mutations have been reported for a number of E. coli genes, the glpFK (glycerol utilization) and the cryptic bglGFB (β-glucoside utilization) systems are among the best characterized where the effects of IS insertion-mediated gene activation are well-characterized at the molecular level. In the glpFK system, starvation of cells incapable of utilizing glycerol leads to an IS5 insertion event that activates the glpFK operon, and enables glycerol utilization. In the case of the cryptic bglGFB operon, insertion of IS5 (and other IS elements) into a specific region in the bglG upstream sequence has the effect of activating the operon in both growing cells, and in starving cells. However, a major unanswered question in the glpFK system, the bgl system, as well as other examples, has been why the insertion events are promoted at specific locations, and how the specific stress condition (glycerol starvation for example) can be mechanistically linked to enhanced insertion at a specific locus. In this paper, we show that a specific DNA structural feature (superhelical stress-induced duplex destabilization, SIDD) is associated with "stress-induced" IS5 insertion in the glpFK, bglGFB, flhDC, fucAO and nfsB systems. We propose a speculative mechanistic model that links specific environmental conditions to the unmasking of an insertional hotspot in the glpFK system. We demonstrate that experimentally altering the predicted stability of a SIDD element in the nfsB gene significantly impacts IS5 insertion at its hotspot.
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Affiliation(s)
- M. Zafri Humayun
- Department of Microbiology, Biochemistry & Molecular Genetics, Rutgers—New Jersey Medical School, Newark, NJ, United States of America
| | - Zhongge Zhang
- Department of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States of America
| | - Anna M. Butcher
- Department of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States of America
| | - Aref Moshayedi
- Department of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States of America
| | - Milton H. Saier
- Department of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States of America
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77
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Pitsawong W, Haynes CA, Koder RL, Rodgers DW, Miller AF. Mechanism-Informed Refinement Reveals Altered Substrate-Binding Mode for Catalytically Competent Nitroreductase. Structure 2017; 25:978-987.e4. [PMID: 28578873 DOI: 10.1016/j.str.2017.05.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 04/02/2017] [Accepted: 05/05/2017] [Indexed: 01/25/2023]
Abstract
Nitroreductase (NR) from Enterobacter cloacae reduces diverse nitroaromatics including herbicides, explosives, and prodrugs, and holds promise for bioremediation, prodrug activation, and enzyme-assisted synthesis. We solved crystal structures of NR complexes with bound substrate or analog for each of its two half-reactions. We complemented these with kinetic isotope effect (KIE) measurements elucidating H-transfer steps essential to each half-reaction. KIEs indicate hydride transfer from NADH to the flavin consistent with our structure of NR with the NADH analog nicotinic acid adenine dinucleotide (NAAD). The KIE on reduction of p-nitrobenzoic acid (p-NBA) also indicates hydride transfer, and requires revision of prior computational mechanisms. Our mechanistic information provided a structural restraint for the orientation of bound substrate, placing the nitro group closer to the flavin N5 in the pocket that binds the amide of NADH. KIEs show that solvent provides a proton, enabling accommodation of different nitro group placements, consistent with the broad repertoire of NR.
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Affiliation(s)
- Warintra Pitsawong
- Department of Chemistry, University of Kentucky, 505 Rose Street, Lexington, KY 40506-0055, USA
| | - Chad A Haynes
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, 741 South Limestone Street, Lexington, KY 40536-0509, USA
| | - Ronald L Koder
- Department of Chemistry, University of Kentucky, 505 Rose Street, Lexington, KY 40506-0055, USA
| | - David W Rodgers
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, 741 South Limestone Street, Lexington, KY 40536-0509, USA.
| | - Anne-Frances Miller
- Department of Chemistry, University of Kentucky, 505 Rose Street, Lexington, KY 40506-0055, USA; Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, 741 South Limestone Street, Lexington, KY 40536-0509, USA.
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Chalansonnet V, Mercier C, Orenga S, Gilbert C. Identification of Enterococcus faecalis enzymes with azoreductases and/or nitroreductase activity. BMC Microbiol 2017; 17:126. [PMID: 28545445 PMCID: PMC5445473 DOI: 10.1186/s12866-017-1033-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 05/15/2017] [Indexed: 01/03/2023] Open
Abstract
Background Nitroreductases, NAD(P)H dependent flavoenzymes, are found in most of bacterial species. Even if Enterococcus faecalis strains seems to present such activity because of their sensitivity to nitrofurans, no enzyme has been described. Nitroreductases were separated of others reductases due to their capacity to reduce nitro compounds. They are further classified based on their preference in cofactor: NADH and/or NADPH. However, recently, azoreductases have been studied for their strong activity on nitro compounds, especially nitro pro-drugs. This result suggests a crossing in azo and nitro reductase activities. For the moment, no nitroreductase was demonstrated to possess azoreductase activity. But due to sequence divergence and activity specificity linked to substrates, activity prediction is not evident and biochemical characterisation remains necessary. Identifying enzymes active on these two classes of compounds: azo and nitro is of interest to consider a common physiological role. Results Four putative nitroreductases, EF0404, EF0648, EF0655 and EF1181 from Enterococcus faecalis V583 were overexpressed as his-tagged recombinant proteins in Escherichia coli and purified following a native or a denaturing/renaturing protocol. EF0648, EF0655 and EF1181 showed nitroreductase activity and their cofactor preferences were in agreement with their protein sequence phylogeny. EF0404 showed both nitroreductase and azoreductase activity. Interestingly, the biochemical characteristics (substrate and cofactor specificity) of EF0404 resembled the properties of the known azoreductase AzoA. But its sequence matched within nitroreductase group, the same as EF0648. Conclusions We here demonstrate nitroreductase activity of the putative reductases identified in the Enterococcus faecalis V583 genome. We identified the first nitroreductase able to reduce directly an azo compound, while its protein sequence is close to others nitroreductases. Consequently, it highlights the difficulty in classifying these enzymes solely on the basis of protein sequence alignment and hereby the necessity to experimentally demonstrate the activity. The results provide additional data to consider a broader functionality of these reductases.
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Affiliation(s)
- Valérie Chalansonnet
- bioMérieux, 3 route de port Michaud, 38390, La Balme les Grottes, France. .,CIRI, International Center for Infectiology Research, Legionella pathogenesis group, Université de Lyon, Lyon, France. .,INSERM, U1111, Lyon, France. .,Ecole Normale Supérieure de Lyon, F-69364, Lyon, France. .,Université Lyon 1, F-69622, Lyon, France. .,CNRS, UMR5308, Lyon, France.
| | - Claire Mercier
- bioMérieux, 3 route de port Michaud, 38390, La Balme les Grottes, France.,CIRI, International Center for Infectiology Research, Legionella pathogenesis group, Université de Lyon, Lyon, France.,INSERM, U1111, Lyon, France.,Ecole Normale Supérieure de Lyon, F-69364, Lyon, France.,Université Lyon 1, F-69622, Lyon, France.,CNRS, UMR5308, Lyon, France
| | - Sylvain Orenga
- bioMérieux, 3 route de port Michaud, 38390, La Balme les Grottes, France
| | - Christophe Gilbert
- CIRI, International Center for Infectiology Research, Legionella pathogenesis group, Université de Lyon, Lyon, France.,INSERM, U1111, Lyon, France.,Ecole Normale Supérieure de Lyon, F-69364, Lyon, France.,Université Lyon 1, F-69622, Lyon, France.,CNRS, UMR5308, Lyon, France
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79
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Huang B, Chen W, Kuang YQ, Liu W, Liu XJ, Tang LJ, Jiang JH. A novel off–on fluorescent probe for sensitive imaging of mitochondria-specific nitroreductase activity in living tumor cells. Org Biomol Chem 2017; 15:4383-4389. [DOI: 10.1039/c7ob00781g] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We have developed a novel fluorescent probe of a benzoindocyanine probe (BICP), which is able to target mitochondria and realize sensitive and selective detection of NTR.
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Affiliation(s)
- Bo Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- College of Biology
- Hunan University
- Changsha
| | - Wen Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- College of Biology
- Hunan University
- Changsha
| | - Yong-Qing Kuang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- College of Biology
- Hunan University
- Changsha
| | - Wei Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- College of Biology
- Hunan University
- Changsha
| | - Xian-Jun Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- College of Biology
- Hunan University
- Changsha
| | - Li-Juan Tang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- College of Biology
- Hunan University
- Changsha
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- College of Biology
- Hunan University
- Changsha
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80
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Valiauga B, Williams EM, Ackerley DF, Čėnas N. Reduction of quinones and nitroaromatic compounds by Escherichia coli nitroreductase A (NfsA): Characterization of kinetics and substrate specificity. Arch Biochem Biophys 2016; 614:14-22. [PMID: 27986535 DOI: 10.1016/j.abb.2016.12.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 12/09/2016] [Accepted: 12/12/2016] [Indexed: 11/16/2022]
Abstract
NfsA, a major FMN-associated nitroreductase of E. coli, reduces nitroaromatic compounds via consecutive two-electron transfers. NfsA has potential applications in the biodegradation of nitroaromatic environment pollutants, e.g. explosives, and is also of interest for the anticancer strategy gene-directed enzyme prodrug therapy. However, the catalytic mechanism of NfsA is poorly characterized. Here we examined the NADPH-dependent reduction of quinones (n = 16) and nitroaromatic compounds (n = 12) by NfsA. We confirmed a general "ping-pong" reaction scheme, and preliminary rapid reaction studies of the enzyme reduction by NADPH showed that this step is much faster than the steady-state turnover number, i.e., the enzyme turnover is limited by the oxidative half-reaction. The reactivity of nitroaromatic compounds (log kcat/Km) followed a linear dependence on their single-electron reduction potential (E17), indicating a limited role for compound structure or active site flexibility in their reactivity. The reactivity of quinones was lower than that of nitroaromatics having similar E17 values, except for the significantly enhanced reactivity of 2-OH-1,4-naphthoquinones, consistent with observations previously made for the group B nitroreductase of Enterobacter cloacae. We present evidence that the reduction of quinones by NfsA is most consistent with a single-step (H-) hydride transfer mechanism.
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Affiliation(s)
- Benjaminas Valiauga
- Institute of Biochemistry of Vilnius University, Mokslininkų 12, LT-08662 Vilnius, Lithuania
| | - Elsie M Williams
- Victoria University of Wellington, School of Biological Sciences, Kelburn Parade, New Zealand
| | - David F Ackerley
- Victoria University of Wellington, School of Biological Sciences, Kelburn Parade, New Zealand
| | - Narimantas Čėnas
- Institute of Biochemistry of Vilnius University, Mokslininkų 12, LT-08662 Vilnius, Lithuania.
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81
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Wang B, Powell SM, Hessami N, Najar FZ, Thomas LM, Karr EA, West AH, Richter-Addo GB. Crystal structures of two nitroreductases from hypervirulent Clostridium difficile and functionally related interactions with the antibiotic metronidazole. Nitric Oxide 2016; 60:32-39. [PMID: 27623089 PMCID: PMC5079799 DOI: 10.1016/j.niox.2016.09.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 09/05/2016] [Accepted: 09/07/2016] [Indexed: 02/04/2023]
Abstract
Nitroreductases (NRs) are flavin mononucleotide (FMN)-dependent enzymes that catalyze the biotransformation of organic nitro compounds (RNO2; R = alkyl, aryl) to the nitroso RN=O, hydroxylamino RNHOH, or amine RNH2 derivatives. Metronidazole (Mtz) is a nitro-containing antibiotic that is commonly prescribed for lower-gut infections caused by the anaerobic bacterium Clostridium difficile. C. difficile infections rank number one among hospital acquired infections, and can result in diarrhea, severe colitis, or even death. Although NRs have been implicated in Mtz resistance of C. difficile, no NRs have been characterized from the hypervirulent R20291 strain of C. difficile. We report the first expression, purification, and three-dimensional X-ray crystal structures of two NRs from the C. difficile R20291 strain. The X-ray crystal structures of the two NRs were solved to 2.1 Å resolution. Their homodimeric structures exhibit the classic NR α+β fold, with each protomer binding one FMN cofactor near the dimer interface. Functional assays demonstrate that these two NRs metabolize Mtz with associated re-oxidation of the proteins. Importantly, these results represent the first isolation and characterization of NRs from the hypervirulent R20291 strain of relevance to organic RNO2 (e.g., Mtz) metabolism.
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Affiliation(s)
- Bing Wang
- Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman 73019, United States; Department of Chemistry and Biochemistry, University of Oklahoma, Norman 73019, United States
| | - Samantha M Powell
- Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman 73019, United States; Department of Chemistry and Biochemistry, University of Oklahoma, Norman 73019, United States
| | - Neda Hessami
- Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman 73019, United States; Department of Chemistry and Biochemistry, University of Oklahoma, Norman 73019, United States
| | - Fares Z Najar
- Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman 73019, United States; Department of Chemistry and Biochemistry, University of Oklahoma, Norman 73019, United States
| | - Leonard M Thomas
- Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman 73019, United States; Department of Chemistry and Biochemistry, University of Oklahoma, Norman 73019, United States
| | - Elizabeth A Karr
- Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman 73019, United States; Department of Microbiology and Plant Biology, University of Oklahoma, Norman 73019, United States
| | - Ann H West
- Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman 73019, United States; Department of Chemistry and Biochemistry, University of Oklahoma, Norman 73019, United States
| | - George B Richter-Addo
- Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman 73019, United States; Department of Chemistry and Biochemistry, University of Oklahoma, Norman 73019, United States.
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82
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N-pentyl-nitrofurantoin induces apoptosis in HL-60 leukemia cell line by upregulating BAX and downregulating BCL-xL gene expression. Pharmacol Rep 2016; 68:1046-53. [DOI: 10.1016/j.pharep.2016.06.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 06/02/2016] [Accepted: 06/06/2016] [Indexed: 12/16/2022]
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83
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Tanner JJ. Empirical power laws for the radii of gyration of protein oligomers. Acta Crystallogr D Struct Biol 2016; 72:1119-1129. [PMID: 27710933 PMCID: PMC5053138 DOI: 10.1107/s2059798316013218] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Accepted: 08/16/2016] [Indexed: 11/10/2022] Open
Abstract
The radius of gyration is a fundamental structural parameter that is particularly useful for describing polymers. It has been known since Flory's seminal work in the mid-20th century that polymers show a power-law dependence, where the radius of gyration is proportional to the number of residues raised to a power. The power-law exponent has been measured experimentally for denatured proteins and derived empirically for folded monomeric proteins using crystal structures. Here, the biological assemblies in the Protein Data Bank are surveyed to derive the power-law parameters for protein oligomers having degrees of oligomerization of 2-6 and 8. The power-law exponents for oligomers span a narrow range of 0.38-0.41, which is close to the value of 0.40 obtained for monomers. This result shows that protein oligomers exhibit essentially the same power-law behavior as monomers. A simple power-law formula is provided for estimating the oligomeric state from an experimental measurement of the radius of gyration. Several proteins in the Protein Data Bank are found to deviate substantially from power-law behavior by having an atypically large radius of gyration. Some of the outliers have highly elongated structures, such as coiled coils. For coiled coils, the radius of gyration does not follow a power law and instead scales linearly with the number of residues in the oligomer. Other outliers are proteins whose oligomeric state or quaternary structure is incorrectly annotated in the Protein Data Bank. The power laws could be used to identify such errors and help prevent them in future depositions.
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Affiliation(s)
- John J. Tanner
- Departments of Biochemistry and Chemistry, University of Missouri-Columbia, Columbia, MO 65211, USA
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84
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You X, Li L, Li X, Ma H, Zhang G, Zhang D. A New Tetraphenylethylene-Derived Fluorescent Probe for Nitroreductase Detection and Hypoxic-Tumor-Cell Imaging. Chem Asian J 2016; 11:2918-2923. [PMID: 27534906 DOI: 10.1002/asia.201600945] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Indexed: 11/05/2022]
Abstract
The fluorescence detection of nitroreductase (NTR) and evaluation of the hypoxia status of tumor cells are vital, not only for clinical diagnoses and therapy, but also for biomedical research. Herein, we report the synthesis and application of a new fluorometric "turn-on" probe for the detection of NTR (TPE-NO2 ) that takes advantage of the aggregation-induced emission of tetraphenylethylene. TPE-NO2 can detect NTR at concentrations as low as 5 ng mL-1 in aqueous solution. The detection mechanism relied on the aggregation and deaggregation of tetraphenylethylene molecules. Moreover, this fluorescent probe can be used to monitor the hypoxia status of tumor cells through the detection of endogenous NTR.
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Affiliation(s)
- Xue You
- Beijing National Laboratory for Molecular Sciences, Laboratories of Organic Solids and Analytical Chemistry for Living, Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Lihong Li
- Beijing National Laboratory for Molecular Sciences, Laboratories of Organic Solids and Analytical Chemistry for Living, Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Xiaohua Li
- Beijing National Laboratory for Molecular Sciences, Laboratories of Organic Solids and Analytical Chemistry for Living, Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Huimin Ma
- Beijing National Laboratory for Molecular Sciences, Laboratories of Organic Solids and Analytical Chemistry for Living, Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Guanxin Zhang
- Beijing National Laboratory for Molecular Sciences, Laboratories of Organic Solids and Analytical Chemistry for Living, Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.
| | - Deqing Zhang
- Beijing National Laboratory for Molecular Sciences, Laboratories of Organic Solids and Analytical Chemistry for Living, Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China. .,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China.
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85
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Ryan A. Azoreductases in drug metabolism. Br J Pharmacol 2016; 174:2161-2173. [PMID: 27487252 DOI: 10.1111/bph.13571] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 07/27/2016] [Accepted: 07/29/2016] [Indexed: 02/06/2023] Open
Abstract
Azoreductases are flavoenzymes that have been characterized in a range of prokaryotes and eukaryotes. Bacterial azoreductases are associated with the activation of two classes of drug, azo drugs for the treatment of inflammatory bowel disease and nitrofuran antibiotics. The mechanism of reduction of azo compounds is presented; it requires tautomerisation of the azo compound to a quinoneimine and provides a unifying mechanism for the reduction of azo and quinone substrates by azoreductases. The importance of further work in the characterization of azoreductases from enteric bacteria is highlighted to aid in the development of novel drugs for the treatment of colon related disorders. Human azoreductases are known to play a crucial role in the metabolism of a number of quinone-containing cancer chemotherapeutic drugs. The mechanism of hydride transfer to quinones, which is shared not only between eukaryotic and prokaryotic azoreductases but also the wider family of NAD(P)H quinone oxidoreductases, is outlined. The importance of common single nucleotide polymorphisms (SNPs) in human azoreductases is described not only in cancer prognosis but also with regard to their effects on the efficacy of quinone drug-based cancer chemotherapeutic regimens. This highlights the need to screen patients for azoreductase SNPs ahead of treatment with these regimens. LINKED ARTICLES This article is part of a themed section on Drug Metabolism and Antibiotic Resistance in Micro-organisms. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v174.14/issuetoc.
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Affiliation(s)
- Ali Ryan
- Faculty of Science, Engineering and Computing, Kingston University, Kingston upon Thames, UK
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86
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Noschese A, Buonerba A, Canton P, Milione S, Capacchione C, Grassi A. Highly efficient and selective reduction of nitroarenes into anilines catalyzed by gold nanoparticles incarcerated in a nanoporous polymer matrix: Role of the polymeric support and insight into the reaction mechanism. J Catal 2016. [DOI: 10.1016/j.jcat.2016.05.005] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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87
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Functional and structural characterization of two Bacillus megaterium nitroreductases biotransforming the herbicide mesotrione. Biochem J 2016; 473:1443-53. [DOI: 10.1042/bj20151366] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 03/22/2016] [Indexed: 01/23/2023]
Abstract
Mesotrione is a selective herbicide belonging to the triketone family, commonly used on maize cultures since 2003. A mesotrione-transforming Bacillus megaterium Mes11 strain isolated from an agricultural soil was used as a model to identify the key enzymes initiating the biotransformation of this herbicide. Two enzymes (called NfrA1 and NfrA2/YcnD) were identified, and functionally and structurally characterized. Both belong to the NfsA FRP family of the nitro-FMN reductase superfamily (type I oxygen-insensitive nitroreductase) and show optimal pH and temperature of 6–6.5 and 23–25°C, respectively. Both undergo a Ping Pong Bi Bi mechanism, with NADPH and NADPH/NADH as cofactors for NfrA1 and NfrA2/YcnD, respectively. It is interesting that both can also reduce various nitro compounds including pesticides, antibiotics, one prodrug and 4-methylsulfonyl-2-nitrobenzoic acid, one of the mesotrione metabolites retrieved from the environment. The present study constitutes the first identification of mesotrione-transforming enzymes. These enzymes (or their corresponding genes) could be used as biomarkers to predict the capacity of ecosystems to transform mesotrione and assess their contamination by both the parent molecule and/or the metabolites.
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88
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Blanco E, Esteve-Adell I, Atienzar P, Casas JA, Hernández P, Quintana C. Cucurbit[7]uril-stabilized gold nanoparticles as catalysts of the nitro compound reduction reaction. RSC Adv 2016. [DOI: 10.1039/c6ra07168f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Catalytic performance of cucurbit[7]uril-stabilized gold nanoparticles on the reduction reaction of 4-nitrophenol and nitrofurantoin.
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Affiliation(s)
- E. Blanco
- Departamento de Química Analítica y Análisis Instrumental
- Universidad Autónoma de Madrid. Cantoblanco
- 28049 Madrid
- Spain
| | - I. Esteve-Adell
- Instituto Universitario de Tecnología Química CSIC-UPV
- Departamento de Química
- Universidad Politécnica de Valencia
- 46022 Valencia
- Spain
| | - P. Atienzar
- Instituto Universitario de Tecnología Química CSIC-UPV
- Departamento de Química
- Universidad Politécnica de Valencia
- 46022 Valencia
- Spain
| | - J. A. Casas
- Departamento de Química Física Aplicada
- Universidad Autónoma de Madrid. Cantoblanco
- 28049 Madrid
- Spain
| | - P. Hernández
- Departamento de Química Analítica y Análisis Instrumental
- Universidad Autónoma de Madrid. Cantoblanco
- 28049 Madrid
- Spain
| | - C. Quintana
- Departamento de Química Analítica y Análisis Instrumental
- Universidad Autónoma de Madrid. Cantoblanco
- 28049 Madrid
- Spain
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89
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Šarlauskas J, Pečiukaitytė-Alksnė M, Misevičienė L, Marozienė A, Polmickaitė E, Staniulytė Z, Čėnas N, Anusevičius Ž. Naphtho[1′,2′:4,5]imidazo[1,2-a]pyridine-5,6-diones: Synthesis, enzymatic reduction and cytotoxic activity. Bioorg Med Chem Lett 2016; 26:512-517. [DOI: 10.1016/j.bmcl.2015.11.084] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 11/22/2015] [Accepted: 11/23/2015] [Indexed: 11/28/2022]
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90
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Giese M, Albrecht M, Rissanen K. Experimental investigation of anion–π interactions – applications and biochemical relevance. Chem Commun (Camb) 2016; 52:1778-95. [DOI: 10.1039/c5cc09072e] [Citation(s) in RCA: 177] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Anion–π interactions, intuitively repulsive forces, turned from controversial to a well-established non-covalent interaction over the past quarter of a century.
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Affiliation(s)
- M. Giese
- Institut für Organische Chemie
- Universität Duisburg Essen
- 45141 Essen
- Germany
| | - M. Albrecht
- Institut für Organische Chemie
- RWTH Aachen University
- 52074 Aachen
- Germany
| | - K. Rissanen
- University of Jyvaskyla
- Department of Chemistry
- Nanoscience Center
- P.O. Box. 35
- FI-40014 University of Jyvaskyla
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91
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Nitroreductase gene-directed enzyme prodrug therapy: insights and advances toward clinical utility. Biochem J 2015; 471:131-53. [PMID: 26431849 DOI: 10.1042/bj20150650] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This review examines the vast catalytic and therapeutic potential offered by type I (i.e. oxygen-insensitive) nitroreductase enzymes in partnership with nitroaromatic prodrugs, with particular focus on gene-directed enzyme prodrug therapy (GDEPT; a form of cancer gene therapy). Important first indications of this potential were demonstrated over 20 years ago, for the enzyme-prodrug pairing of Escherichia coli NfsB and CB1954 [5-(aziridin-1-yl)-2,4-dinitrobenzamide]. However, it has become apparent that both the enzyme and the prodrug in this prototypical pairing have limitations that have impeded their clinical progression. Recently, substantial advances have been made in the biodiscovery and engineering of superior nitroreductase variants, in particular development of elegant high-throughput screening capabilities to enable optimization of desirable activities via directed evolution. These advances in enzymology have been paralleled by advances in medicinal chemistry, leading to the development of second- and third-generation nitroaromatic prodrugs that offer substantial advantages over CB1954 for nitroreductase GDEPT, including greater dose-potency and enhanced ability of the activated metabolite(s) to exhibit a local bystander effect. In addition to forging substantial progress towards future clinical trials, this research is supporting other fields, most notably the development and improvement of targeted cellular ablation capabilities in small animal models, such as zebrafish, to enable cell-specific physiology or regeneration studies.
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92
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Mukherjee A, Rokita SE. Single Amino Acid Switch between a Flavin-Dependent Dehalogenase and Nitroreductase. J Am Chem Soc 2015; 137:15342-5. [PMID: 26616824 PMCID: PMC4684082 DOI: 10.1021/jacs.5b07540] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
A single
mutation within a flavoprotein is capable of switching
the catalytic activity of a dehalogenase into a nitroreductase.
This change in function correlates with a destabilization of the one-electron-reduced
flavin semiquinone that is differentially expressed in the nitro-FMN
reductase superfamily during redox cycling. The diversity of
function within such a superfamily therefore has the potential
to arise from rapid evolution, and its members should provide a convenient
basis for developing new catalysts with an altered specificity of
choice.
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Affiliation(s)
- Arnab Mukherjee
- Department of Chemistry, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Steven E Rokita
- Department of Chemistry, Johns Hopkins University , Baltimore, Maryland 21218, United States
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93
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Identification of novel members of the bacterial azoreductase family in Pseudomonas aeruginosa. Biochem J 2015; 473:549-58. [PMID: 26621870 DOI: 10.1042/bj20150856] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 11/30/2015] [Indexed: 11/17/2022]
Abstract
Azoreductases are a family of diverse enzymes found in many pathogenic bacteria as well as distant homologues being present in eukarya. In addition to having azoreductase activity, these enzymes are also suggested to have NAD(P)H quinone oxidoreductase (NQO) activity which leads to a proposed role in plant pathogenesis. Azoreductases have also been suggested to play a role in the mammalian pathogenesis of Pseudomonas aeruginosa. In view of the importance of P. aeruginosa as a pathogen, we therefore characterized recombinant enzymes following expression of a group of putative azoreductase genes from P. aeruginosa expressed in Escherichia coli. The enzymes include members of the arsenic-resistance protein H (ArsH), tryptophan repressor-binding protein A (WrbA), modulator of drug activity B (MdaB) and YieF families. The ArsH, MdaB and YieF family members all show azoreductase and NQO activities. In contrast, WrbA is the first enzyme to show NQO activity but does not reduce any of the 11 azo compounds tested under a wide range of conditions. These studies will allow further investigation of the possible role of these enzymes in the pathogenesis of P. aeruginosa.
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94
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Xu J, Sun S, Li Q, Yue Y, Li Y, Shao S. A rapid response "Turn-On" fluorescent probe for nitroreductase detection and its application in hypoxic tumor cell imaging. Analyst 2015; 140:574-81. [PMID: 25422882 DOI: 10.1039/c4an01934b] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A novel "Turn-On" fluorescent probe, quaternarized 4-pyridinyl-substituted BODIPY dye by incorporating a 5-nitrofuran moiety, was developed and applied for imaging the hypoxic status of tumor cells by the indirect detection of nitroreductase. The design was based on a nitroreductase-catalyzed reduction of the nitrofuran moiety in the presence of reduced nicotinamide adenine dinucleotide (NADH) as an electron donor and followed by the 1,6-rearrangement-elimination and the release of free 4-pyridinyl-substituted BODIPY dye . This probe displayed desired properties such as high specificity, "Turn-On" fluorescence response with suitable sensitivity, appreciable water solubility and rapid response time (within 5 min). Moreover, as a biocompatible molecule, the probe has been successfully applied for imaging the hypoxic status of tumor cells (e.g. A549 cells) and especially used for real-time determination of nitroreductase produced by Escherichia coli. Therefore, we hope to apply this novel method in the biomedical research fields for the imaging of disease-relevant hypoxia and detection of pathogenic microorganisms.
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Affiliation(s)
- Jian Xu
- Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, P. R. China.
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95
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Transformation pathway of 2,4,6-trinitrotoluene by Escherichia coli nitroreductases and improvement of activity using structure-based mutagenesis. Process Biochem 2015. [DOI: 10.1016/j.procbio.2015.01.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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96
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Song HN, Jeong DG, Bang SY, Paek SH, Park BC, Park SG, Woo EJ. Crystal structure of the fungal nitroreductase Frm2 from Saccharomyces cerevisiae. Protein Sci 2015; 24:1158-63. [PMID: 25864423 DOI: 10.1002/pro.2686] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Accepted: 03/31/2015] [Indexed: 11/09/2022]
Abstract
Nitroreductases are flavoenzymes that catalyze nitrocompounds and are widely utilized in industrial applications due to their detoxification potential and activation of biomedicinal prodrugs. Type I nitroreductases are classified into subgroups depending on the use of NADPH or NADH as the electron donor. Here, we report the crystal structure of the fungal nitroreductase Frm2 from Saccharomyces cerevisiae, one of the uncharacterized subgroups of proteins, to reveal its minimal architecture previously observed in bacterial nitroreductases such as CinD and YdjA. The structure lacks protruding helical motifs that form part of the cofactor and substrate binding site, resulting in an open and wide active site geometry. Arg82 is uniquely conserved in proximity to the substrate binding site in Frm2 homologues and plays a crucial role in the activity of the active site. Frm2 primarily utilizes NADH to reduce 4-NQO. Because missing helical elements are involved in the direct binding to the NAD(P)H in group A or group B in Type I family, Frm2 and its homologues may represent a distinctive subgroup with an altered binding mode for the reducing compound. This result provides a structural basis for the rational design of novel prodrugs with the ability to reduce nitrogen-containing hazardous molecules.
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Affiliation(s)
- Hyung-Nam Song
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, Republic of Korea.,Department of Biotechnology and Bioinformatics, Korea University, Sejong, 339-700, Republic of Korea
| | - Dae-Gwin Jeong
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, Republic of Korea.,Bio-Analytical Science Division, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Seo-Young Bang
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, Republic of Korea
| | - Se-Hwan Paek
- Department of Biotechnology and Bioinformatics, Korea University, Sejong, 339-700, Republic of Korea
| | - Byoung-Chul Park
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, Republic of Korea.,Bio-Analytical Science Division, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Sung-Goo Park
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, Republic of Korea.,Bio-Analytical Science Division, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Eui-Jeon Woo
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, Republic of Korea.,Bio-Analytical Science Division, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
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97
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Bai J, Zhou Y, Chen Q, Yang Q, Yang J. Altering the regioselectivity of a nitroreductase in the synthesis of arylhydroxylamines by structure-based engineering. Chembiochem 2015; 16:1219-25. [PMID: 25917861 DOI: 10.1002/cbic.201500070] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Indexed: 11/07/2022]
Abstract
Nitroreductases have great potential for the highly efficient reduction of aryl nitro compounds to arylhydroxylamines. However, regioselective reduction of the desired nitro group in polynitroarenes is still a challenge. Here, we describe the structure-based engineering of Escherichia coli nitroreductase NfsB to alter its regioselectivity, in order to achieve reduction of a target nitro group. When 2,4-dinitrotoluene was used as the substrate, the wild-type enzyme regioselectively reduced the 4-NO2 group, but the T41L/N71S/F124W mutant primarily reduced the 2-NO2 group, without loss of activity. The crystal structure of T41L/N71S/F124W and docking experiments indicated that the regioselectivity change (from 4-NO2 to 2-NO2 ) might result from the increased hydrophobicity of residues 41 and 124 (proximal to FMN) and conformational changes in residues 70 and 124.
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Affiliation(s)
- Jing Bai
- School of Life Science and Biotechnology, Dalian University of Technology, No. 2 Linggong Road, Dalian-116023 (China)
| | - Yong Zhou
- School of Software Technology, Dalian University of Technology, 321 Tuqiang Street, Development Zone, Dalian (China)
| | - Qi Chen
- School of Life Science and Biotechnology, Dalian University of Technology, No. 2 Linggong Road, Dalian-116023 (China)
| | - Qing Yang
- School of Life Science and Biotechnology, Dalian University of Technology, No. 2 Linggong Road, Dalian-116023 (China)
| | - Jun Yang
- School of Life Science and Biotechnology, Dalian University of Technology, No. 2 Linggong Road, Dalian-116023 (China).
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98
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Hou F, Miyakawa T, Kitamura N, Takeuchi M, Park SB, Kishino S, Ogawa J, Tanokura M. Structure and reaction mechanism of a novel enone reductase. FEBS J 2015; 282:1526-37. [PMID: 25702712 DOI: 10.1111/febs.13239] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 01/28/2015] [Accepted: 02/16/2015] [Indexed: 11/28/2022]
Abstract
UNLABELLED Recently, a novel gut-bacterial fatty acid metabolism, saturation of polyunsaturated fatty acid, that modifies fatty acid composition of the host and is expected to improve our health by altering lipid metabolism related to the onset of metabolic syndrome, was discovered in Lactobacillus plantarum AKU 1009a. Enzymes constituting the pathway catalyze sequential reactions of free fatty acids without CoA or acyl carrier protein. Among these enzymes, CLA-ER was identified as an enone reductase that can saturate the C=C bond in the 10-oxo-trans-11-octadecenoic acid (KetoB) to produce 10-oxo-octadecanoic acid (KetoC). This enzyme is the sole member of the NADH oxidase/flavin reductase family that has been identified to exert an enone reduction activity. Here, we report both the structure of holo CLA-ER with cofactor FMN and the KetoC-bound structure, which elucidate the structural basis of enone group recognition of free fatty acids and provide the unique catalytic mechanism as an enone reductase in the NADH oxidase/flavin reductase family. A 'cap' structure of CLA-ER underwent a large conformational change upon KetoC binding. The resulting binding site adopts a sandglass shape and is positively charged at one side, which is suitable to recognize a fatty acid molecule with enone group. Based on the crystal structures and enzymatic activities of several mutants, we identified C51, F126 and Y101 as the critical residues for the reaction and proposed an alternative electron transfer pathway of CLA-ER. These findings expand our understanding of the complexity of fatty acid metabolism. DATABASE The atomic coordinates have been deposited in the Protein Data Bank (PDB), www.pdb.org (PDB ID 4QLX, 4QLY).
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Affiliation(s)
- Feng Hou
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Japan
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99
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Anion-π Interactions in Supramolecular Chemistry and Catalysis. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2015. [DOI: 10.1007/978-3-319-14163-3_16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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100
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de Carvalho AS, Salomão K, de Castro SL, Conde TR, Zamith HPDS, Caffarena ER, Hall BS, Wilkinson SR, Boechat N. Megazol and its bioisostere 4H-1,2,4-triazole: comparing the trypanocidal, cytotoxic and genotoxic activities and their in vitro and in silico interactions with the Trypanosoma brucei nitroreductase enzyme. Mem Inst Oswaldo Cruz 2014; 109:315-23. [PMID: 24676659 PMCID: PMC4131783 DOI: 10.1590/0074-0276140497] [Citation(s) in RCA: 13] [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: 10/11/2013] [Accepted: 02/13/2014] [Indexed: 11/22/2022] Open
Abstract
Megazol (7) is a 5-nitroimidazole that is highly active against Trypanosoma cruzi and Trypanosoma brucei, as well as drug-resistant forms of trypanosomiasis. Compound 7 is not used clinically due to its mutagenic and genotoxic properties, but has been largely used as a lead compound. Here, we compared the activity of 7 with its 4H-1,2,4-triazole bioisostere (8) in bloodstream forms of T. brucei and T. cruzi and evaluated their activation by T. brucei type I nitroreductase (TbNTR) enzyme. We also analysed the cytotoxic and genotoxic effects of these compounds in whole human blood using Comet and fluorescein diacetate/ethidium bromide assays. Although the only difference between 7 and 8 is the substitution of sulphur (in the thiadiazole in 7) for nitrogen (in the triazole in 8), the results indicated that 8 had poorer antiparasitic activity than 7 and was not genotoxic, whereas 7 presented this effect. The determination of Vmax indicated that although 8 was metabolised more rapidly than 7, it bounds to the TbNTR with better affinity, resulting in equivalent kcat/KM values. Docking assays of 7 and 8 performed within the active site of a homology model of the TbNTR indicating that 8 had greater affinity than 7.
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Affiliation(s)
| | - Kelly Salomão
- Laboratório de Biologia Celular, Instituto Oswaldo Cruz-Fiocruz, Rio de
Janeiro, RJ, Brasil
| | | | - Taline Ramos Conde
- Departamento de Farmacologia e Toxicologia, Instituto Nacional de
Controle de Qualidade em Saúde - Fiocruz, Rio de Janeiro, RJ,
Brasil
| | - Helena Pereira da Silva Zamith
- Departamento de Farmacologia e Toxicologia, Instituto Nacional de
Controle de Qualidade em Saúde - Fiocruz, Rio de Janeiro, RJ,
Brasil
| | | | - Belinda Suzette Hall
- School of Biological and Chemical Sciences, Queen Mary University of
London, London, UK
| | | | - Núbia Boechat
- Departamento de Síntese de Fármacos, Farmanguinhos - Fiocruz, Rio de
Janeiro, RJ, Brasil
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