1
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Rich MH, Sharrock AV, Mulligan TS, Matthews F, Brown AS, Lee-Harwood HR, Williams EM, Copp JN, Little RF, Francis JJB, Horvat CN, Stevenson LJ, Owen JG, Saxena MT, Mumm JS, Ackerley DF. A metagenomic library cloning strategy that promotes high-level expression of captured genes to enable efficient functional screening. Cell Chem Biol 2023; 30:1680-1691.e6. [PMID: 37898120 PMCID: PMC10842177 DOI: 10.1016/j.chembiol.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 06/17/2023] [Accepted: 10/02/2023] [Indexed: 10/30/2023]
Abstract
Functional screening of environmental DNA (eDNA) libraries is a potentially powerful approach to discover enzymatic "unknown unknowns", but is usually heavily biased toward the tiny subset of genes preferentially transcribed and translated by the screening strain. We have overcome this by preparing an eDNA library via partial digest with restriction enzyme FatI (cuts CATG), causing a substantial proportion of ATG start codons to be precisely aligned with strong plasmid-encoded promoter and ribosome-binding sequences. Whereas we were unable to select nitroreductases from standard metagenome libraries, our FatI strategy yielded 21 nitroreductases spanning eight different enzyme families, each conferring resistance to the nitro-antibiotic niclosamide and sensitivity to the nitro-prodrug metronidazole. We showed expression could be improved by co-expressing rare tRNAs and encoded proteins purified directly using an embedded His6-tag. In a transgenic zebrafish model of metronidazole-mediated targeted cell ablation, our lead MhqN-family nitroreductase proved ∼5-fold more effective than the canonical nitroreductase NfsB.
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Affiliation(s)
- Michelle H Rich
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Abigail V Sharrock
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Timothy S Mulligan
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Frazer Matthews
- Department of Genetic Medicine, McKusick-Nathans Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Alistair S Brown
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Hannah R Lee-Harwood
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Elsie M Williams
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Janine N Copp
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Rory F Little
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Jenni J B Francis
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Claire N Horvat
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Luke J Stevenson
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Jeremy G Owen
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Meera T Saxena
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Jeff S Mumm
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Genetic Medicine, McKusick-Nathans Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Center for Nanomedicine, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - David F Ackerley
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand.
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2
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Sharrock AV, Mumm JS, Bagdžiūnas G, Čėnas N, Arcus VL, Ackerley DF. The Crystal Structure of Engineered Nitroreductase NTR 2.0 and Impact of F70A and F108Y Substitutions on Substrate Specificity. Int J Mol Sci 2023; 24:ijms24076633. [PMID: 37047605 PMCID: PMC10095097 DOI: 10.3390/ijms24076633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/25/2023] [Accepted: 03/30/2023] [Indexed: 04/05/2023] Open
Abstract
Bacterial nitroreductase enzymes that convert prodrugs to cytotoxins are valuable tools for creating transgenic targeted ablation models to study cellular function and cell-specific regeneration paradigms. We recently engineered a nitroreductase (“NTR 2.0”) for substantially enhanced reduction of the prodrug metronidazole, which permits faster cell ablation kinetics, cleaner interrogations of cell function, ablation of previously recalcitrant cell types, and extended ablation paradigms useful for modelling chronic diseases. To provide insight into the enhanced enzymatic mechanism of NTR 2.0, we have solved the X-ray crystal structure at 1.85 Angstroms resolution and compared it to the parental enzyme, NfsB from Vibrio vulnificus. We additionally present a survey of reductive activity with eight alternative nitroaromatic substrates, to provide access to alternative ablation prodrugs, and explore applications such as remediation of dinitrotoluene pollutants. The predicted binding modes of four key substrates were investigated using molecular modelling.
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Affiliation(s)
- Abigail V. Sharrock
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Jeff S. Mumm
- Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Gintautas Bagdžiūnas
- Institute of Biochemistry, University of Vilnius, Saulėtekio 7, LT-10257 Vilnius, Lithuania
| | - Narimantas Čėnas
- Institute of Biochemistry, University of Vilnius, Saulėtekio 7, LT-10257 Vilnius, Lithuania
| | - Vickery L. Arcus
- Te Aka Mātuatua-School of Science, University of Waikato, Hamilton 3240, New Zealand
| | - David F. Ackerley
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
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3
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Rich MH, Sharrock AV, Mulligan TS, Matthews F, Brown AS, Lee-Harwood HR, Williams EM, Copp JN, Little RF, Francis JJB, Horvat CN, Stevenson LJ, Owen JG, Saxena MT, Mumm JS, Ackerley DF. A metagenomic library cloning strategy that promotes high-level expression of captured genes to enable efficient functional screening. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.24.534183. [PMID: 36993673 PMCID: PMC10055417 DOI: 10.1101/2023.03.24.534183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Functional screening of environmental DNA (eDNA) libraries is a potentially powerful approach to discover enzymatic "unknown unknowns", but is usually heavily biased toward the tiny subset of genes preferentially transcribed and translated by the screening strain. We have overcome this by preparing an eDNA library via partial digest with restriction enzyme FatI (cuts CATG), causing a substantial proportion of ATG start codons to be precisely aligned with strong plasmid-encoded promoter and ribosome-binding sequences. Whereas we were unable to select nitroreductases from standard metagenome libraries, our FatI strategy yielded 21 nitroreductases spanning eight different enzyme families, each conferring resistance to the nitro-antibiotic niclosamide and sensitivity to the nitro-prodrug metronidazole. We showed expression could be improved by co-expressing rare tRNAs and encoded proteins purified directly using an embedded His6-tag. In a transgenic zebrafish model of metronidazole-mediated targeted cell ablation, our lead MhqN-family nitroreductase proved ~5-fold more effective than the canonical nitroreductase NfsB.
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Affiliation(s)
- Michelle H Rich
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Abigail V Sharrock
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Timothy S Mulligan
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Frazer Matthews
- Department of Genetic Medicine, McKusick-Nathans Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Alistair S Brown
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Hannah R Lee-Harwood
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Elsie M Williams
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
- Current address: Burnet Institute, Melbourne, Victoria 3004, Australia
| | - Janine N Copp
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
- Current addresses: Michael Smith Laboratories, University of British Columbia, Vancouver BC V6T 1Z4, Canada; Abcellera Biologics Inc, Vancouver BC V5Y 0A1, Canada
| | - Rory F Little
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
- Current address: Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Jenni JB Francis
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Claire N Horvat
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
- Current address: Teva Pharmaceuticals, Sydney, New South Wales 2113, Australia
| | - Luke J Stevenson
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Jeremy G Owen
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Meera T Saxena
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Jeff S Mumm
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Genetic Medicine, McKusick-Nathans Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Center for Nanomedicine, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - David F Ackerley
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
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4
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Singleton DC, Mowday AM, Guise CP, Syddall SP, Bai SY, Li D, Ashoorzadeh A, Smaill JB, Wilson WR, Patterson AV. Bioreductive prodrug PR-104 improves the tumour distribution and titre of the nitroreductase-armed oncolytic adenovirus ONYX-411 NTR leading to therapeutic benefit. Cancer Gene Ther 2022; 29:1021-1032. [PMID: 34837065 DOI: 10.1038/s41417-021-00409-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 10/05/2021] [Accepted: 11/09/2021] [Indexed: 11/09/2022]
Abstract
Advances in the field of cancer immunotherapy have stimulated renewed interest in adenoviruses as oncolytic agents. Clinical experience has shown that oncolytic adenoviruses are safe and well tolerated but possess modest single-agent activity. One approach to improve the potency of oncolytic viruses is to utilise their tumour selectivity to deliver genes encoding prodrug-activating enzymes. These enzymes can convert prodrugs into cytotoxic species within the tumour; however, these cytotoxins can interfere with viral replication and limit utility. In this work, we evaluated the activity of a nitroreductase (NTR)-armed oncolytic adenovirus ONYX-411NTR in combination with the clinically tested bioreductive prodrug PR-104. Both NTR-expressing cells in vitro and xenografts containing a minor population of NTR-expressing cells were highly sensitive to PR-104. Pharmacologically relevant prodrug exposures did not interfere with ONYX-411NTR replication in vitro. In vivo, prodrug administration increased virus titre and improved virus distribution within tumour xenografts. Colonisation of tumours with high ONYX-411NTR titre resulted in NTR expression and prodrug activation. The combination of ONYX-411NTR with PR-104 was efficacious against HCT116 xenografts, whilst neither prodrug nor virus were active as single agents. This work highlights the potential for future clinical development of NTR-armed oncolytic viruses in combination with bioreductive prodrugs.
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Affiliation(s)
- Dean C Singleton
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand. .,Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand. .,Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand.
| | - Alexandra M Mowday
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
| | - Chris P Guise
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand
| | - Sophie P Syddall
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand
| | - Sally Y Bai
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand
| | - Dan Li
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand
| | - Amir Ashoorzadeh
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
| | - Jeff B Smaill
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
| | - William R Wilson
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
| | - Adam V Patterson
- Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
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5
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Sharrock AV, Mulligan TS, Hall KR, Williams EM, White DT, Zhang L, Emmerich K, Matthews F, Nimmagadda S, Washington S, Le KD, Meir-Levi D, Cox OL, Saxena MT, Calof AL, Lopez-Burks ME, Lander AD, Ding D, Ji H, Ackerley DF, Mumm JS. NTR 2.0: a rationally engineered prodrug-converting enzyme with substantially enhanced efficacy for targeted cell ablation. Nat Methods 2022; 19:205-215. [PMID: 35132245 PMCID: PMC8851868 DOI: 10.1038/s41592-021-01364-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 11/29/2021] [Indexed: 11/12/2022]
Abstract
Transgenic expression of bacterial nitroreductase (NTR) enzymes sensitizes eukaryotic cells to prodrugs such as metronidazole (MTZ), enabling selective cell-ablation paradigms that have expanded studies of cell function and regeneration in vertebrates. However, first-generation NTRs required confoundingly toxic prodrug treatments to achieve effective cell ablation, and some cell types have proven resistant. Here we used rational engineering and cross-species screening to develop an NTR variant, NTR 2.0, which exhibits ~100-fold improvement in MTZ-mediated cell-specific ablation efficacy, eliminating the need for near-toxic prodrug treatment regimens. NTR 2.0 therefore enables sustained cell-loss paradigms and ablation of previously resistant cell types. These properties permit enhanced interrogations of cell function, extended challenges to the regenerative capacities of discrete stem cell niches, and novel modeling of chronic degenerative diseases. Accordingly, we have created a series of bipartite transgenic reporter/effector resources to facilitate dissemination of NTR 2.0 to the research community.
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Affiliation(s)
- Abigail V Sharrock
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Timothy S Mulligan
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Kelsi R Hall
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Elsie M Williams
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - David T White
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Liyun Zhang
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Kevin Emmerich
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Frazer Matthews
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Saumya Nimmagadda
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Selena Washington
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Katherine D Le
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Danielle Meir-Levi
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Olivia L Cox
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Meera T Saxena
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA
- Luminomics, Baltimore, MD, USA
| | - Anne L Calof
- Department of Anatomy and Neurobiology, University of California, Irvine, CA, USA
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Martha E Lopez-Burks
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Arthur D Lander
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Ding Ding
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Hongkai Ji
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - David F Ackerley
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand.
- Centre for Biodiscovery and Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington, New Zealand.
| | - Jeff S Mumm
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA.
- The Center for Nanomedicine, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA.
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD, USA.
- Department of Genetic Medicine, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.
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6
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Use of an optimised enzyme/prodrug combination for Clostridia directed enzyme prodrug therapy induces a significant growth delay in necrotic tumours. Cancer Gene Ther 2022; 29:178-188. [PMID: 33558701 DOI: 10.1038/s41417-021-00296-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 12/20/2020] [Accepted: 01/12/2021] [Indexed: 01/30/2023]
Abstract
Necrosis is a typical histological feature of solid tumours that provides a selective environment for growth of the non-pathogenic anaerobic bacterium Clostridium sporogenes. Modest anti-tumour activity as a single agent encouraged the use of C. sporogenes as a vector to express therapeutic genes selectively in tumour tissue, a concept termed Clostridium Directed Enzyme Prodrug Therapy (CDEPT). Here, we examine the ability of a recently identified Neisseria meningitidis type I nitroreductase (NmeNTR) to metabolise the prodrug PR-104A in an in vivo model of CDEPT. Human HCT116 colon cancer cells stably over-expressing NmeNTR demonstrated significant sensitivity to PR-104A, the imaging agent EF5, and several nitro(hetero)cyclic anti-infective compounds. Chemical induction of necrosis in human H1299 xenografts by the vascular disrupting agent vadimezan promoted colonisation by NmeNTR-expressing C. sporogenes, and efficacy studies demonstrated moderate but significant anti-tumour activity of spores when compared to untreated controls. Inclusion of the pre-prodrug PR-104 into the treatment schedule provided significant additional activity, indicating proof-of-principle. Successful preclinical evaluation of a transferable gene that enables metabolism of both PET imaging agents (for vector visualisation) and prodrugs (for conditional enhancement of efficacy) is an important step towards the prospect of CDEPT entering clinical evaluation.
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7
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Interrogation of the Structure–Activity Relationship of a Lipophilic Nitroaromatic Prodrug Series Designed for Cancer Gene Therapy Applications. Pharmaceuticals (Basel) 2022; 15:ph15020185. [PMID: 35215297 PMCID: PMC8877822 DOI: 10.3390/ph15020185] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/25/2022] [Accepted: 01/27/2022] [Indexed: 11/17/2022] Open
Abstract
PR-104A is a dual hypoxia/nitroreductase gene therapy prodrug by virtue of its ability to undergo either one- or two-electron reduction to its cytotoxic species. It has been evaluated extensively in pre-clinical GDEPT studies, yet off-target human aldo-keto reductase AKR1C3-mediated activation has limited its use. Re-evaluation of this chemical scaffold has previously identified SN29176 as an improved hypoxia-activated prodrug analogue of PR-104A that is free from AKR1C3 activation. However, optimization of the bystander effect of SN29176 is required for use in a GDEPT setting to compensate for the non-uniform distribution of therapeutic gene transfer that is often observed with current gene therapy vectors. A lipophilic series of eight analogues were synthesized from commercially available 3,4-difluorobenzaldehyde. Calculated octanol-water partition coefficients (LogD7.4) spanned > 2 orders of magnitude. 2D anti-proliferative and 3D multicellular layer assays were performed using isogenic HCT116 cells expressing E. coli NfsA nitroreductase (NfsA_Ec) or AKR1C3 to determine enzyme activity and measure bystander effect. A variation in potency for NfsA_Ec was observed, while all prodrugs appeared AKR1C3-resistant by 2D assay. However, 3D assays indicated that increasing prodrug lipophilicity correlated with increased AKR1C3 activation and NfsA_Ec activity, suggesting that metabolite loss from the cell of origin into media during 2D monolayer assays could mask cytotoxicity. Three prodrugs were identified as bono fide AKR1C3-negative candidates whilst maintaining activity with NfsA_Ec. These were converted to their phosphate ester pre-prodrugs before being taken forward into in vivo therapeutic efficacy studies. Ultimately, 2-(5-(bis(2-bromoethyl)amino)-4-(ethylsulfonyl)-N-methyl-2-nitrobenzamido)ethyl dihydrogen phosphate possessed a significant 156% improvement in median survival in mixed NfsA_Ec/WT tumors compared to untreated controls (p = 0.005), whilst still maintaining hypoxia selectivity comparable to PR-104A.
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8
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Liu T, Wang Y, Feng L, Tian X, Cui J, Yu Z, Wang C, Zhang B, James TD, Ma X. 2D Strategy for the Construction of an Enzyme-Activated NIR Fluorophore Suitable for the Visual Sensing and Profiling of Homologous Nitroreductases from Various Bacterial Species. ACS Sens 2021; 6:3348-3356. [PMID: 34469146 PMCID: PMC8477384 DOI: 10.1021/acssensors.1c01216] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/19/2021] [Indexed: 12/15/2022]
Abstract
Nitroreductases (NTRs) mediate the reduction of nitroaromatic compounds to the corresponding nitrite, hydroxylamine, or amino derivatives. The activity of NTRs in bacteria facilitates the metabolic activation and antibacterial activity of 5-nitroimidazoles. Therefore, NTR activity correlates with the drug susceptibility and resistance of pathogenic bacteria. As such, it is important to develop a rapid and visual assay for the real-time sensing of bacterial NTRs for the evaluation and development of antibiotics. Herein, an activatable near-infrared fluorescent probe (HC-NO2) derived from a hemicyanine fluorophore was designed and developed based on two evaluation factors, including the calculated partition coefficient (Clog P) and fluorescence wavelength. Using HC-NO2 as the special substrate of NTRs, NTR activity can be assayed efficiently, and then, bacteria can be imaged based on the detection of NTRs. More importantly, a sensitive in-gel assay using HC-NO2 has been developed to selectively identify NTRs and sensitively determine NTR activity. Using the in-gel assay, NTRs from various bacterial species have been profiled visually from the "fluorescence fingerprints", which facilitates the rapid identification of NTRs from bacterial lysates. Thus, various homologous NTRs were identified from three metronidazole-susceptible bacterial species as well as seven unsusceptible species, which were confirmed by the whole-genome sequence. As such, the evaluation of NTRs from different bacterial species should help improve the rational usage of 5-nitroimidazole drugs as antibiotics.
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Affiliation(s)
- Tao Liu
- Dalian
Key Laboratory of Metabolic Target Characterization and Traditional
Chinese Medicine Intervention, College of Pharmacy, Dalian Medical University, Dalian 116044, China
- State
Key Laboratory of Fine Chemicals, Dalian
University of Technology, Dalian 116024, China
| | - Yifei Wang
- Dalian
Key Laboratory of Metabolic Target Characterization and Traditional
Chinese Medicine Intervention, College of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Lei Feng
- Dalian
Key Laboratory of Metabolic Target Characterization and Traditional
Chinese Medicine Intervention, College of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Xiangge Tian
- Dalian
Key Laboratory of Metabolic Target Characterization and Traditional
Chinese Medicine Intervention, College of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Jingnan Cui
- State
Key Laboratory of Fine Chemicals, Dalian
University of Technology, Dalian 116024, China
| | - Zhenlong Yu
- Dalian
Key Laboratory of Metabolic Target Characterization and Traditional
Chinese Medicine Intervention, College of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Chao Wang
- Dalian
Key Laboratory of Metabolic Target Characterization and Traditional
Chinese Medicine Intervention, College of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Baojing Zhang
- Dalian
Key Laboratory of Metabolic Target Characterization and Traditional
Chinese Medicine Intervention, College of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Tony D. James
- Department
of Chemistry, University of Bath, Bath BA2 7AY, U.K.
- School
of Chemistry and Chemical Engineering, Henan
Normal University, Xinxiang 453007, China
| | - Xiaochi Ma
- Dalian
Key Laboratory of Metabolic Target Characterization and Traditional
Chinese Medicine Intervention, College of Pharmacy, Dalian Medical University, Dalian 116044, China
- Jiangsu
Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou 221004, China
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9
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Čėnas N, Nemeikaitė-Čėnienė A, Kosychova L. Single- and Two-Electron Reduction of Nitroaromatic Compounds by Flavoenzymes: Mechanisms and Implications for Cytotoxicity. Int J Mol Sci 2021; 22:ijms22168534. [PMID: 34445240 PMCID: PMC8395237 DOI: 10.3390/ijms22168534] [Citation(s) in RCA: 4] [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: 07/13/2021] [Revised: 07/30/2021] [Accepted: 08/04/2021] [Indexed: 12/14/2022] Open
Abstract
Nitroaromatic compounds (ArNO2) maintain their importance in relation to industrial processes, environmental pollution, and pharmaceutical application. The manifestation of toxicity/therapeutic action of nitroaromatics may involve their single- or two-electron reduction performed by various flavoenzymes and/or their physiological redox partners, metalloproteins. The pivotal and still incompletely resolved questions in this area are the identification and characterization of the specific enzymes that are involved in the bioreduction of ArNO2 and the establishment of their contribution to cytotoxic/therapeutic action of nitroaromatics. This review addresses the following topics: (i) the intrinsic redox properties of ArNO2, in particular, the energetics of their single- and two-electron reduction in aqueous medium; (ii) the mechanisms and structure-activity relationships of reduction in ArNO2 by flavoenzymes of different groups, dehydrogenases-electrontransferases (NADPH:cytochrome P-450 reductase, ferredoxin:NADP(H) oxidoreductase and their analogs), mammalian NAD(P)H:quinone oxidoreductase, bacterial nitroreductases, and disulfide reductases of different origin (glutathione, trypanothione, and thioredoxin reductases, lipoamide dehydrogenase), and (iii) the relationships between the enzymatic reactivity of compounds and their activity in mammalian cells, bacteria, and parasites.
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Affiliation(s)
- Narimantas Čėnas
- Institute of Biochemistry of Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania;
- Correspondence: ; Tel.: +370-5-223-4392
| | - Aušra Nemeikaitė-Čėnienė
- State Research Institute Center for Innovative Medicine, Santariškių St. 5, LT-08406 Vilnius, Lithuania;
| | - Lidija Kosychova
- Institute of Biochemistry of Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania;
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10
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Sharrock AV, McManaway SP, Rich MH, Mumm JS, Hermans IF, Tercel M, Pruijn FB, Ackerley DF. Engineering the Escherichia coli Nitroreductase NfsA to Create a Flexible Enzyme-Prodrug Activation System. Front Pharmacol 2021; 12:701456. [PMID: 34163368 PMCID: PMC8215503 DOI: 10.3389/fphar.2021.701456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 05/24/2021] [Indexed: 11/13/2022] Open
Abstract
Bacterial nitroreductase enzymes that can efficiently convert nitroaromatic prodrugs to a cytotoxic form have numerous applications in targeted cellular ablation. For example, the generation of cytotoxic metabolites that have low bystander potential (i.e., are largely confined to the activating cell) has been exploited for precise ablation of specific cell types in animal and cell-culture models; while enzyme-prodrug combinations that generate high levels of bystander cell killing are useful for anti-cancer strategies such as gene-directed enzyme-prodrug therapy (GDEPT). Despite receiving substantial attention for such applications, the canonical nitroreductase NfsB from Escherichia coli has flaws that limit its utility, in particular a low efficiency of conversion of most prodrugs. Here, we sought to engineer a superior broad-range nitroreductase, E. coli NfsA, for improved activity with three therapeutically-relevant prodrugs: the duocarmycin analogue nitro-CBI-DEI, the dinitrobenzamide aziridine CB1954 and the 5-nitroimidazole metronidazole. The former two prodrugs have applications in GDEPT, while the latter has been employed for targeted ablation experiments and as a precise 'off-switch' in GDEPT models to eliminate nitroreductase-expressing cells. Our lead engineered NfsA (variant 11_78, with the residue substitutions S41Y, L103M, K222E and R225A) generated reduced metabolites of CB1954 and nitro-CBI-DEI that exhibited high bystander efficiencies in both bacterial and 2D HEK-293 cell culture models, while no cell-to-cell transfer was evident for the reduced metronidazole metabolite. We showed that the high bystander efficiency for CB1954 could be attributed to near-exclusive generation of the 2-hydroxylamine reduction product, which has been shown in 3D cell culture to cause significantly greater bystander killing than the 4-hydroxylamine species that is also produced by NfsB. We similarly observed a high bystander effect for nitro-CBI-DEI in HCT-116 tumor spheroids in which only a small proportion of cells were expressing variant 11_78. Collectively, our data identify variant 11_78 as a broadly improved prodrug-activating nitroreductase that offers advantages for both targeted cellular ablation and suicide gene therapy applications.
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Affiliation(s)
- Abigail V. Sharrock
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
- Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - Sarah P. McManaway
- Auckland Cancer Society Research Centre, The University of Auckland, Auckland, New Zealand
| | - Michelle H. Rich
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Jeff S. Mumm
- The Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, United States
| | - Ian F. Hermans
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | - Moana Tercel
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
- Auckland Cancer Society Research Centre, The University of Auckland, Auckland, New Zealand
| | - Frederik B. Pruijn
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
- Auckland Cancer Society Research Centre, The University of Auckland, Auckland, New Zealand
| | - David F. Ackerley
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
- Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
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11
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The YfkO Nitroreductase from Bacillus Licheniformis on Gold-Coated Superparamagnetic Nanoparticles: Towards a Novel Directed Enzyme Prodrug Therapy Approach. Pharmaceutics 2021; 13:pharmaceutics13040517. [PMID: 33918536 PMCID: PMC8070144 DOI: 10.3390/pharmaceutics13040517] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 11/17/2022] Open
Abstract
The bacterial nitroreductase NfnB has been the focus of a great deal of research for its use in directed enzyme prodrug therapy in combination with the nitroreductase prodrug CB1954 with this combination of enzyme and prodrug even entering clinical trials. Despite some promising results, there are major limitations to this research, such as the fact that the lowest reported Km for this enzyme far exceeds the maximum dosage of CB1954. Due to these limitations, new enzymes are now being investigated for their potential use in directed enzyme prodrug therapy. One such enzyme that has proved promising is the YfkO nitroreductase from Bacillus Licheniformis. Upon investigation, the YfkO nitroreductase was shown to have a much lower Km (below the maximum dosage) than that of NfnB as well as the fact that when reacting with the prodrug it produces a much more favourable ratio of enzymatic products than NfnB, forming more of the desired 4-hydroxylamine derivative of CB1954.
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12
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Hall KR, Robins KJ, Williams EM, Rich MH, Calcott MJ, Copp JN, Little RF, Schwörer R, Evans GB, Patrick WM, Ackerley DF. Intracellular complexities of acquiring a new enzymatic function revealed by mass-randomisation of active-site residues. eLife 2020; 9:59081. [PMID: 33185191 PMCID: PMC7738182 DOI: 10.7554/elife.59081] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 11/12/2020] [Indexed: 11/17/2022] Open
Abstract
Selection for a promiscuous enzyme activity provides substantial opportunity for competition between endogenous and newly-encountered substrates to influence the evolutionary trajectory, an aspect that is often overlooked in laboratory directed evolution studies. We selected the Escherichia coli nitro/quinone reductase NfsA for chloramphenicol detoxification by simultaneously randomising eight active-site residues and interrogating ~250,000,000 reconfigured variants. Analysis of every possible intermediate of the two best chloramphenicol reductases revealed complex epistatic interactions. In both cases, improved chloramphenicol detoxification was only observed after an R225 substitution that largely eliminated activity with endogenous quinones. Error-prone PCR mutagenesis reinforced the importance of R225 substitutions, found in 100% of selected variants. This strong activity trade-off demonstrates that endogenous cellular metabolites hold considerable potential to shape evolutionary outcomes. Unselected prodrug-converting activities were mostly unaffected, emphasising the importance of negative selection to effect enzyme specialisation, and offering an application for the evolved genes as dual-purpose selectable/counter-selectable markers. In the cell, most tasks are performed by big molecules called proteins, which behave like molecular machines. Although proteins are often described as having one job each, this is not always true, and many proteins can perform different roles. Enzymes are a type of protein that facilitate chemical reactions. They are often specialised to one reaction, but they can also accelerate other side-reactions. During evolution, these side-reactions can become more useful and, as a result, the role of the enzyme may change over time. The main role of the enzyme called NfsA in Escherichia coli bacteria is thought to be to convert molecules called quinones into hydroquinones, which can protect the cell from toxic molecules produced in oxidation reactions. As a side-reaction, NfsA has the potential to protect bacteria from an antibiotic called chloramphenicol, but it generally does this with such low efficacy that the effects are negligible. Producing hydroquinones is helpful to the cell in some situations, but if bacteria are regularly exposed to chloramphenicol, NfsA’s role aiding antibiotic resistance could become more important. Over time, the enzyme could evolve to become better at neutralising chloramphenicol. Therefore, NfsA provides an opportunity to study the evolution of proteins and how bacteria adapt to antibiotics. To see how evolution might affect the activity of NfsA, Hall et al. generated 250 million E. coli with either random or targeted changes to the gene that codes for the NfsA enzyme. The resulting variants of NfsA that were most effective against chloramphenicol all had a change that eliminated the enzyme’s ability to convert quinones. This result demonstrates a key trade-off between roles for NfsA, where one must be lost for the other to improve. These results demonstrate the interplay between a protein’s different roles and provide insight into bacterial drug resistance. Additionally, the experiments showed that the bacteria with improved resistance to chloramphenicol also became more sensitive to another antibiotic, metronidazole. These findings could inform the fight against drug-resistant bacterial infections and may also be helpful in guiding the design of proteins with different roles.
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Affiliation(s)
- Kelsi R Hall
- School of Biological Sciences, Victoria University of Wellington, Wellington, Wellington, New Zealand.,Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
| | - Katherine J Robins
- School of Biological Sciences, Victoria University of Wellington, Wellington, Wellington, New Zealand
| | - Elsie M Williams
- School of Biological Sciences, Victoria University of Wellington, Wellington, Wellington, New Zealand.,Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
| | - Michelle H Rich
- School of Biological Sciences, Victoria University of Wellington, Wellington, Wellington, New Zealand
| | - Mark J Calcott
- School of Biological Sciences, Victoria University of Wellington, Wellington, Wellington, New Zealand.,Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
| | - Janine N Copp
- School of Biological Sciences, Victoria University of Wellington, Wellington, Wellington, New Zealand
| | - Rory F Little
- School of Biological Sciences, Victoria University of Wellington, Wellington, Wellington, New Zealand
| | - Ralf Schwörer
- Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand.,Ferrier Institute, Victoria University of Wellington, Wellington, New Zealand
| | - Gary B Evans
- Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand.,Ferrier Institute, Victoria University of Wellington, Wellington, New Zealand
| | - Wayne M Patrick
- School of Biological Sciences, Victoria University of Wellington, Wellington, Wellington, New Zealand.,Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
| | - David F Ackerley
- School of Biological Sciences, Victoria University of Wellington, Wellington, Wellington, New Zealand.,Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
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13
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Ball P, Halliwell J, Anderson S, Gwenin V, Gwenin C. Evaluation of two xenobiotic reductases from Pseudomonas putida for their suitability for magnetic nanoparticle-directed enzyme prodrug therapy as a novel approach to cancer treatment. Microbiologyopen 2020; 9:e1110. [PMID: 32979040 PMCID: PMC7568253 DOI: 10.1002/mbo3.1110] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/28/2020] [Accepted: 07/30/2020] [Indexed: 02/03/2023] Open
Abstract
Directed enzyme prodrug therapy (DEPT) is a cancer chemotherapy strategy in which bacterial enzymes are delivered to a cancer site before prodrug administration, resulting in prodrug activation at the cancer site and more localized treatment. A major limitation to DEPT is the poor effectiveness of the most studied enzyme for the CB1954 prodrug, NfnB from Escherichia coli, at concentrations suitable for human use. Much research into finding alternative enzymes to NfnB has resulted in the identification of the Xenobiotic reductases, XenA and XenB, which have been shown in the literature to reduce environmentally polluting nitro‐compounds. In this study, they were assessed for their potential use in cancer prodrug therapy strategies. Both proteins were cloned into the pET28a+ expression vector to give the genetically modified proteins XenA‐his and XenB‐his, of which only XenB‐his was active when tested with CB1954. XenB‐his was further modified to include a cysteine‐tag to facilitate direct immobilization on to a gold surface for future magnetic nanoparticle DEPT (MNDEPT) treatments and was named XenB‐cys. When tested using high‐performance liquid chromatography (HPLC), XenB‐his and XenB‐cys both demonstrated a preference for reducing CB1954 at the 4‐nitro position. Furthermore, XenB‐his and XenB‐cys successfully induced cell death in SK‐OV‐3 cells when combined with CB1954. This led to XenB‐cys being identified as a promising candidate for use in future MNDEPT treatments.
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14
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Directed evolution of the B. subtilis nitroreductase YfkO improves activation of the PET-capable probe SN33623 and CB1954 prodrug. Biotechnol Lett 2020; 43:203-211. [PMID: 32851465 DOI: 10.1007/s10529-020-02992-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 08/13/2020] [Indexed: 10/23/2022]
Abstract
OBJECTIVES To use directed evolution to improve YfkO-mediated reduction of the 5-nitroimidazole PET-capable probe SN33623 without impairing conversion of the anti-cancer prodrug CB1954. RESULTS Two iterations of error-prone PCR, purifying selection, and FACS sorting in a DNA damage quantifying GFP reporter strain were used to identify three YfkO variants able to sensitize E. coli host cells to at least 2.4-fold lower concentrations of SN33623 than the native enzyme. Two of these variants were able to be purified in a functional form, and in vitro assays revealed these were twofold and fourfold improved in kcat/KM with SN33623 over wild type YfkO. Serendipitously, the more-active variant was also nearly fourfold improved in kcat/KM versus wild type YfkO in converting CB1954 to a genotoxic drug. CONCLUSIONS The enhanced activation of the PET imaging probe SN33623 and CB1954 prodrug exhibited by the lead evolved variant of YfkO offers prospects for improved enzyme-prodrug therapy.
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15
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Mowday AM, Copp JN, Syddall SP, Dubois LJ, Wang J, Lieuwes NG, Biemans R, Ashoorzadeh A, Abbattista MR, Williams EM, Guise CP, Lambin P, Ackerley DF, Smaill JB, Theys J, Patterson AV. E. coli nitroreductase NfsA is a reporter gene for non-invasive PET imaging in cancer gene therapy applications. Theranostics 2020; 10:10548-10562. [PMID: 32929365 PMCID: PMC7482819 DOI: 10.7150/thno.46826] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 07/30/2020] [Indexed: 12/13/2022] Open
Abstract
The use of reporter genes to non-invasively image molecular processes inside cells has significant translational potential, particularly in the context of systemically administered gene therapy vectors and adoptively administered cells such as immune or stem cell based therapies. Bacterial nitroreductase enzymes possess ideal properties for reporter gene imaging applications, being of non-human origin and possessing the ability to metabolize a range of clinically relevant nitro(hetero)cyclic substrates. Methods: A library of eleven Escherichia coli nitroreductase candidates were screened for the ability to efficiently metabolize 2-nitroimidazole based positron emission tomography (PET) probes originally developed as radiotracers for hypoxic cell imaging. Several complementary methods were utilized to detect formation of cell-entrapped metabolites, including various in vitro and in vivo models to establish the capacity of the 2-nitroimidazole PET agent EF5 to quantify expression of a nitroreductase candidate. Proof-of-principle PET imaging studies were successfully conducted using 18F-HX4. Results: Recombinant enzyme kinetics, bacterial SOS reporter assays, anti-proliferative assays and flow cytometry approaches collectively identified the major oxygen-insensitive nitroreductase NfsA from E. coli (NfsA_Ec) as the most promising nitroreductase reporter gene. Cells expressing NfsA_Ec were demonstrably labelled with the imaging agent EF5 in a manner that was quantitatively superior to hypoxia, in monolayers (2D), multicellular layers (3D), and in human tumor xenograft models. EF5 retention correlated with NfsA_Ec positive cell density over a range of EF5 concentrations in 3D in vitro models and in xenografts in vivo and was predictive of in vivo anti-tumor activity of the cytotoxic prodrug PR-104. Following PET imaging with 18F-HX4, a significantly higher tumor-to-blood ratio was observed in two xenograft models for NfsA_Ec expressing tumors compared to the parental tumors thereof, providing verification of this reporter gene imaging approach. Conclusion: This study establishes that the bacterial nitroreductase NfsA_Ec can be utilized as an imaging capable reporter gene, with the ability to metabolize and trap 2-nitroimidazole PET imaging agents for non-invasive imaging of gene expression.
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16
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Protocol for evaluating the abilities of diverse nitroaromatic prodrug metabolites to exit a model Gram negative bacterial vector. MethodsX 2020; 7:100797. [PMID: 32021829 PMCID: PMC6995258 DOI: 10.1016/j.mex.2020.100797] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 01/13/2020] [Indexed: 01/29/2023] Open
Abstract
Bacterial-directed enzyme-prodrug therapy (BDEPT) uses tumour-tropic bacteria armed with a genetically-encoded prodrug-converting enzyme to sensitise tumours to a systemically-administered prodrug. A strong bystander effect (i.e., efficient bacteria-to-tumour transfer of activated prodrug metabolites) is critical to maximise tumour cell killing and avoid bacterial self-sterilisation. To investigate the bystander effect in bacteria we developed a sensitive screen that utilised two Escherichia coli strains grown in co-culture. The first of these was an activator strain that overexpressed the E. coli nitroreductase NfsA, and the second was a nitroreductase null recipient strain bearing an SOS-GFP DNA damage responsive gene construct. In this system, induction of GFP by genotoxic prodrug metabolites can only occur following their transfer from the activator to the recipient cells. This can be monitored both in fluorescence based microtitre plate assays and by flow-cytometry, enabling modelling of the abilities of diverse nitroaromatic prodrug metabolites to exit a Gram negative vector.
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17
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Tokay E, Güngör T, Hacıoğlu N, Önder FC, Gülhan ÜG, Tok TT, Çelik A, Ay M, Köçkar F. Prodrugs for nitroreductase-based cancer therapy-3: Antitumor activity of the novel dinitroaniline prodrugs/Ssap-NtrB enzyme suicide gene system: Synthesis, in vitro and in silico evaluation in prostate cancer. Eur J Med Chem 2019; 187:111937. [PMID: 31841727 DOI: 10.1016/j.ejmech.2019.111937] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 11/29/2019] [Accepted: 11/30/2019] [Indexed: 01/18/2023]
Abstract
Prodrugs for targeted tumor therapies have been extensively studied in recent years due to not only maximising therapeutic effects on tumor cells but also reducing or eliminating serious side effects on healthy cells. This strategy uses prodrugs which are safe for normal cells and form toxic metabolites (drugs) after selective reduction by enzymes in tumor tissues. In this study, prodrug candidates (1-36) containing nitro were designed, synthesized and characterized within the scope of chemical experiments. Drug-likeness properties of prodrug candidates were analyzed using DS 2018 to investigate undesired toxicity effects. In vitro cytotoxic effects of prodrug canditates were performed with MTT assay for human hepatoma cells (Hep3B) and prostate cancer cells (PC3) and human umbilical vein endothelial cells (HUVEC) as healthy control. Non-toxic compounds (3, 5, 7, 10, 12, 15, 17, 19 and 21-23), and also compounds (1, 2, 5, 6, 9, 11, 14, 16, 20 and 24) which had low toxic effects, were selected to examine their suitability as prodrug canditates. The reduction profiles and kinetic studies of prodrug/Ssap-NtrB combinations were performed with biochemical analyses. Then, selected prodrug/Ssap-NtrB combinations were applied to prostate cancer cells to determine toxicity. The results of theoretical, in vitro cytotoxic and biochemical studies suggest 14/Ssap-NtrB, 22/Ssap-NtrB and 24/Ssap-NtrB may be potential prodrug/enzyme combinations for nitroreductase (Ntr)-based prostate cancer therapy.
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Affiliation(s)
- Esra Tokay
- Department of Molecular Biology and Genetic, Faculty of Sciences and Arts, Balıkesir University, Balıkesir, 10145, Turkey
| | - Tuğba Güngör
- Department of Chemistry, Faculty of Sciences and Arts, Natural Products and Drug Research Laboratory, Çanakkale Onsekiz Mart University, Çanakkale, 17020, Turkey
| | - Nelin Hacıoğlu
- Department of Molecular Biology and Genetic, Faculty of Sciences and Arts, Balıkesir University, Balıkesir, 10145, Turkey
| | - Ferah Cömert Önder
- Department of Chemistry, Faculty of Sciences and Arts, Natural Products and Drug Research Laboratory, Çanakkale Onsekiz Mart University, Çanakkale, 17020, Turkey
| | - Ünzile Güven Gülhan
- Department of Chemistry, Faculty of Science, Gebze Technical University, Gebze-Kocaeli, 41400, Turkey
| | - Tuğba Taşkın Tok
- Department of Chemistry, Faculty of Sciences and Arts, Gaziantep University, Gaziantep, 27310, Turkey
| | - Ayhan Çelik
- Department of Chemistry, Faculty of Science, Gebze Technical University, Gebze-Kocaeli, 41400, Turkey
| | - Mehmet Ay
- Department of Chemistry, Faculty of Sciences and Arts, Natural Products and Drug Research Laboratory, Çanakkale Onsekiz Mart University, Çanakkale, 17020, Turkey.
| | - Feray Köçkar
- Department of Molecular Biology and Genetic, Faculty of Sciences and Arts, Balıkesir University, Balıkesir, 10145, Turkey.
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18
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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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19
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Williams EM, Rich MH, Mowday AM, Ashoorzadeh A, Copp JN, Guise CP, Anderson RF, Flanagan JU, Smaill JB, Patterson AV, Ackerley DF. Engineering Escherichia coli NfsB To Activate a Hypoxia-Resistant Analogue of the PET Probe EF5 To Enable Non-Invasive Imaging during Enzyme Prodrug Therapy. Biochemistry 2019; 58:3700-3710. [PMID: 31403283 DOI: 10.1021/acs.biochem.9b00376] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Gene-directed enzyme prodrug therapy (GDEPT) uses tumor-tropic vectors to deliver prodrug-converting enzymes such as nitroreductases specifically to the tumor environment. The nitroreductase NfsB from Escherichia coli (NfsB_Ec) has been a particular focal point for GDEPT and over the past 25 years has been the subject of several engineering studies seeking to improve catalysis of prodrug substrates. To facilitate clinical development, there is also a need to enable effective non-invasive imaging capabilities. SN33623, a 5-nitroimidazole analogue of 2-nitroimidazole hypoxia probe EF5, has potential for PET imaging exogenously delivered nitroreductases without generating confounding background due to tumor hypoxia. However, we show here that SN33623 is a poor substrate for NfsB_Ec. To address this, we used assay-guided sequence and structure analysis to identify two conserved residues that block SN33623 activation in NfsB_Ec and close homologues. Introduction of the rational substitutions F70A and F108Y into NfsB_Ec conferred high levels of SN33623 activity and enabled specific labeling of E. coli expressing the engineered enzyme. Serendipitously, the F70A and F108Y substitutions also substantially improved activity with the anticancer prodrug CB1954 and the 5-nitroimidazole antibiotic prodrug metronidazole, which is a potential biosafety agent for targeted ablation of nitroreductase-expressing vectors.
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Affiliation(s)
- Elsie M Williams
- School of Biological Sciences , Victoria University of Wellington , Wellington 6012 , New Zealand
| | - Michelle H Rich
- School of Biological Sciences , Victoria University of Wellington , Wellington 6012 , New Zealand
| | - Alexandra M Mowday
- Auckland Cancer Society Research Centre, School of Medical Sciences , The University of Auckland , Auckland 1023 , New Zealand
| | - Amir Ashoorzadeh
- Auckland Cancer Society Research Centre, School of Medical Sciences , The University of Auckland , Auckland 1023 , New Zealand
| | - Janine N Copp
- School of Biological Sciences , Victoria University of Wellington , Wellington 6012 , New Zealand
| | - Christopher P Guise
- Auckland Cancer Society Research Centre, School of Medical Sciences , The University of Auckland , Auckland 1023 , New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery , Auckland 1023 , New Zealand
| | - Robert F Anderson
- Auckland Cancer Society Research Centre, School of Medical Sciences , The University of Auckland , Auckland 1023 , New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery , Auckland 1023 , New Zealand
| | - Jack U Flanagan
- Auckland Cancer Society Research Centre, School of Medical Sciences , The University of Auckland , Auckland 1023 , New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery , Auckland 1023 , New Zealand
| | - Jeff B Smaill
- Auckland Cancer Society Research Centre, School of Medical Sciences , The University of Auckland , Auckland 1023 , New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery , Auckland 1023 , New Zealand
| | - Adam V Patterson
- Auckland Cancer Society Research Centre, School of Medical Sciences , The University of Auckland , Auckland 1023 , New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery , Auckland 1023 , New Zealand
| | - David F Ackerley
- School of Biological Sciences , Victoria University of Wellington , Wellington 6012 , New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery , Auckland 1023 , New Zealand
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20
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A cofactor consumption screen identifies promising NfsB family nitroreductases for dinitrotoluene remediation. Biotechnol Lett 2019; 41:1155-1162. [DOI: 10.1007/s10529-019-02716-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 08/01/2019] [Indexed: 11/26/2022]
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21
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Güngör T, Önder FC, Tokay E, Gülhan ÜG, Hacıoğlu N, Tok TT, Çelik A, Köçkar F, Ay M. PRODRUGS FOR NITROREDUCTASE BASED CANCER THERAPY- 2: Novel amide/Ntr combinations targeting PC3 cancer cells. Eur J Med Chem 2019; 171:383-400. [DOI: 10.1016/j.ejmech.2019.03.035] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 02/26/2019] [Accepted: 03/14/2019] [Indexed: 02/06/2023]
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22
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Pardeshi KA, Kumar TA, Ravikumar G, Shukla M, Kaul G, Chopra S, Chakrapani H. Targeted Antibacterial Activity Guided by Bacteria-Specific Nitroreductase Catalytic Activation to Produce Ciprofloxacin. Bioconjug Chem 2019; 30:751-759. [DOI: 10.1021/acs.bioconjchem.8b00887] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Kundansingh A. Pardeshi
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pune-411 008, Maharashtra, India
| | - T. Anand Kumar
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pune-411 008, Maharashtra, India
| | - Govindan Ravikumar
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pune-411 008, Maharashtra, India
| | - Manjulika Shukla
- Division of Microbiology, CSIR-Central Drug Research Institute, Lucknow-226031, Uttar Pradesh, India
| | - Grace Kaul
- Division of Microbiology, CSIR-Central Drug Research Institute, Lucknow-226031, Uttar Pradesh, India
| | - Sidharth Chopra
- Division of Microbiology, CSIR-Central Drug Research Institute, Lucknow-226031, Uttar Pradesh, India
| | - Harinath Chakrapani
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pune-411 008, Maharashtra, India
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23
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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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24
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Evaluating the abilities of diverse nitroaromatic prodrug metabolites to exit a model Gram negative vector for bacterial-directed enzyme-prodrug therapy. Biochem Pharmacol 2018; 158:192-200. [PMID: 30352235 DOI: 10.1016/j.bcp.2018.10.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 10/17/2018] [Indexed: 12/12/2022]
Abstract
Gene-directed enzyme-prodrug therapy (GDEPT) employs tumour-tropic vectors including viruses and bacteria to deliver a genetically-encoded prodrug-converting enzyme to the tumour environment, thereby sensitising the tumour to the prodrug. Nitroreductases, able to activate a range of promising nitroaromatic prodrugs to genotoxic metabolites, are of great interest for GDEPT. The bystander effect (cell-to-cell transfer of activated prodrug metabolites) has been quantified for some nitroaromatic prodrugs in mixed multilayer human cell cultures, however while these provide a good model for viral DEPT (VDEPT) they do not inform on the ability of these prodrug metabolites to exit bacterial vectors (relevant to bacterial-DEPT (BDEPT)). To investigate this we grew two Escherichia coli strains in co-culture; an activator strain expressing the nitroreductase E. coli NfsA and a recipient strain containing an SOS-GFP DNA damage responsive gene construct. In this system, induction of GFP by reduced prodrug metabolites can only occur following their transfer from the activator to the recipient cells. We used this to investigate five clinically relevant prodrugs: metronidazole, CB1954, nitro-CBI-DEI, and two dinitrobenzamide mustard prodrug analogues, PR-104A and SN27686. Consistent with the bystander efficiencies previously measured in human cell multilayers, reduced metronidazole exhibited little bacterial cell-to-cell transfer, whereas nitro-CBI-DEI was passed very efficiently from activator to recipient cells post-reduction. However, in contrast with observations in human cell multilayers, the nitrogen mustard prodrug metabolites were not effectively passed between the two bacterial strains, whereas reduced CB1954 was transferred efficiently. Using nitroreductase enzymes that exhibit different biases for the 2- versus 4-nitro substituents of CB1954, we further showed that the 2-nitro reduction products exhibit substantially higher levels of bacterial cell-to-cell transfer than the 4-nitro reduction products, consistent with their relative bystander efficiencies in human cell culture. Overall, our data suggest that prodrugs may differ in their suitability for VDEPT versus BDEPT applications and emphasise the importance of evaluating an enzyme-prodrug partnership in an appropriate context for the intended vector.
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25
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Copp JN, Akiva E, Babbitt PC, Tokuriki N. Revealing Unexplored Sequence-Function Space Using Sequence Similarity Networks. Biochemistry 2018; 57:4651-4662. [PMID: 30052428 DOI: 10.1021/acs.biochem.8b00473] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The rapidly expanding number of protein sequences found in public databases can improve our understanding of how protein functions evolve. However, our current knowledge of protein function likely represents a small fraction of the diverse repertoire that exists in nature. Integrative computational methods can facilitate the discovery of new protein functions and enzymatic reactions through the observation and investigation of the complex sequence-structure-function relationships within protein superfamilies. Here, we highlight the use of sequence similarity networks (SSNs) to identify previously unexplored sequence and function space. We exemplify this approach using the nitroreductase (NTR) superfamily. We demonstrate that SSN investigations can provide a rapid and effective means to classify groups of proteins, therefore exposing experimentally unexplored sequences that may exhibit novel functionality. Integration of such approaches with systematic experimental characterization will expand our understanding of the functional diversity of enzymes and their associated physiological roles.
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Affiliation(s)
- Janine N Copp
- Michael Smith Laboratories , University of British Columbia , 2185 East Mall , Vancouver , British Columbia V6T 1Z4 , Canada
| | - Eyal Akiva
- Department of Bioengineering and Therapeutic Sciences , University of California , San Francisco , California 94158 , United States.,Quantitative Biosciences Institute , University of California , San Francisco , California 94143 , United States
| | - Patricia C Babbitt
- Department of Bioengineering and Therapeutic Sciences , University of California , San Francisco , California 94158 , United States.,Quantitative Biosciences Institute , University of California , San Francisco , California 94143 , United States
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories , University of British Columbia , 2185 East Mall , Vancouver , British Columbia V6T 1Z4 , Canada
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26
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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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27
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Rich MH, Sharrock AV, Hall KR, Ackerley DF, MacKichan JK. Evaluation of NfsA-like nitroreductases from Neisseria meningitidis and Bartonella henselae for enzyme-prodrug therapy, targeted cellular ablation, and dinitrotoluene bioremediation. Biotechnol Lett 2017; 40:359-367. [DOI: 10.1007/s10529-017-2472-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 10/31/2017] [Indexed: 10/18/2022]
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28
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Akiva E, Copp JN, Tokuriki N, Babbitt PC. Evolutionary and molecular foundations of multiple contemporary functions of the nitroreductase superfamily. Proc Natl Acad Sci U S A 2017; 114:E9549-E9558. [PMID: 29078300 PMCID: PMC5692541 DOI: 10.1073/pnas.1706849114] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Insight regarding how diverse enzymatic functions and reactions have evolved from ancestral scaffolds is fundamental to understanding chemical and evolutionary biology, and for the exploitation of enzymes for biotechnology. We undertook an extensive computational analysis using a unique and comprehensive combination of tools that include large-scale phylogenetic reconstruction to determine the sequence, structural, and functional relationships of the functionally diverse flavin mononucleotide-dependent nitroreductase (NTR) superfamily (>24,000 sequences from all domains of life, 54 structures, and >10 enzymatic functions). Our results suggest an evolutionary model in which contemporary subgroups of the superfamily have diverged in a radial manner from a minimal flavin-binding scaffold. We identified the structural design principle for this divergence: Insertions at key positions in the minimal scaffold that, combined with the fixation of key residues, have led to functional specialization. These results will aid future efforts to delineate the emergence of functional diversity in enzyme superfamilies, provide clues for functional inference for superfamily members of unknown function, and facilitate rational redesign of the NTR scaffold.
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Affiliation(s)
- Eyal Akiva
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158
| | - Janine N Copp
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada V6T 1Z4;
| | - Patricia C Babbitt
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158;
- California Institute for Quantitative Biosciences, University of California, San Francisco, CA 94158
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29
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Lehouritis P, Hogan G, Tangney M. Designer bacteria as intratumoural enzyme biofactories. Adv Drug Deliv Rev 2017; 118:8-23. [PMID: 28916496 DOI: 10.1016/j.addr.2017.09.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 08/18/2017] [Accepted: 09/07/2017] [Indexed: 02/07/2023]
Abstract
Bacterial-directed enzyme prodrug therapy (BDEPT) is an emerging form of treatment for cancer. It is a biphasic variant of gene therapy in which a bacterium, armed with an enzyme that can convert an inert prodrug into a cytotoxic compound, induces tumour cell death following tumour-specific prodrug activation. BDEPT combines the innate ability of bacteria to selectively proliferate in tumours, with the capacity of prodrugs to undergo contained, compartmentalised conversion into active metabolites in vivo. Although BDEPT has undergone clinical testing, it has received limited clinical exposure, and has yet to achieve regulatory approval. In this article, we review BDEPT from the system designer's perspective, and provide detailed commentary on how the designer should strategize its development de novo. We report on contemporary advancements in this field which aim to enhance BDEPT in terms of safety and efficacy. Finally, we discuss clinical and regulatory barriers facing BDEPT, and propose promising approaches through which these hurdles may best be tackled.
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30
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Copp JN, Mowday AM, Williams EM, Guise CP, Ashoorzadeh A, Sharrock AV, Flanagan JU, Smaill JB, Patterson AV, Ackerley DF. Engineering a Multifunctional Nitroreductase for Improved Activation of Prodrugs and PET Probes for Cancer Gene Therapy. Cell Chem Biol 2017; 24:391-403. [DOI: 10.1016/j.chembiol.2017.02.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 12/31/2016] [Accepted: 02/01/2017] [Indexed: 12/20/2022]
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31
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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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32
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Malekshah OM, Chen X, Nomani A, Sarkar S, Hatefi A. Enzyme/Prodrug Systems for Cancer Gene Therapy. ACTA ACUST UNITED AC 2016; 2:299-308. [PMID: 28042530 DOI: 10.1007/s40495-016-0073-y] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The use of enzyme/prodrug system has gained attention because it could help improve the efficacy and safety of conventional cancer chemotherapies. In this approach, cancer cells are first transfected with a gene that can express an enzyme with ability to convert a non-toxic prodrug into its active cytotoxic form. As a result, the activated prodrug could kill the transfected cancer cells. Despite the significant progress of different suicide gene therapy protocols in preclinical studies and early clinical trials, none has reached the clinic due to several shortcomings. These include slow prodrug-drug conversion rate, low transfection/transduction efficiency of the vectors and nonspecific toxicity/immunogenicity related to the delivery systems, plasmid DNA, enzymes and/or prodrugs. This mini review aims at providing an overview of the most widely used enzyme/prodrug systems with emphasis on reporting the results of the recent preclinical and clinical studies.
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Affiliation(s)
- Obeid M Malekshah
- Department of Pharmaceutics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, United States
| | - Xuguang Chen
- Department of Pharmaceutics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, United States
| | - Alireza Nomani
- Department of Pharmaceutics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, United States
| | - Siddik Sarkar
- Department of Pharmaceutics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, United States
| | - Arash Hatefi
- Department of Pharmaceutics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, United States; Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, United States
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33
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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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34
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Mowday AM, Ashoorzadeh A, Williams EM, Copp JN, Silva S, Bull MR, Abbattista MR, Anderson RF, Flanagan JU, Guise CP, Ackerley DF, Smaill JB, Patterson AV. Rational design of an AKR1C3-resistant analog of PR-104 for enzyme-prodrug therapy. Biochem Pharmacol 2016; 116:176-87. [PMID: 27453434 DOI: 10.1016/j.bcp.2016.07.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 07/20/2016] [Indexed: 12/28/2022]
Abstract
The clinical stage anti-cancer agent PR-104 has potential utility as a cytotoxic prodrug for exogenous bacterial nitroreductases expressed from replicating vector platforms. However substrate selectivity is compromised due to metabolism by the human one- and two-electron oxidoreductases cytochrome P450 oxidoreductase (POR) and aldo-keto reductase 1C3 (AKR1C3). Using rational drug design we developed a novel mono-nitro analog of PR-104A that is essentially free of this off-target activity in vitro and in vivo. Unlike PR-104A, there was no biologically relevant cytotoxicity in cells engineered to express AKR1C3 or POR, under aerobic or anoxic conditions, respectively. We screened this inert prodrug analog, SN34507, against a type I bacterial nitroreductase library and identified E. coli NfsA as an efficient bioactivator using a DNA damage response assay and recombinant enzyme kinetics. Expression of E. coli NfsA in human colorectal cancer cells led to selective cytotoxicity to SN34507 that was associated with cell cycle arrest and generated a robust 'bystander effect' at tissue-like cell densities when only 3% of cells were NfsA positive. Anti-tumor activity of SN35539, the phosphate pre-prodrug of SN34507, was established in 'mixed' tumors harboring a minority of NfsA-positive cells and demonstrated marked tumor control following heterogeneous suicide gene expression. These experiments demonstrate that off-target metabolism of PR-104 can be avoided and identify the suicide gene/prodrug partnership of E. coli NfsA/SN35539 as a promising combination for development in armed vectors.
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Affiliation(s)
- Alexandra M Mowday
- Auckland Cancer Society Research Centre, School of Medical Sciences, The University of Auckland, Auckland 1023, New Zealand
| | - Amir Ashoorzadeh
- Auckland Cancer Society Research Centre, School of Medical Sciences, The University of Auckland, Auckland 1023, New Zealand
| | - Elsie M Williams
- School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand
| | - Janine N Copp
- School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand
| | - Shevan Silva
- Auckland Cancer Society Research Centre, School of Medical Sciences, The University of Auckland, Auckland 1023, New Zealand
| | - Matthew R Bull
- Auckland Cancer Society Research Centre, School of Medical Sciences, The University of Auckland, Auckland 1023, New Zealand
| | - Maria R Abbattista
- Auckland Cancer Society Research Centre, School of Medical Sciences, The University of Auckland, Auckland 1023, New Zealand
| | - Robert F Anderson
- Auckland Cancer Society Research Centre, School of Medical Sciences, The University of Auckland, Auckland 1023, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, School of Biological Sciences, The University of Auckland, Auckland 1023, New Zealand
| | - Jack U Flanagan
- Auckland Cancer Society Research Centre, School of Medical Sciences, The University of Auckland, Auckland 1023, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, School of Biological Sciences, The University of Auckland, Auckland 1023, New Zealand
| | - Christopher P Guise
- Auckland Cancer Society Research Centre, School of Medical Sciences, The University of Auckland, Auckland 1023, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, School of Biological Sciences, The University of Auckland, Auckland 1023, New Zealand
| | - David F Ackerley
- School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, School of Biological Sciences, The University of Auckland, Auckland 1023, New Zealand
| | - Jeff B Smaill
- Auckland Cancer Society Research Centre, School of Medical Sciences, The University of Auckland, Auckland 1023, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, School of Biological Sciences, The University of Auckland, Auckland 1023, New Zealand
| | - Adam V Patterson
- Auckland Cancer Society Research Centre, School of Medical Sciences, The University of Auckland, Auckland 1023, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, School of Biological Sciences, The University of Auckland, Auckland 1023, New Zealand.
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35
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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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Progress and problems with the use of suicide genes for targeted cancer therapy. Adv Drug Deliv Rev 2016; 99:113-128. [PMID: 26004498 DOI: 10.1016/j.addr.2015.05.009] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 02/19/2015] [Accepted: 05/14/2015] [Indexed: 12/16/2022]
Abstract
Among various gene therapy methods for cancer, suicide gene therapy attracts a special attention because it allows selective conversion of non-toxic compounds into cytotoxic drugs inside cancer cells. As a result, therapeutic index can be increased significantly by introducing high concentrations of cytotoxic molecules to the tumor environment while minimizing impact on normal tissues. Despite significant success at the preclinical level, no cancer suicide gene therapy protocol has delivered the desirable clinical significance yet. This review gives a critical look at the six main enzyme/prodrug systems that are used in suicide gene therapy of cancer and familiarizes readers with the state-of-the-art research and practices in this field. For each enzyme/prodrug system, the mechanisms of action, protein engineering strategies to enhance enzyme stability/affinity and chemical modification techniques to increase prodrug kinetics and potency are discussed. In each category, major clinical trials that have been performed in the past decade with each enzyme/prodrug system are discussed to highlight the progress to date. Finally, shortcomings are underlined and areas that need improvement in order to produce clinical significance are delineated.
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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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Gwenin VV, Poornima P, Halliwell J, Ball P, Robinson G, Gwenin CD. Identification of novel nitroreductases from Bacillus cereus and their interaction with the CB1954 prodrug. Biochem Pharmacol 2015; 98:392-402. [PMID: 26415543 DOI: 10.1016/j.bcp.2015.09.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 09/15/2015] [Indexed: 10/23/2022]
Abstract
Directed enzyme prodrug therapy is a form of cancer chemotherapy in which bacterial prodrug-activating enzymes, or their encoding genes, are directed to the tumour before administration of a prodrug. The prodrug can then be activated into a toxic drug at the tumour site, reducing off-target effects. The bacterial nitroreductases are a class of enzymes used in this therapeutic approach and although very promising, the low turnover rate of prodrug by the most studied nitroreductase enzyme, NfnB from Escherichia coli (NfnB_Ec), is a major limit to this technology. There is a continual search for enzymes with greater efficiency, and as part of the search for more efficient bacterial nitroreductase enzymes, two novel enzymes from Bacillus cereus (strain ATCC 14579) have been identified and shown to reduce the CB1954 (5-(aziridin-1-yl)-2,4-dinitrobenzamide) prodrug to its respective 2'-and 4'-hydroxylamine products. Both enzymes shared features characteristic of the nitro-FMN-reductase superfamily including non-covalently associated FMN, requirement for the NAD(P)H cofactor, homodimeric, could be inhibited by Dicoumarol (3,3'-methylenebis(4-hydroxy-2H-chromen-2-one)), and displayed ping pong bi bi kinetics. Based on the biochemical characteristics and nucleotide alignment with other nitroreductase enzymes, one enzyme was named YdgI_Bc and the other YfkO_Bc. Both B. cereus enzymes had greater turnover for the CB1954 prodrug compared with NfnB_Ec, and in the presence of added NADPH cofactor, YfkO_Bc had superior cell killing ability, and produced mainly the 4'-hydroxylamine product at low prodrug concentration. The YfkO_Bc was identified as a promising candidate for future enzyme prodrug therapy.
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Affiliation(s)
- Vanessa V Gwenin
- School of Chemistry, Bangor University, Bangor, Gwynedd, LL57 2DG Wales, UK
| | | | - Jennifer Halliwell
- School of Chemistry, Bangor University, Bangor, Gwynedd, LL57 2DG Wales, UK
| | - Patrick Ball
- School of Chemistry, Bangor University, Bangor, Gwynedd, LL57 2DG Wales, UK
| | - George Robinson
- School of Chemistry, Bangor University, Bangor, Gwynedd, LL57 2DG Wales, UK
| | - Chris D Gwenin
- School of Chemistry, Bangor University, Bangor, Gwynedd, LL57 2DG Wales, UK.
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Uzlikova M, Nohynkova E. The effect of metronidazole on the cell cycle and DNA in metronidazole-susceptible and -resistant Giardia cell lines. Mol Biochem Parasitol 2015; 198:75-81. [PMID: 25681616 DOI: 10.1016/j.molbiopara.2015.01.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 01/30/2015] [Accepted: 01/30/2015] [Indexed: 01/29/2023]
Abstract
Metronidazole (MTZ) is used as the drug of choice to treat Giardia infections. It is believed that the prodrug is transformed intracellularly into toxic intermediates that interact with cellular components, leading to cell death. The present study aimed to describe the effects of MTZ treatment on DNA and cell cycle progression in MTZ-sensitive and in vitro-derived MTZ-resistant cell lines. Detection of the phosphorylated form of histone H2A in cell nuclei together with electrophoresis of genomic DNA, flow cytometry analysis and incubation of cells with other drugs (albendazole or neomycin) demonstrated that DNA damage in MTZ-treated cells is clearly conditioned by the presence of this drug. The flow cytometry analysis and a BrdU labeling assay showed that the sublethal drug concentration affects the replication phase of the cell cycle. Cells incubated with lethal drug concentration exhibit unchanged DNA profile, only about 50% of cells are positive for γH2A and lose an ability to attach to a surface after few hours of incubation. It is likely that the early reaction of cells to lethal concentration of MTZ is not primarily initiated by the reaction to DNA damage but rather by the immediate interaction of MTZ with biomolecules where activated MTZ is generated. Interestingly, in MTZ-resistant lines incubated in the presence of the drug, about 40% of cells remain permanently positive for γH2A without any effects on the cell cycle progression suggesting that DNA damage caused by MTZ treatment persists in these cells. Accelerated mutagenesis caused by MTZ-induced DNA damage may therefore be a new factor contributing to the development of natural resistance.
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Affiliation(s)
- Magdalena Uzlikova
- Department of Tropical Medicine, First Faculty of Medicine, Charles University in Prague, Studnickova 7, Prague 2 128 00, Czech Republic.
| | - Eva Nohynkova
- Department of Tropical Medicine, First Faculty of Medicine, Charles University in Prague, Studnickova 7, Prague 2 128 00, Czech Republic.
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Prosser GA, Williams EM, Sissons JA, Walmsley KE, Parker MR, Ackerley DF. A gain-of-function positive-selection expression plasmid that enables high-efficiency cloning. Biotechnol Lett 2014; 37:383-9. [DOI: 10.1007/s10529-014-1673-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 09/11/2014] [Indexed: 10/24/2022]
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Green LK, La Flamme AC, Ackerley DF. Pseudomonas aeruginosa MdaB and WrbA are water-soluble two-electron quinone oxidoreductases with the potential to defend against oxidative stress. J Microbiol 2014; 52:771-7. [DOI: 10.1007/s12275-014-4208-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 06/25/2014] [Accepted: 07/02/2014] [Indexed: 10/25/2022]
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Copp JN, Williams EM, Rich MH, Patterson AV, Smaill JB, Ackerley DF. Toward a high-throughput screening platform for directed evolution of enzymes that activate genotoxic prodrugs. Protein Eng Des Sel 2014; 27:399-403. [PMID: 24996412 DOI: 10.1093/protein/gzu025] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Engineering of enzymes to more efficiently activate genotoxic prodrugs holds great potential for improving anticancer gene or antibody therapies. We report the development of a new, GFP-based, high-throughput screening platform to enable engineering of prodrug-activating enzymes by directed evolution. By fusing an inducible SOS promoter to an engineered GFP reporter gene, we were able to measure levels of DNA damage in intact Escherichia coli and separate cell populations by fluorescence activating cell sorting (FACS). In two FACS iterations, we were able to achieve a 90,000-fold enrichment of a functional prodrug-activating nitroreductase from a null library background.
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Affiliation(s)
- J N Copp
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand Centre for Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand Present address: Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - E M Williams
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand Centre for Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - M H Rich
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand Centre for Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - A V Patterson
- Maurice Wilkins Centre for Molecular Biodiscovery, School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand Auckland Cancer Society Research Centre, University of Auckland, Grafton, Auckland 1023, New Zealand
| | - J B Smaill
- Maurice Wilkins Centre for Molecular Biodiscovery, School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand Auckland Cancer Society Research Centre, University of Auckland, Grafton, Auckland 1023, New Zealand
| | - D F Ackerley
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand Centre for Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand Maurice Wilkins Centre for Molecular Biodiscovery, School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
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The Flavin Reductase MsuE Is a Novel Nitroreductase that Can Efficiently Activate Two Promising Next-Generation Prodrugs for Gene-Directed Enzyme Prodrug Therapy. Cancers (Basel) 2013; 5:985-97. [PMID: 24202330 PMCID: PMC3795375 DOI: 10.3390/cancers5030985] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 07/23/2013] [Accepted: 07/26/2013] [Indexed: 11/20/2022] Open
Abstract
Bacterial nitroreductase enzymes that can efficiently catalyse the oxygen-independent reduction of prodrugs originally developed to target tumour hypoxia offer great potential for expanding the therapeutic range of these molecules to aerobic tumour regions, via the emerging cancer strategy of gene-directed enzyme prodrug therapy (GDEPT). Two promising hypoxia prodrugs for GDEPT are the dinitrobenzamide mustard PR-104A, and the nitrochloromethylbenzindoline prodrug nitro-CBI-DEI. We describe here use of a nitro-quenched fluorogenic probe to identify MsuE from Pseudomonas aeruginosa as a novel nitroreductase candidate for GDEPT. In SOS and bacteria-delivered enzyme prodrug cytotoxicity assays MsuE was less effective at activating CB1954 (a first-generation GDEPT prodrug) than the “gold standard” nitroreductases NfsA and NfsB from Escherichia coli. However, MsuE exhibited comparable levels of activity with PR-104A and nitro-CBI-DEI, and is the first nitroreductase outside of the NfsA and NfsB enzyme families to do so. These in vitro findings suggest that MsuE is worthy of further evaluation in in vivo models of GDEPT.
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Green LK, Syddall SP, Carlin KM, Bell GD, Guise CP, Mowday AM, Hay MP, Smaill JB, Patterson AV, Ackerley DF. Pseudomonas aeruginosa NfsB and nitro-CBI-DEI--a promising enzyme/prodrug combination for gene directed enzyme prodrug therapy. Mol Cancer 2013; 12:58. [PMID: 23758947 PMCID: PMC3695803 DOI: 10.1186/1476-4598-12-58] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 06/05/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The nitro-chloromethylbenzindoline prodrug nitro-CBI-DEI appears a promising candidate for the anti-cancer strategy gene-directed enzyme prodrug therapy, based on its ability to be converted to a highly cytotoxic cell-permeable derivative by the nitroreductase NfsB from Escherichia coli. However, relative to some other nitroaromatic prodrugs, nitro-CBI-DEI is a poor substrate for E. coli NfsB. To address this limitation we evaluated other nitroreductase candidates from E. coli and Pseudomonas aeruginosa. FINDINGS Initial screens of candidate genes in the E. coli reporter strain SOS-R2 identified two additional nitroreductases, E. coli NfsA and P. aeruginosa NfsB, as being more effective activators of nitro-CBI-DEI than E. coli NfsB. In monolayer cytotoxicity assays, human colon carcinoma (HCT-116) cells transfected with P. aeruginosa NfsB were >4.5-fold more sensitive to nitro-CBI-DEI than cells expressing either E. coli enzyme, and 23.5-fold more sensitive than untransfected HCT-116. In three dimensional mixed cell cultures, not only were the P. aeruginosa NfsB expressing cells 540-fold more sensitive to nitro-CBI-DEI than pure cultures of untransfected HCT-116, the activated drug that they generated also displayed an unprecedented local bystander effect. CONCLUSION We posit that the discrepancy in the fold-sensitivity to nitro-CBI-DEI between the two and three dimensional cytotoxicity assays stems from loss of activated drug into the media in the monolayer cultures. This emphasises the importance of evaluating high-bystander GDEPT prodrugs in three dimensional models. The high cytotoxicity and bystander effect exhibited by the NfsB_Pa/nitro-CBI-DEI combination suggest that further preclinical development of this GDEPT pairing is warranted.
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Affiliation(s)
- Laura K Green
- School of Biological Sciences, Victoria University of Wellington, Kelburn Parade, Wellington, New Zealand
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Robins KJ, Hooks DO, Rehm BHA, Ackerley DF. Escherichia coli NemA is an efficient chromate reductase that can be biologically immobilized to provide a cell free system for remediation of hexavalent chromium. PLoS One 2013; 8:e59200. [PMID: 23527133 PMCID: PMC3596305 DOI: 10.1371/journal.pone.0059200] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2012] [Accepted: 02/14/2013] [Indexed: 11/19/2022] Open
Abstract
Hexavalent chromium is a serious and widespread environmental pollutant. Although many bacteria have been identified that can transform highly water-soluble and toxic Cr(VI) to insoluble and relatively non-toxic Cr(III), bacterial bioremediation of Cr(VI) pollution is limited by a number of issues, in particular chromium toxicity to the remediating cells. To address this we sought to develop an immobilized enzymatic system for Cr(VI) remediation. To identify novel Cr(VI) reductase enzymes we first screened cell extracts from an Escherichia coli library of soluble oxidoreductases derived from a range of bacteria, but found that a number of these enzymes can reduce Cr(VI) indirectly, via redox intermediates present in the crude extracts. Instead, activity assays for 15 candidate enzymes purified as His6-tagged proteins identified E. coli NemA as a highly efficient Cr(VI) reductase (kcat/KM = 1.1×105 M−1s−1 with NADH as cofactor). Fusion of nemA to the polyhydroxyalkanoate synthase gene phaC from Ralstonia eutropha enabled high-level biosynthesis of functionalized polyhydroxyalkanoate granules displaying stable and active NemA on their surface. When these granules were combined with either Bacillus subtilis glucose dehydrogenase or Candida boidinii formate dehydrogenase as a cofactor regenerating partner, high levels of chromate transformation were observed with only low initial concentrations of expensive NADH cofactor being required, the overall reaction being powered by consumption of the cheap sacrificial substrates glucose or formic acid, respectively. This system therefore offers promise as an economic solution for ex situ Cr(VI) remediation.
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Affiliation(s)
- Katherine J. Robins
- School of Biological Sciences, Victoria University of Wellington, Kelburn Parade, Wellington, New Zealand
| | - David O. Hooks
- Institute of Fundamental Sciences, Massey University, Tennent Drive, Palmerston North, New Zealand
- MacDiarmid Institute for Advanced Materials and Nanotechnology, Victoria University of Wellington, Kelburn Parade, Wellington, New Zealand
| | - Bernd H. A. Rehm
- Institute of Fundamental Sciences, Massey University, Tennent Drive, Palmerston North, New Zealand
- MacDiarmid Institute for Advanced Materials and Nanotechnology, Victoria University of Wellington, Kelburn Parade, Wellington, New Zealand
| | - David F. Ackerley
- School of Biological Sciences, Victoria University of Wellington, Kelburn Parade, Wellington, New Zealand
- Centre for Biodiscovery, Victoria University of Wellington, Kelburn Parade, Wellington, New Zealand
- * E-mail:
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