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Jiang S, Xu L, Zhong Y, Zhang C, Yu X, Li K, Ding L, Wang X. Hemicyanine-Based Highly Water-Soluble Probe for Extracellular Nitroreductase. Chembiochem 2024; 25:e202400257. [PMID: 38847484 DOI: 10.1002/cbic.202400257] [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: 03/20/2024] [Revised: 05/29/2024] [Indexed: 07/19/2024]
Abstract
Nitroreductase (NTR) has long been a target of interest for its important role involved in the nitro compounds metabolism. Various probes have been reported for NTR analysis, but rarely able to distinguish the extracellular NTR from intracellular ones. Herein we reported a new NTR sensor, HCyS-NO2, which was a hemicyanine molecule with one nitro and two sulfo groups attached. The nitro group acted as the reporting group to respond NTR reduction. Direct linkage of nitro group into the hemicyanine π conjugate system facilitated the intramolecular electron transfer (IET) process and thus quenched the fluorescence of hemicyanine core. Upon reduction with NTR, the nitro group was rapidly converted into the hydroxylamino and then the amino group, eliminating IET process and thus restoring the fluorescence. The sulfo groups installed significantly increased the hydrophilicity of the molecule, and introduced negative charges at physiological pH, preventing the diffusion into bacteria. Both gram-negative and gram-positive bacteria were able to turn on the fluorescence of HCyS-NO2, without detectable diffusion into cells, providing a useful tool to probe the extracellular reduction process.
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Affiliation(s)
- Shaoli Jiang
- Institute of Advanced Synthesis, Institute of Chemical Biology and Functional Molecules, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Le Xu
- Institute of Advanced Synthesis, Institute of Chemical Biology and Functional Molecules, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Yihong Zhong
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Chuangchuang Zhang
- Institute of Advanced Synthesis, Institute of Chemical Biology and Functional Molecules, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Xiaoyu Yu
- Institute of Advanced Synthesis, Institute of Chemical Biology and Functional Molecules, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Ke Li
- Institute of Advanced Synthesis, Institute of Chemical Biology and Functional Molecules, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Lin Ding
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Xiaojian Wang
- Institute of Advanced Synthesis, Institute of Chemical Biology and Functional Molecules, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, China
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Kancherla AD, Liu L, Tillery L, Shek R, Craig JK, Machen AJ, Seibold S, Battaile KP, Fradi S, Barrett LK, Subramanian S, Myler P, Van Voorhis WC, Lovell S. Crystal structures of NAD(P)H nitroreductases from Klebsiella pneumoniae. Acta Crystallogr F Struct Biol Commun 2024; 80:173-182. [PMID: 38990055 PMCID: PMC11299736 DOI: 10.1107/s2053230x24006472] [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: 03/01/2024] [Accepted: 07/02/2024] [Indexed: 07/12/2024] Open
Abstract
Klebsiella pneumoniae (Kp) is an infectious disease pathogen that poses a significant global health threat due to its potential to cause severe infections and its tendency to exhibit multidrug resistance. Understanding the enzymatic mechanisms of the oxygen-insensitive nitroreductases (Kp-NRs) from Kp is crucial for the development of effective nitrofuran drugs, such as nitrofurantoin, that can be activated as antibiotics. In this paper, three crystal structures of two Kp-NRs (PDB entries 7tmf/7tmg and 8dor) are presented, and an analysis of their crystal structures and their flavin mononucleotide (FMN)-binding mode is provided. The structures with PDB codes 7tmf (Kp-NR1a), 7tmg (Kp-NR1b) and 8dor (Kp-NR2) were determined at resolutions of 1.97, 1.90 and 1.35 Å, respectively. The Kp-NR1a and Kp-NR1b structures adopt an αβ fold, in which four-stranded antiparallel β-sheets are surrounded by five helices. With domain swapping, the β-sheet was expanded with a β-strand from the other molecule of the dimer. The difference between the structures lies in the loop spanning Leu173-Ala185: in Kp-NR1a the loop is disordered, whereas the loop adopts multiple conformations in Kp-NR1b. The FMN interactions within Kp-NR1/NR2 involve hydrogen-bond and π-stacking interactions. Kp-NR2 contains four-stranded antiparallel β-sheets surrounded by eight helices with two short helices and one β-sheet. Structural and sequence alignments show that Kp-NR1a/b and Kp-NR2 are homologs of the Escherichia coli oxygen-insensitive NRs YdjA and NfnB and of Enterobacter cloacae NR, respectively. By homology inference from E. coli, Kp-NR1a/b and Kp-NR2 may detoxify polynitroaromatic compounds and Kp-NR2 may activate nitrofuran drugs to cause bactericidal activity through a ping-pong bi-bi mechanism, respectively.
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Affiliation(s)
- Abhishek D. Kancherla
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA98109, USA
- Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases, Department of MedicineUniversity of WashingtonSeattleWA98109USA
| | - Lijun Liu
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA98109, USA
- Protein Structure and X-ray Crystallography LaboratoryUniversity of Kansas2034 Becker DriveLawrenceKS66047USA
| | - Logan Tillery
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA98109, USA
- Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases, Department of MedicineUniversity of WashingtonSeattleWA98109USA
| | - Roger Shek
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA98109, USA
- Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases, Department of MedicineUniversity of WashingtonSeattleWA98109USA
| | - Justin K. Craig
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA98109, USA
- Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases, Department of MedicineUniversity of WashingtonSeattleWA98109USA
| | - Alexandra J. Machen
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA98109, USA
- Protein Structure and X-ray Crystallography LaboratoryUniversity of Kansas2034 Becker DriveLawrenceKS66047USA
| | - Steve Seibold
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA98109, USA
- Protein Structure and X-ray Crystallography LaboratoryUniversity of Kansas2034 Becker DriveLawrenceKS66047USA
| | | | - Selma Fradi
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA98109, USA
- Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases, Department of MedicineUniversity of WashingtonSeattleWA98109USA
| | - Lynn K. Barrett
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA98109, USA
- Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases, Department of MedicineUniversity of WashingtonSeattleWA98109USA
| | - Sandhya Subramanian
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA98109, USA
- Center for Global Infectious Disease ResearchSeattle Children’s Research Institute307 Westlake Avenue North Suite 500SeattleWA98109USA
| | - Peter Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA98109, USA
- Center for Global Infectious Disease ResearchSeattle Children’s Research Institute307 Westlake Avenue North Suite 500SeattleWA98109USA
| | - Wesley C. Van Voorhis
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA98109, USA
- Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases, Department of MedicineUniversity of WashingtonSeattleWA98109USA
| | - Scott Lovell
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA98109, USA
- Protein Structure and X-ray Crystallography LaboratoryUniversity of Kansas2034 Becker DriveLawrenceKS66047USA
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Dulyayangkul P, Sealey JE, Lee WWY, Satapoomin N, Reding C, Heesom KJ, Williams PB, Avison MB. Improving nitrofurantoin resistance prediction in Escherichia coli from whole-genome sequence by integrating NfsA/B enzyme assays. Antimicrob Agents Chemother 2024; 68:e0024224. [PMID: 38767379 PMCID: PMC11232377 DOI: 10.1128/aac.00242-24] [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: 02/19/2024] [Accepted: 04/13/2024] [Indexed: 05/22/2024] Open
Abstract
Nitrofurantoin resistance in Escherichia coli is primarily caused by mutations damaging two enzymes, NfsA and NfsB. Studies based on small isolate collections with defined nitrofurantoin MICs have found significant random genetic drift in nfsA and nfsB, making it extremely difficult to predict nitrofurantoin resistance from whole-genome sequence (WGS) where both genes are not obviously disrupted by nonsense or frameshift mutations or insertional inactivation. Here, we report a WGS survey of 200 oqxAB-negative E. coli from community urine samples, of which 34 were nitrofurantoin resistant. We characterized individual non-synonymous mutations seen in nfsA and nfsB among this collection using complementation cloning and NfsA/B enzyme assays in cell extracts. We definitively identified R203C, H11Y, W212R, A112E, and A112T in NfsA and R121C, Q142H, F84S, P163H, W46R, K57E, and V191G in NfsB as amino acid substitutions that reduce enzyme activity sufficiently to cause resistance. In contrast, E58D, I117T, K141E, L157F, A172S, G187D, and A188V in NfsA and G66D, M75I, V93A, and A174E in NfsB are functionally silent in this context. We identified that 9/166 (5.4%) nitrofurantoin-susceptible isolates were "pre-resistant," defined as having loss of function mutations in nfsA or nfsB. Finally, using NfsA/B enzyme assays and proteomics, we demonstrated that 9/34 (26.5%) ribE wild-type nitrofurantoin-resistant isolates also carried functionally wild-type nfsB or nfsB/nfsA. In these cases, NfsA/B activity was reduced through downregulated gene expression. Our biological understanding of nitrofurantoin resistance is greatly improved by this analysis but is still insufficient to allow its reliable prediction from WGS data.
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Affiliation(s)
- Punyawee Dulyayangkul
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
- Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand
| | - Jordan E Sealey
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Winnie W Y Lee
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Naphat Satapoomin
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Carlos Reding
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Kate J Heesom
- University of Bristol Proteomics Facility, Bristol, United Kingdom
| | - Philip B Williams
- University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, United Kingdom
| | - Matthew B Avison
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
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Russo S, Luján AP, Fraaije MW, Poelarends GJ. Synthesis of Pharmaceutically Relevant Arylamines Enabled by a Nitroreductase from Bacillus tequilensis. Chembiochem 2024; 25:e202300846. [PMID: 38502784 DOI: 10.1002/cbic.202300846] [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: 02/03/2024] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 03/21/2024]
Abstract
Arylamines are essential building blocks for the manufacture of valuable pharmaceuticals, pigments and dyes. However, their current industrial production involves the use of chemocatalytic procedures with a significant environmental impact. As a result, flavin-dependent nitroreductases (NRs) have received increasing attention as sustainable catalysts for more ecofriendly synthesis of arylamines. In this study, we assessed a novel NR from Bacillus tequilensis, named BtNR, for the synthesis of pharmaceutically relevant arylamines, including valuable synthons used in the manufacture of blockbuster drugs such as vismodegib, sonidegib, linezolid and sildenafil. After optimizing the enzymatic reaction conditions, high conversion of nitroaromatics to arylamines (up to 97 %) and good product yields (up to 56 %) were achieved. Our results indicate that BtNR has a broad substrate scope, including bulky nitro benzenes, nitro pyrazoles and nitro pyridines. Hence, BtNR is an interesting biocatalyst for the synthesis of pharmaceutically relevant amine-functionalized aromatics, providing an attractive alternative to traditional chemical synthesis methodologies.
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Affiliation(s)
- Sara Russo
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
- Molecular Enzymology Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Alejandro Prats Luján
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Marco W Fraaije
- Molecular Enzymology Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Gerrit J Poelarends
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
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Day MA, Jarrom D, Rajah N, Searle PF, Hyde EI, White SA. Oxygen-insensitive nitroreductase E. coli NfsA, but not NfsB, is inhibited by fumarate. Proteins 2023; 91:585-592. [PMID: 36443029 PMCID: PMC10953011 DOI: 10.1002/prot.26451] [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: 08/19/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 11/30/2022]
Abstract
Escherichia coli NfsA and NfsB are founding members of two flavoprotein families that catalyze the oxygen-insensitive reduction of nitroaromatics and quinones by NAD(P)H. This reduction is required for the activity of nitrofuran antibiotics and the enzymes have also been proposed for use with nitroaromatic prodrugs in cancer gene therapy and biocatalysis, but the roles of the proteins in vivo in bacteria are not known. NfsA is NADPH-specific whereas NfsB can also use NADH. The crystal structures of E. coli NfsA and NfsB and several analogs have been determined previously. In our crystal trials, we unexpectedly observed NfsA bound to fumarate. We here present the X-ray structure of the E. coli NfsA-fumarate complex and show that fumarate acts as a weak inhibitor of NfsA but not of NfsB. The structural basis of this differential inhibition is conserved in the two protein families and occurs at fumarate concentrations found in vivo, so impacting the efficacy of these proteins.
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Affiliation(s)
- Martin A. Day
- School of BiosciencesUniversity of BirminghamBirminghamUK
- Institute for Cancer and Genomic SciencesUniversity of BirminghamBirminghamUK
| | - David Jarrom
- School of BiosciencesUniversity of BirminghamBirminghamUK
| | - Navina Rajah
- School of BiosciencesUniversity of BirminghamBirminghamUK
| | - Peter F. Searle
- Institute for Cancer and Genomic SciencesUniversity of BirminghamBirminghamUK
| | - Eva I. Hyde
- School of BiosciencesUniversity of BirminghamBirminghamUK
| | - Scott A. White
- School of BiosciencesUniversity of BirminghamBirminghamUK
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Day MA, Christofferson AJ, Anderson JLR, Vass SO, Evans A, Searle PF, White SA, Hyde EI. Structure and Dynamics of Three Escherichia coli NfsB Nitro-Reductase Mutants Selected for Enhanced Activity with the Cancer Prodrug CB1954. Int J Mol Sci 2023; 24:ijms24065987. [PMID: 36983061 PMCID: PMC10051150 DOI: 10.3390/ijms24065987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/16/2023] [Accepted: 02/27/2023] [Indexed: 03/30/2023] Open
Abstract
Escherichia coli NfsB has been studied extensively for its potential for cancer gene therapy by reducing the prodrug CB1954 to a cytotoxic derivative. We have previously made several mutants with enhanced activity for the prodrug and characterised their activity in vitro and in vivo. Here, we determine the X-ray structure of our most active triple and double mutants to date, T41Q/N71S/F124T and T41L/N71S. The two mutant proteins have lower redox potentials than wild-type NfsB, and the mutations have lowered activity with NADH so that, in contrast to the wild-type enzyme, the reduction of the enzyme by NADH, rather than the reaction with CB1954, has a slower maximum rate. The structure of the triple mutant shows the interaction between Q41 and T124, explaining the synergy between these two mutations. Based on these structures, we selected mutants with even higher activity. The most active one contains T41Q/N71S/F124T/M127V, in which the additional M127V mutation enlarges a small channel to the active site. Molecular dynamics simulations show that the mutations or reduction of the FMN cofactors of the protein has little effect on its dynamics and that the largest backbone fluctuations occur at residues that flank the active site, contributing towards its broad substrate range.
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Affiliation(s)
- Martin A Day
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
- Institute for Cancer Studies, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | | | | | - Simon O Vass
- Institute for Cancer Studies, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Adam Evans
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Peter F Searle
- Institute for Cancer Studies, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Scott A White
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Eva I Hyde
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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