Characterization of Escherichia coli nitroreductase NfsB in the metabolism of nitrobenzodiazepines

MicrobeRX: a tool for enzymatic-reaction-based metabolite prediction in the gut microbiome

BACKGROUND

The gut microbiome functions as a metabolic organ, producing numerous enzymes that influence host health; however, their substrates and metabolites remain largely unknown.

RESULTS

We present MicrobeRX, an enzyme-based metabolite prediction tool that employs 5487 human reactions and 4030 unique microbial reactions from 6286 genome-scale models, as well as 3650 drug metabolic reactions from the DrugBank database (v.5.1.12). MicrobeRX includes additional analysis modules for metabolite visualization and enzymatic and taxonomic analyses. When we applied MicrobeRX to 1083 orally administered drugs that have been approved in at least one jurisdiction at some point in time (DrugBank), it predicted metabolites with physicochemical properties and structures similar to metabolites found in biosamples (from MiMeDB). It also outperformed another existing metabolite prediction tool (BioTransformer 3.0) in terms of predictive potential, molecular diversity, reduction of redundant predictions, and enzyme annotation.

CONCLUSIONS

Our analysis revealed both unique and overlapping metabolic capabilities in human and microbial metabolism and chemo- and taxa-specific microbial biotransformations. MicrobeRX bridges the genomic and chemical spaces of the gut microbiome, making it a valuable tool for unlocking the chemical potential of the gut microbiome in human health, the food and pharmaceutical industries, and environmental safety. Video Abstract.

Carbon and Nitrogen Isotope Fractionations During Biotic and Abiotic Transformations of 2,4-Dinitroanisole (DNAN)

2,4-Dinitroanisole (DNAN) is a main constituent in various new insensitive munition formulations. Although DNAN is susceptible to biotic and abiotic transformations, in many environmental instances, transformation mechanisms are difficult to resolve, distinguish, or apportion on the basis solely of analysis of concentrations. We used compound-specific isotope analysis (CSIA) to investigate the characteristic isotope fractionations of the biotic (by three microbial consortia and three pure cultures) and abiotic (by 9,10-anthrahydroquinone-2-sulfonic acid [AHQS]) transformations of DNAN. The correlations of isotope enrichment factors (ΛN/C) for biotic transformations had a range of values from 4.93 ± 0.53 to 12.19 ± 1.23, which is entirely distinct from ΛN/C values reported previously for alkaline hydrolysis, enzymatic hydrolysis, reduction by Fe2+-bearing minerals and iron-oxide-bound Fe2+, and UV-driven phototransformations. The ΛN/C value associated with the abiotic reduction by AHQS was 38.76 ± 2.23, within the range of previously reported values for DNAN reduction by Fe2+-bearing minerals and iron-oxide-bound Fe2+, albeit the mean ΛN/C was lower. These results enhance the database of isotope effects accompanying DNAN transformations under environmentally relevant conditions, allowing better evaluation of the extents of biotic and abiotic transformations of DNAN that occur in soils, groundwaters, surface waters, and the marine environment.

Development of a Fluorescence Probe for Detecting Nitroreductase Activity Based on Steric Repulsion-Induced Twisted Intramolecular Charge Transfer (sr-TICT)

Twisted intramolecular charge transfer (TICT) is a phenomenon involving intramolecular charge transfer together with intramolecular rotation upon photoexcitation, and in general this excited state of fluorescent dyes undergoes non-radiative decay (producing no fluorescence). We recently discovered that the magnitude of TICT in rhodamine derivatives could be regulated by altering the size of the substituents on the xanthene moiety, generating differing degrees of intramolecular steric repulsion. To further illustrate the usefulness and generality of this strategy, we describe here an application of quinone methide chemistry, which is widely used as a fluorescence off/on switching reaction for fluorescence probes detecting enzymatic activity, to construct a steric repulsion-induced (sr)-TICT-based fluorescence probe targeting nitroreductase (NTR) activity. The developed probe was almost non-fluorescent in phosphate-buffered saline (PBS) due to strong induction of the TICT state. On the other hand, when the probe was incubated with NTR and nicotinamide adenine dinucleotide (NADH), a large fluorescence increase was observed over time. We confirmed that the enzymatic reaction proceeded as expected, i.e., the nitro group of the probe was reduced to the corresponding amino group, followed by spontaneous elimination of iminoquinone methide. These results suggest that our simple design strategy based on the sr-TICT mechanism, i.e., controlling intramolecular steric repulsion, would be applicable to the development of fluorescence probes for a variety of enzymes.

Microbial metabolism marvels: a comprehensive review of microbial drug transformation capabilities

This comprehensive review elucidates the pivotal role of microbes in drug metabolism, synthesizing insights from an exhaustive analysis of over two hundred papers. Employing a structural classification system grounded in drug atom involvement, the review categorizes the microbiome-mediated drug-metabolizing capabilities of over 80 drugs. Additionally, it compiles pharmacodynamic and enzymatic details related to these reactions, striving to include information on encoding genes and specific involved microorganisms. Bridging biochemistry, pharmacology, genetics, and microbiology, this review not only serves to consolidate diverse research fields but also highlights the potential impact of microbial drug metabolism on future drug design and in silico studies. With a visionary outlook, it also lays the groundwork for personalized medicine interventions, emphasizing the importance of interdisciplinary collaboration for advancing drug development and enhancing therapeutic strategies.

From-Toilet-to-Freezer: A Review on Requirements for an Automatic Protocol to Collect and Store Human Fecal Samples for Research Purposes

The composition, viability and metabolic functionality of intestinal microbiota play an important role in human health and disease. Studies on intestinal microbiota are often based on fecal samples, because these can be sampled in a non-invasive way, although procedures for sampling, processing and storage vary. This review presents factors to consider when developing an automated protocol for sampling, processing and storing fecal samples: donor inclusion criteria, urine-feces separation in smart toilets, homogenization, aliquoting, usage or type of buffer to dissolve and store fecal material, temperature and time for processing and storage and quality control. The lack of standardization and low-throughput of state-of-the-art fecal collection procedures promote a more automated protocol. Based on this review, an automated protocol is proposed. Fecal samples should be collected and immediately processed under anaerobic conditions at either room temperature (RT) for a maximum of 4 h or at 4 °C for no more than 24 h. Upon homogenization, preferably in the absence of added solvent to allow addition of a buffer of choice at a later stage, aliquots obtained should be stored at either -20 °C for up to a few months or -80 °C for a longer period-up to 2 years. Protocols for quality control should characterize microbial composition and viability as well as metabolic functionality.

The Interplay between Gut Microbiota and Oral Medications and Its Impact on Advancing Precision Medicine

Trillions of diverse microbes reside in the gut and are deeply interwoven with the human physiological process, from food digestion, immune system maturation, and fighting invading pathogens, to drug metabolism. Microbial drug metabolism has a profound impact on drug absorption, bioavailability, stability, efficacy, and toxicity. However, our knowledge of specific gut microbial strains, and their genes that encode enzymes involved in the metabolism, is limited. The microbiome encodes over 3 million unique genes contributing to a huge enzymatic capacity, vastly expanding the traditional drug metabolic reactions that occur in the liver, manipulating their pharmacological effect, and, ultimately, leading to variation in drug response. For example, the microbial deactivation of anticancer drugs such as gemcitabine can lead to resistance to chemotherapeutics or the crucial role of microbes in modulating the efficacy of the anticancer drug, cyclophosphamide. On the other hand, recent findings show that many drugs can shape the composition, function, and gene expression of the gut microbial community, making it harder to predict the outcome of drug-microbiota interactions. In this review, we discuss the recent understanding of the multidirectional interaction between the host, oral medications, and gut microbiota, using traditional and machine-learning approaches. We analyze gaps, challenges, and future promises of personalized medicine that consider gut microbes as a crucial player in drug metabolism. This consideration will enable the development of personalized therapeutic regimes with an improved outcome, ultimately leading to precision medicine.

Enhancing the Contrast of Tumor Imaging for Image-Guided Surgery Using a Tumor-Targeting Probiotic with the Continuous Expression of a Biomarker

Tumor recurrence commonly results from tumor-positive resection margins and metastatic lesions. The complete removal of tumor-positive margins is particularly essential in clinics. Thus, we designed a strategy based on Escherichia coli Nissle 1917 (EcN) nitroreductase (NTR) with a polyethylene glycol (PEG) polymer coating (PC-EcN-NTR) to specifically target and colonize in tumors for high-contrast tumor imaging by providing a large amount of NTR as biomarkers in situ. NTR is a favorable biomarker for tumor detection and imaging. The nfsB-encoding plasmid with a 16S promoter was transfected into EcN for the continuous and stable expression of NTR (E. coli. NfsB). PC-EcN-NTR can accumulate and proliferate for a long time in tumors to substantially express NTR. When the NTR-activated fluorescence (FL) probe was sprayed on the tumor, the tumor region showed fluorescence signals within 5 min. Compared to the tumor without colonization with bacteria, the PC-EcN-NTR-colonized tumors displayed 3.15× enhanced fluorescence signals. Furthermore, the fluorescence signals of the whole tumor can last at least 3 h, which is suitable for a long and meticulous surgical operation. More importantly, in the PC-EcN-NTR-harboring tumor, obvious FL appeared even at the very edge (approximately 200 μm away from the edge) of the tumor tissue. A TCF-Based near-infrared-II fluorescent probe (probe 2) was designed and synthesized. Results similar to those of probe 1 were observed when probe 2 was used for in vivo tumor imaging, which further proved the generality of the enhancing ability of the tumor-targeting probiotic. This strategy will hopefully guide the surgical resection of tumors via monitoring intense NTR activity. It may spur the use of tumor-targeting probiotic and enzyme-activated fluorescent probes for the processes of tumor diagnosis and image-guided surgery.

Biotransformation of the insensitive munition constituents 3-nitro-1,2,4-triazol-5-one (NTO) and 2,4-dinitroanisole (DNAN) by aerobic methane-oxidizing consortia and pure cultures

We present the first report of biotransformation of 3-nitro-1,2,4-triazol-5-one (NTO) and 2,4-dinitroanisole (DNAN), replacements for the explosives 1,3,5-trinitro-1,3,5-triazine (RDX) and 2,4,6-trinitrotoluene (TNT), respectively, by methane-oxidizing cultures under aerobic conditions. Two consortia, dominated by Methylosinus spp., degraded both compounds with transient production of reduced NTO products, and non-stoichiometric production of reduced DNAN products. No release of inorganic nitrogen was observed with either compound, indicating that NTO and DNAN may be utilized as nitrogen sources by these consortia. The pure culture Methylosinus trichosporium OB3b also degraded both compounds. Degradation was observed in the presence of acetylene (a known inhibitor of methane monooxygenase; MMO) when methanol was supplied, indicating that MMO was not involved. Furthermore, studies with purified soluble MMO (sMMO) from OB3b indicated that neither compound was a substrate for sMMO. Degradation was inhibited by 2-iodosobenzoic acid, but not by dicoumarol, suggesting involvement of an oxygen- and dicoumarol-insensitive (nitro)reductase. These results indicate methanotrophs can aerobically degrade NTO and DNAN via one or more (nitro)reductases, with sMMO serving a supporting role deriving reducing equivalents from methane. This finding is important because methanotrophic bacteria are widely dispersed, and may represent a previously unrecognized route of NTO and DNAN biotransformation in aerobic environments.

Gut microbiota in reductive drug metabolism

Gut bacteria are predominant microorganisms in the gut microbiota and have been recognized to mediate a variety of biotransformations of xenobiotic compounds in the gut. This review is focused on one of the gut bacterial xenobiotic metabolisms, reduction. Xenobiotics undergo different types of reductive metabolisms depending on chemically distinct groups: azo (-NN-), nitro (-NO₂), alkene (-CC-), ketone (-CO), N-oxide (-NO), and sulfoxide (-SO). In this review, we have provided select examples of drugs in six chemically distinct groups that are known or suspected to be subjected to the reduction by gut bacteria. For some drugs, responsible enzymes in specific gut bacteria have been identified and characterized, but for many drugs, only circumstantial evidence is available that indicates gut bacteria-mediated reductive metabolism. The physiological roles of even known gut bacterial enzymes have not been well defined.

The gut microbiome: an orchestrator of xenobiotic metabolism

Microbes inhabiting the intestinal tract of humans represent a site for xenobiotic metabolism. The gut microbiome, the collection of microorganisms in the gastrointestinal tract, can alter the metabolic outcome of pharmaceuticals, environmental toxicants, and heavy metals, thereby changing their pharmacokinetics. Direct chemical modification of xenobiotics by the gut microbiome, either through the intestinal tract or re-entering the gut via enterohepatic circulation, can lead to increased metabolism or bioactivation, depending on the enzymatic activity within the microbial niche. Unique enzymes encoded within the microbiome include those that reverse the modifications imparted by host detoxification pathways. Additionally, the microbiome can limit xenobiotic absorption in the small intestine by increasing the expression of cell-cell adhesion proteins, supporting the protective mucosal layer, and/or directly sequestering chemicals. Lastly, host gene expression is regulated by the microbiome, including CYP450s, multi-drug resistance proteins, and the transcription factors that regulate them. While the microbiome affects the host and pharmacokinetics of the xenobiotic, xenobiotics can also influence the viability and metabolism of the microbiome. Our understanding of the complex interconnectedness between host, microbiome, and metabolism will advance with new modeling systems, technology development and refinement, and mechanistic studies focused on the contribution of human and microbial metabolism.

Discovery and Characterization of a Nitroreductase Capable of Conferring Bacterial Resistance to Chloramphenicol

Widespread antibiotic resistance has led to the reappraisal of abandoned antibiotics including chloramphenicol. However, enzyme(s) underlying one form of chloramphenicol resistance, nitroreduction, have eluded identification. Here we demonstrate that expression of the Haemophilus influenzae nitroreductase gene nfsB confers chloramphenicol resistance in Escherichia coli. We characterized the enzymatic product of H. influenzae NfsB acting on chloramphenicol and found it to be amino-chloramphenicol. Kinetic analysis revealed reduction of diverse substrates including the incomplete reduction of 5-nitro antibiotics metronidazole and nitrofurantoin, likely resulting in activation of these antibiotic pro-drugs to their cytotoxic forms. We observed that expression of the H. influenzae nfsB gene in E. coli results in significantly increased susceptibility to metronidazole. Finally, we found that in this strain metronidazole attenuates chloramphenicol resistance synergistically, and in vitro metronidazole weakly inhibits chloramphenicol reduction by NfsB. Our findings reveal the underpinnings of a chloramphenicol resistance mechanism nearly 70 years after its description.

Nitrothiophene carboxamides, a novel narrow spectrum antibacterial series: Mechanism of action and Efficacy

The mechanism of efflux is a tour-de-force in the bacterial armoury that has thwarted the development of novel antibiotics. We report the discovery of a novel chemical series with potent antibacterial properties that was engineered to overcome efflux liability. Compounds liable to efflux specifically via the Resistance Nodulation and cell Division (RND) pump, AcrAB-TolC were chosen for a hit to lead progression. Using structure-based design, the compounds were optimised to lose their binding to the efflux pump, thereby making them potent on wild-type bacteria. We discovered these compounds to be pro-drugs that require activation in E. coli by specific bacterial nitroreductases NfsA and NfsB. Hit to lead chemistry led to the generation of compounds that were potent on wild-type and multi-drug resistant clinical isolates of E. coli, Shigella spp., and Salmonella spp. These compounds are bactericidal and efficacious in a mouse thigh infection model.

Effects of bacterial and presystemic nitroreductase metabolism of 2-chloro-5-nitro-N-phenylbenzamide on its mutagenicity and bioavailability

2-Chloro-5-nitro-N-phenylbenzamide (GW9662), a potent irreversible PPAR-γ antagonist, has shown promise as a cancer chemopreventive agent and is undergoing preclinical evaluations. Studies were initiated to assess its bacterial mutagenicity and pharmacokinetic profile in two animal species prior to subchronic oral toxicity evaluations and the results are reported here. GW9662 was mutagenic in both TA98 and TA100 bacterial strains with and without metabolic activation but was negative in the nitroreductase-deficient strains (TA98NR and TA100NR) also with and without metabolic activation, indicating that GW9662 mutagenicity is dependent on nitroreduction. The mutagenic activity was predominantly via a base-substitution mechanism. Following oral dosing in rats and dogs, the parent compound, GW9662, was virtually absent from plasma samples, but there was chromatographic evidence for the presence of metabolites in the plasma as a result of oral dosing. Metabolite identification studies showed that an amine metabolite ACPB (5-amino-2-chloro-N-phenylbenzamide), a product of nitro reduction, was the predominant species exhibiting large and persistent plasma levels. Thus systemic circulation of GW9662 has been attained largely in the form of its reduced metabolite, probably a product of gut bacterial metabolism. GW9662 was detectable in plasma of rats and dogs after intravenous dose albeit at low concentrations. Pharmacokinetic analysis following intravenous dosing in rats showed a rapid clearance and an extensive tissue distribution which could have accounted for the very low plasma levels. Of note, the amine metabolite was absent following intravenous dosing in both rats and dogs, confirming it being a product of presystemic metabolism. The potential utility of GW9662 as a chemopreventive agent, especially as an Estrogen Receptor-α (ER-α) inducer in an otherwise ER-α negative breast tissue, is of great interest. However, the results shown here suggest that additional animal toxicological and bioavailability studies are required to establish a role of GW9662 as a chemopreventive agent.

Structure-based development of bacterial nitroreductase against nitrobenzodiazepine-induced hypnosis

Nitrobenzodiazepine (NBDZ) is an addictive drug of the abused substances that causes severe neurological effects and even death. Bacterial type I nitroreductase NfsB (EC 1.5.1.34) has been reported to catalyze NBDZ into inactive metabolite 7-amino-benzodiazepine (7ABDZ) with promising activity, so as to become an attractive candidate for treatment of NBDZ overdose and addiction. Here, we investigate the nitroreduction of an NBDZ, flunitrazepam (FZ), by various mutants of NfsB designed from the solved crystal structure and characterize their in vitro and in vivo potency. Conformational changes occurred in the active site of N71S/F124W in contrast to the wild-type, including the flipping on the aromatic rings of W124 and F70 as well as the extension on the hydrogen bond network between flavin mononucleotide (FMN) and S71, which allow the significant enlargement in the active site pocket. In the complex structure of N71S/F124W and nicotinamide (NIA), stacking sandwich attractions of W124-FMN-NIA were also found, implying the importance of W124 in substrate accessibility. Consequently, N71S/F124W exhibited increased 7AFZ production in vitro with nearly no toxicity and reduced 50% sleeping time (hypnosis) in vivo. Taken together, we demonstrate for the first time that N71S/F124W can serve as an effective antidote for NBDZ-induced hypnosis and provide the molecular basis for designing NfsB and the like in the future.

The intestinal microbiota, gastrointestinal environment and colorectal cancer: a putative role for probiotics in prevention of colorectal cancer?

Colorectal cancer (CRC) is the third most commonly diagnosed cancer in the United States, and, even though 5-15% of the total CRC cases can be attributed to individual genetic predisposition, environmental factors could be considered major factors in susceptibility to CRC. Lifestyle factors increasing the risks of CRC include elevated body mass index, obesity, and reduced physical activity. Additionally, a number of dietary elements have been associated with higher or lower incidence of CRC. In this context, it has been suggested that diets high in fruit and low in meat might have a protective effect, reducing the incidence of colorectal adenomas by modulating the composition of the normal nonpathogenic commensal microbiota. In addition, it has been demonstrated that changes in abundance of taxonomic groups have a profound impact on the gastrointestinal physiology, and an increasing number of studies are proposing that the microbiota mediates the generation of dietary factors triggering colon cancer. High-throughput sequencing and molecular taxonomic technologies are rapidly filling the knowledge gaps left by conventional microbiology techniques to obtain a comprehensive catalog of the human intestinal microbiota and their associated metabolic repertoire. The information provided by these studies will be essential to identify agents capable of modulating the massive amount of gut bacteria in safe noninvasive manners to prevent CRC. Probiotics, defined as "live microorganisms which, when administered in adequate amounts, confer a health benefit on the host" (219), are capable of transient modulation of the microbiota, and their beneficial effects include reinforcement of the natural defense mechanisms and protection against gastrointestinal disorders. Probiotics have been successfully used to manage infant diarrhea, food allergies, and inflammatory bowel disease; hence, the purpose of this review was to examine probiotic metabolic activities that may have an effect on the prevention of CRC by scavenging toxic compounds or preventing their generation in situ. Additionally, a brief consideration is given to safety evaluation and production methods in the context of probiotics efficacy.

Biological and structural characterization of the Mycobacterium smegmatis nitroreductase NfnB, and its role in benzothiazinone resistance

Tuberculosis is still a leading cause of death in developing countries, for which there is an urgent need for new pharmacological agents. The synthesis of the novel antimycobacterial drug class of benzothiazinones (BTZs) and the identification of their cellular target as DprE1 (Rv3790), a component of the decaprenylphosphoryl-β-d-ribose 2'-epimerase complex, have been reported recently. Here, we describe the identification and characterization of a novel resistance mechanism to BTZ in Mycobacterium smegmatis. The overexpression of the nitroreductase NfnB leads to the inactivation of the drug by reduction of a critical nitro-group to an amino-group. The direct involvement of NfnB in the inactivation of the lead compound BTZ043 was demonstrated by enzymology, microbiological assays and gene knockout experiments. We also report the crystal structure of NfnB in complex with the essential cofactor flavin mononucleotide, and show that a common amino acid stretch between NfnB and DprE1 is likely to be essential for the interaction with BTZ. We performed docking analysis of NfnB-BTZ in order to understand their interaction and the mechanism of nitroreduction. Although Mycobacterium tuberculosis seems to lack nitroreductases able to inactivate these drugs, our findings are valuable for the design of new BTZ molecules, which may be more effective in vivo.