Authors: John A Bouranis, Laura M Beaver, Jaewoo Choi...

Isothiocyanates, such as sulforaphane and iberin, derived from glucosinolates (GLS) in cruciferous vegetables, are known to prevent and suppress cancer development. GLS can also be converted by bacteria to biologically inert nitriles, such as sulforaphane-nitrile (SFN-NIT) and iberin-nitrile (IBN-NIT), but the role of the gut microbiome in this process is relatively undescribed and SFN-NIT excretion in humans is unknown. An ex vivo fecal incubation model with in vitro digested broccoli sprouts and 16S sequencing was utilized to explore the role of the gut microbiome in SFN- and IBN-NIT production. SFN-NIT excretion was measured among human subjects following broccoli sprout consumption. The fecal culture model showed high inter-individual variability in nitrile production and identified two sub-populations of microbial communities among the fecal cultures, which coincided with a differing abundance of nitriles. The Clostridiaceae family was associated with high levels, while individuals with a low abundance of nitriles were more enriched with taxa from the Enterobacteriaceae family. High levels of inter-individual variation in urine SFN-NIT levels were also observed, with peak excretion of SFN-NIT at 24 h post broccoli sprout consumption. These results suggest that nitrile production from broccoli, as opposed to isothiocyanates, could be influenced by gut microbiome composition, potentially lowering efficacy of cruciferous vegetable interventions.

Topics: Brassica; Clostridiaceae; Enterobacteriaceae; Female; Gastrointestinal Microbiome; Glucosinolates; Humans; Isothiocyanates; Male; Nitriles; Plant Shoots; Sulfoxides; Thiocyanates

PubMed: 34578891
DOI: 10.3390/nu13093013

Authors: Sarah Kim, Sein Min, Heelim Chae...

Signal Amplification by Reversible Exchange (SABRE), a hyperpolarization technique, has been harnessed as a powerful tool to achieve useful hyperpolarized materials by polarization transfer from parahydrogen. In this study, we systemically applied SABRE to a series of nitrile compounds, which have been rarely investigated. By performing SABRE in various magnetic fields and concentrations on nitrile compounds, we unveiled its hyperpolarization properties to maximize the spin polarization and its transfer to the next spins. Through this sequential study, we obtained a ~130-fold enhancement for several nitrile compounds, which is the highest number ever reported for the nitrile compounds. Our study revealed that the spin polarization on hydrogens decreases with longer distances from the nitrile group, and its maximum polarization is found to be approximately 70 G with 5 μL of substrates in all structures. Interestingly, more branched structures in the ligand showed less effective polarization transfer mechanisms than the structural isomers of butyronitrile and isobutyronitrile. These first systematic SABRE studies on a series of nitrile compounds will provide new opportunities for further research on the hyperpolarization of various useful nitrile materials.

Topics: Hydrogen; Magnetic Fields; Magnetic Resonance Spectroscopy; Molecular Structure; Nitriles

PubMed: 32717970
DOI: 10.3390/molecules25153347

Authors: Shannon Kilmartin-Lynch, Rajeev Roychand, Mohammad Saberian...

The use of single-use nitrile gloves has been on a sharp incline since the Coronavirus pandemic first started in late 2019. This led to a significant increase in the generation of this clinical waste that requires various recycling solutions to reduce its environmental impact from disposal or incineration. This paper explores its application in structural concrete by adding shredded nitrile gloves at 0.1%, 0.2%, and 0.3% of the volume of concrete. The compressive strength, modulus of elasticity, ultrasonic pulse velocity, and SEM-EDS analysis were undertaken to ascertain the effect of different concentrations of shredded nitrile gloves on the mechanical properties, quality of concrete, and its bond performance with the cement matrix. The results demonstrate that the inclusion of up to 0.2% of shredded nitrile gloves can provide ~22% improvement in the compressive strength of blended concrete composites at 28-days of curing. In comparison, the inclusion of 0.3% of shredded nitrile gloves shows improvements of ~20% in compressive strength at 28-days. The SEM-EDS analysis shows a very good bond formation between the nitrile rubber and the cement matrix with no gap identified in the interfacial transition zone (ITZ).

Topics: COVID-19; Construction Materials; Humans; Nitriles; Rubber; SARS-CoV-2

PubMed: 34742992
DOI: 10.1016/j.scitotenv.2021.151423

Authors: Hilmi Yavuzer, Yasuhisa Asano, Harald Gröger...

In this contribution, the unique and unprecedented stereochemical phenomenon of an aldoxime dehydratase-catalyzed enantioselective dehydration of racemic E- and Z-aldoximes with selective formation of both enantiomeric forms of a chiral nitrile is rationalized by means of molecular modelling, comprising in silico mutations and docking studies. This theoretical investigation gave detailed insight into why with the same enzyme the use of racemic E- and Z-aldoximes leads to opposite forms of the chiral nitrile. The calculated mutants with a larger or smaller cavity in the active site were then prepared and used in biotransformations, showing the theoretically predicted decrease and increase of the enantioselectivities in these nitrile syntheses. This validated model also enabled the rational design of mutants with a smaller cavity, which gave superior enantioselectivities compared to the known wild-type enzyme, with excellent E-values of up to E>200 when the mutant OxdRE-Leu145Phe was utilized.

Topics: Hydro-Lyases; Molecular Docking Simulation; Molecular Structure; Nitriles; Stereoisomerism

PubMed: 33886145
DOI: 10.1002/anie.202017234

Authors: Jihye Jung, Jan Braun, Tibor Czabany...

The nitrile reductase QueF catalyzes NADPH-dependent reduction of the nitrile group of preQ (7-cyano-7-deazaguanine) into the primary amine of preQ (7-aminomethyl-7-deazaguanine), a biologically unique reaction important in bacterial nucleoside biosynthesis. Here we have discovered that the QueF from Escherichia coli-its D197A and E89L variants in particular (apparent k ≈10  min )-also catalyze the slow hydration of the C5=C6 double bond of the dihydronicotinamide moiety of NADPH. The enzymatically C6-hydrated NADPH is a 3.5:1 mixture of R and S forms and rearranges spontaneously through anomeric epimerization (β→α) and cyclization at the tetrahydronicotinamide C6 and the ribosyl O2. NADH and 1-methyl- or 1-benzyl-1,4-dihydronicotinamide are not substrates of the enzymatic hydration. Mutagenesis results support a QueF hydratase mechanism, in which Cys190-the essential catalytic nucleophile for nitrile reduction-acts as the general acid for protonation at the dihydronicotinamide C5 of NADPH. Thus, the NADPH hydration in the presence of QueF bears mechanistic resemblance to the C=C double bond hydration in natural hydratases.

Topics: Catalysis; Cysteine; Escherichia coli; Escherichia coli Proteins; Hydro-Lyases; Mutagenesis, Site-Directed; Mutation; NADP; Nitriles; Oxidoreductases

PubMed: 31850614
DOI: 10.1002/cbic.201900679

Authors: O K L Rapheeha, M P Roux-van der Merwe, J Badenhorst...

AIMS

The aim of this study was to explore bacterial soil diversity for nitrile biocatalysts, in particular, those for hydrolysis of β-substituted nitriles, to the corresponding carboxamides and acids that may be incorporated into peptidomimetics. To achieve this, we needed to compare the efficiency of isolation methods and determine the influence of land use and geographical origin of the soil sample.

METHODS AND RESULTS

Nitrile-utilizing bacteria were isolated from various soil environments across a 1000 km long transect of South Africa, including agricultural soil, a gold mine tailing dam and uncultivated soil. The substrate profile of these isolates was determined through element-limited growth studies on seven different aliphatic or aromatic nitriles. A subset of these organisms expressing broad substrate ranges was evaluated for their ability to hydrolyse β-substituted nitriles (3-amino-3-phenylpropionitrile and 3-hydroxy-4-phenoxybutyronitrile) and the active organisms were found to be Rhodococcus erythropolis from uncultivated soil and Rhodococcus rhodochrous from agricultural soils.

CONCLUSIONS

The capacity for hydrolysis of β-substituted nitriles appears to reside almost exclusively in Rhodococci. Land use has a much greater effect on the biocatalysis substrate profile than geographical location.

SIGNIFICANCE AND IMPACT OF THE STUDY

Enzymes are typically substrate specific in their catalytic reactions, and this means that a wide diversity of enzymes is required to provide a comprehensive biocatalysis toolbox. This paper shows that the microbial diversity of nitrile hydrolysis activity can be targeted according to land utilization. Nitrile biocatalysis is a green chemical method for the enzymatic production of amides and carboxylic acids that has industrial applications, such as in the synthesis of acrylamide and nicotinamide. The biocatalysts discovered in this study may be applied to the synthesis of peptidomimetics which are an important class of therapeutic compounds.

Topics: Amides; Carboxylic Acids; Catalysis; Hydrolysis; Nitriles; Rhodococcus; Soil Microbiology; South Africa

PubMed: 27930842
DOI: 10.1111/jam.13367

Review

Authors: Hideji Tanii

OBJECTIVES

Allyl nitrile (3-butenenitrile) occurs naturally in the environment, in particular, in cruciferous vegetables, indicating a possible daily intake of the compound. There is no report on actual health effects of allyl nitrile in humans, although it is possible that individuals in the environment are at a risk of exposure to allyl nitrile. However, little is known about its quantitative assessment for the environment and bioactivity in the body. This study provides a review of previous accumulated studies on allyl nitrile.

METHODS

Published literature on allyl nitrile was examined for findings on toxicity, metabolism, risk of various cancers, generation, intake estimates, and low-dose effects in the body.

RESULTS

High doses of allyl nitrile produce toxicity characterized by behavioral abnormalities, which are considered to be produced by an active metabolite, 3,4-epoxybutyronitrile. Cruciferous vegetables have been shown to have a potential role in reducing various cancers. Hydrolysis of the glucosinolate sinigrin, rich in cruciferous vegetables, results in the generation of allyl nitrile. An intake of allyl nitrile is estimated at 0.12 μmol/kg body weight in Japan. Repeated exposure to low doses of allyl nitrile upregulates antioxidant/phase II enzymes in various tissues; this may contribute to a reduction in neurotoxicity and skin inflammation. These high and low doses are far more than the intake estimate.

CONCLUSION

Allyl nitrile in the environment is a compound with diverse bioactivities in the body, characterized by inducing behavioral abnormalities at high doses and some antioxidant/phase II enzymes at low doses.

Topics: Animals; Antioxidants; Disease Models, Animal; Glucosinolates; Humans; Mental Disorders; Mice; Neoplasms; Nitriles; Rats; Vegetables

PubMed: 28132970
DOI: 10.1539/joh.16-0147-RA

Review

Authors: Simone Brogi, Roberta Ibba, Sara Rossi...

In the field of drug discovery, the nitrile group is well represented among drugs and biologically active compounds. It can form both non-covalent and covalent interactions with diverse biological targets, and it is amenable as an electrophilic warhead for covalent inhibition. The main advantage of the nitrile group as a warhead is mainly due to its milder electrophilic character relative to other more reactive groups (e.g., -CHO), reducing the possibility of unwanted reactions that would hinder the development of safe drugs, coupled to the ease of installation through different synthetic approaches. The covalent inhibition is a well-assessed design approach for serine, threonine, and cysteine protease inhibitors. The mechanism of hydrolysis of these enzymes involves the formation of a covalent acyl intermediate, and this mechanism can be exploited by introducing electrophilic warheads in order to mimic this covalent intermediate. Due to the relevant role played by the cysteine protease in the survival and replication of infective agents, spanning from viruses to protozoan parasites, we will review the most relevant and recent examples of protease inhibitors presenting a nitrile group that have been introduced to form or to facilitate the formation of a covalent bond with the catalytic cysteine active site residue.

Topics: Cysteine; Cysteine Proteases; Cysteine Proteinase Inhibitors; Drug Discovery; Humans; Nitriles; Parasitic Diseases

PubMed: 35458759
DOI: 10.3390/molecules27082561

Review

Authors: Pablo Domínguez de María

Nitriles comprise a broad group of chemicals that are currently being industrially produced and used in fine chemicals and pharmaceuticals, as well as in bulk applications, polymer chemistry, solvents, etc. Aldoxime dehydratases catalyze the cyanide-free synthesis of nitriles starting from aldoximes under mild conditions, holding potential to become sustainable alternatives for industrial processes. Different aldoxime dehydratases accept a broad range of aldoximes with impressive high substrate loadings of up to >1 Kg L and can efficiently catalyze the reaction in aqueous media as well as in non-aqueous systems, such as organic solvents and solvent-free (neat substrates). This paper provides an overview of the recent developments in this field with emphasis on strategies that may be of relevance for industry and sustainability. When possible, potential links to biorefineries and to the use of biogenic raw materials are discussed.

Topics: Biocatalysis; Green Chemistry Technology; Hydro-Lyases; Nitriles

PubMed: 34361620
DOI: 10.3390/molecules26154466

Authors: Joni Frederick, Fritha Hennessy, Uli Horn...

BACKGROUND

Rhodococci are industrially important soil-dwelling Gram-positive bacteria that are well known for both nitrile hydrolysis and oxidative metabolism of aromatics. Rhodococcus rhodochrous ATCC BAA-870 is capable of metabolising a wide range of aliphatic and aromatic nitriles and amides. The genome of the organism was sequenced and analysed in order to better understand this whole cell biocatalyst.

RESULTS

The genome of R. rhodochrous ATCC BAA-870 is the first Rhodococcus genome fully sequenced using Nanopore sequencing. The circular genome contains 5.9 megabase pairs (Mbp) and includes a 0.53 Mbp linear plasmid, that together encode 7548 predicted protein sequences according to BASys annotation, and 5535 predicted protein sequences according to RAST annotation. The genome contains numerous oxidoreductases, 15 identified antibiotic and secondary metabolite gene clusters, several terpene and nonribosomal peptide synthetase clusters, as well as 6 putative clusters of unknown type. The 0.53 Mbp plasmid encodes 677 predicted genes and contains the nitrile converting gene cluster, including a nitrilase, a low molecular weight nitrile hydratase, and an enantioselective amidase. Although there are fewer biotechnologically relevant enzymes compared to those found in rhodococci with larger genomes, such as the well-known Rhodococcus jostii RHA1, the abundance of transporters in combination with the myriad of enzymes found in strain BAA-870 might make it more suitable for use in industrially relevant processes than other rhodococci.

CONCLUSIONS

The sequence and comprehensive description of the R. rhodochrous ATCC BAA-870 genome will facilitate the additional exploitation of rhodococci for biotechnological applications, as well as enable further characterisation of this model organism. The genome encodes a wide range of enzymes, many with unknown substrate specificities supporting potential applications in biotechnology, including nitrilases, nitrile hydratase, monooxygenases, cytochrome P450s, reductases, proteases, lipases, and transaminases.

Topics: Amino Acid Sequence; Drug Resistance, Bacterial; Genome, Bacterial; Molecular Sequence Annotation; Nitriles; Oxidoreductases; Rhodococcus; Whole Genome Sequencing

PubMed: 31898479
DOI: 10.1186/s12864-019-6405-7