Bioactive metabolites of Streptomyces misakiensis display broad-spectrum antimicrobial activity against multidrug-resistant bacteria and fungi.

Background: Antimicrobial resistance is a serious threat to public health globally. It is a slower-moving pandemic than COVID-19, so we are fast running out of treatment options. Purpose: Thus, this study was designed to search for an alternative biomaterial with broad-spectrum activity for the treatment of multidrug-resistant (MDR) bacterial and fungal pathogen-related infections. Methods: We isolated Streptomyces species from soil samples and identified the most active strains with antimicrobial activity. The culture filtrates of active species were purified, and the bioactive metabolite extracts were identified by thin-layer chromatography (TLC), preparative high-performance liquid chromatography (HPLC), nuclear magnetic resonance (NMR) spectroscopy, and gas chromatography-mass spectrometry (GC-MS). The minimum inhibitory concentrations (MICs) of the bioactive metabolites against MDR bacteria and fungi were determined using the broth microdilution method. Results: Preliminary screening revealed that Streptomyces misakiensis and S. coeruleorubidus exhibited antimicrobial potential. The MIC50 and MIC90 of S. misakiensis antibacterial bioactive metabolite (ursolic acid methyl ester) and antifungal metabolite (tetradecamethylcycloheptasiloxane) against all tested bacteria and fungi were 0.5 µg/ml and 1 µg/mL, respectively, versus S. coeruleorubidus metabolites: thiocarbamic acid, N,N-dimethyl, S-1,3-diphenyl-2-butenyl ester against bacteria (MIC50: 2 µg/ml and MIC90: 4 µg/mL) and fungi (MIC50: 4 µg/ml and MIC90: 8 µg/mL). Ursolic acid methyl ester was active against ciprofloxacin-resistant strains of Streptococcus pyogenes, S. agalactiae, Escherichia coli, Klebsiella pneumoniae, and Salmonella enterica serovars, colistin-resistant Aeromonas hydrophila and K. pneumoniae, and vancomycin-resistant Staphylococcus aureus. Tetradecamethylcycloheptasiloxane was active against azole- and amphotericin B-resistant Candida albicans, Cryptococcus neoformans, C. gattii, Aspergillus flavus, A. niger, and A. fumigatus. Ursolic acid methyl ester was applied in vivo for treating S. aureus septicemia and K. pneumoniae pneumonia models in mice. In the septicemia model, the ursolic acid methyl ester-treated group had a significant 4.00 and 3.98 log CFU/g decrease (P < 0.05) in liver and spleen tissue compared to the infected, untreated control group. Lung tissue in the pneumonia model showed a 2.20 log CFU/g significant decrease in the ursolic acid methyl ester-treated group in comparison to the control group. The haematological and biochemical markers in the ursolic acid methyl ester-treated group did not change in a statistically significant way. Moreover, no abnormalities were found in the histopathology of the liver, kidneys, lungs, and spleen of ursolic acid methyl ester-treated mice in comparison with the control group. Conclusion: S. misakiensis metabolite extracts are broad-spectrum antimicrobial biomaterials that can be further investigated for the potential against MDR pathogen infections. Hence, it opens up new horizons for exploring alternative drugs for current and reemerging diseases.

An inaugural survey of cereal, oilseed and vegetable crop diseases in the Yukon Territory in 2020

Various kinds of field crops growing on two commercial farms in the Whitehorse area of the southern Yukon Territory were surveyed for diseases in summer 2020 by staff of the Agriculture Branch of the Government of Yukon. They included barley, wheat, canola, beets, broccoli, cabbage, carrots, potatoes and turnips. Fields were visited one or more times during July and August. The incidence and severity of diseases were visually assessed on a crop-by-crop basis and samples were collected for laboratory analysis of the pathogens present, if any. Both infectious and non-infectious diseases were present on most crops. The infectious diseases were caused by various species of plant pathogenic bacteria and fungi that were common on these crops growing in other areas of Canada. INTRODUCTION AND METHODS: The 2020 field crop disease survey is believed to be the first organized study of its kind on agricultural crops in the Territory. In his book, "An Annotated Index of Plant Diseases in Canada . . . ", I.L. Conners lists over 300 records of plant diseases on trees, shrubs, herbs and grasses in the Yukon that were published by individuals who were surveying forests and native vegetation mainly for federal government departments, universities and other agencies (Conners 1967). The objectives of the 2020 survey were: (1) to determine the kinds and levels of diseases on selected Yukon crops, (2) to identify the major pathogen species attacking Yukon crops, and (3) to use the results to plan future surveillance activities aimed at helping producers to improve their current disease management programs. All of the fields included in the 2020 survey were situated on two commercial farms, which were designated as Farm #1 and #2, in the Whitehorse area in the southern Yukon (Fig. 1). The crops surveyed included cereals (barley and wheat), oilseeds (canola) and vegetables (beets, broccoli, cabbage, carrots, potatoes and turnips). Fields were visited one or more times in the mid- to late growing season (July/August) at a time when damage from diseases was most noticeable. Symptoms were visually assessed on a crop-by-crop basis by determining their incidence and severity. Incidence was represented by the percentage of plants, leaves, heads, kernels, etc., damaged in the target crop, while severity was estimated to be the proportion of the leaf, fruit, head, root/canopy area, etc., affected by a specific disease as follows: Proportion of the canopy affected based on a 0-4 rating scale, where: 0 = no disease symptoms, 1 = 1-10% of the crop canopy showing symptoms;2 = 11-25% showing symptoms, 3 = 26- 50% showing symptoms, and 4 = > 50% showing symptoms. Photographs of affected plants were taken and sent to plant pathologists across Western Canada for their opinions on causation. Where possible, representative samples of plants with disease symptoms were packaged and sent to the Alberta Plant Health Lab (APHL) in Edmonton, AB for diagnostic analyses. Background information, such as the general cultural practices and cropping history, was obtained from the producers wherever possible. GPS coordinates were obtained for each field to enable future mapping Cereals: Individual fields of barley (11 ha) and wheat (30 ha) located at Farm #1 were surveyed. The barley was a two-row forage cultivar 'CDC Maverick', while the wheat was an unspecified cultivar of Canada Prairie Spring (CPS) Wheat. Plant samples were taken along a W-shaped transect for a total of five sampling points for the barley field (< 20 ha) and ten sampling points for the wheat field (> 20 ha). The first visit, which occurred on July 30, involved visual inspection and destructive sampling wherein plants were collected and removed from the field for a detailed disease assessment at a lab space in Whitehorse. There, the roots were rinsed off and the plants were examined for disease symptoms. The second visit to these fields, which occurred on August 27, only involved visual examination of the standing crop. Oilseeds: A single 40 ha field of Polish canola (cv. 'Synergy') was examined o

Molecular and therapeutic insights of rapamycin: a multi-faceted drug from Streptomyces hygroscopicus.

The advancement in pharmaceutical research has led to the discovery and development of new combinatorial life-saving drugs. Rapamycin is a macrolide compound produced from Streptomyces hygroscopicus. Rapamycin and its derivatives are one of the promising sources of drug with broad spectrum applications in the medical field. In recent times, rapamycin has gained significant attention as of its activity against cytokine storm in COVID-19 patients. Rapamycin and its derivatives have more potency when compared to other prevailing drugs. Initially, it has been used exclusively as an anti-fungal drug. Currently rapamycin has been widely used as an immunosuppressant. Rapamycin is a multifaceted drug; it has anti-cancer, anti-viral and anti-aging potentials. Rapamycin has its specific action on mTOR signaling pathway. mTOR has been identified as a key regulator of different pathways. There will be an increased demand for rapamycin, because it has lesser adverse effects when compared to steroids. Currently researchers are focused on the production of effective rapamycin derivatives to combat the growing demand of this wonder drug. The main focus of the current review is to explore the origin, development, molecular mechanistic action, and the current therapeutic aspects of rapamycin. Also, this review article revealed the potential of rapamycin and the progress of rapamycin research. This helps in understanding the exact potency of the drug and could facilitate further studies that could fill in the existing knowledge gaps. The study also gathers significant data pertaining to the gene clusters and biosynthetic pathways involved in the synthesis and production of this multi-faceted drug. In addition, an insight into the mechanism of action of the drug and important derivatives of rapamycin has been expounded. The fillings of the current review, aids in understanding the underlying molecular mechanism, strain improvement, optimization and production of rapamycin derivatives.

Investigation of Streptomyces sp. Strain EMB24 Secondary Metabolite Profile Has Unraveled Its Extraordinary Antibacterial Potency Against Drug-Resistant Bacteria.

With the overuse and misuse of antibiotics amid COVID-19 pandemic, the antimicrobial resistance, which is already a global challenge, has accelerated its pace significantly. Finding novel and potential antibiotics seems one of the probable solutions. In this work, a novel Streptomyces sp. strain EMB24 was isolated and found to be an excellent source of antimicrobials as confirmed by agar-plug assay. It showed antibacterial activity against infection-causing bacteria, namely Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa. In addition, Streptomyces sp. strain EMB24 inhibited the growth methicillin-resistant Staphylococcus aureus (MRSA), tetracycline-resistant Neisseria gonorrhoeae, and ampicillin-resistant Neisseria gonorrhoeae. Furthermore, to get deep insights about the genome and biosynthetic gene clusters producing antibiotics, whole genome sequencing was done. The strain EMB24 is closely related to the Streptomyces longispororuber as revealed by phylogenetic analysis which is a potential source of antibiotics and pigments as undecylprodigiosin and metacycloprodigiosin belonging to the class prodigiosin. Naphthyridinomycin, alkylresorcinols, desferrioxamine B and E, venezuelin, aborycin, MS-271, and siamycin are potent therapeutics that shared 100% similarity with the reference strain as revealed by the online antiSMASH tool.

Ivermectin: Evaluation of Efficacy and Safety in COVID-19

The search for an effective and safe COVID-19 therapy involves, among other things, assessment of efficacy of medicines already used for the treatment of other diseases, and having potential antiviral activity against SARSCoV-2. The relevance of the presented study stems from ambiguous data on the off-label use of the antiparasitic medicine ivermectin for the treatment of COVID-19 patients. The aim of the study was to analyse ivermectin efficacy and safety for COVID-19 treatment, as reflected in the scientific literature. Ivermectin, an antiparasitic medicine from the group of macrocyclic lactones produced by Streptomyces avermitilis, stimulates release of the inhibitory neurotransmitter gamma-aminobutyric acid, which leads to impaired transmission of nerve impulses, paralysis and death of parasites. The results of preclinical studies show ivermectin's inhibitory activity against a number of RNA and DNA viruses, including SARS-CoV-2. The results of ivermectin clinical studies are ambiguous: a number of studies demonstrated a positive effect on the condition of COVID-19 patients, however, there is currently no convincing evidence of the validity and efficacy of ivermectin use for the prevention and treatment of COVID-19 patients. The safety profile of ivermectin is relatively favourable. Large randomised controlled trials are needed to fully assess the feasibility of using ivermectin in COVID-19.

The Potential Effect of Nigericin from Streptomyces hygroscopicus subsp. Hygroscopicus Against the Syndemic of Malaria and COVID-19 through Molecular Docking Perspective

Background: Malaria is a constantly challenging problem, notably in the Coronavirus Disease-19 (COVID-19) pandemic. The syndemic condition, malaria-COVID-19 co-infections, had been reported. Our previous study successfully revealed several compounds from Streptomyces hygroscopicus subsp. Hygroscopicus, including nigericin that has both antimalarial and antiviral effects. In malaria infection, Plasmodium falciparum Chloroquine Resistance Transporter (PfCRT) is the potential target for eliminating Plasmodium. Meanwhile, for SARS-CoV-2 infection, MPro is an essential protein for SARS-CoV-2 survival. This research aims to examine the potential effect of nigericin towards Plasmodium and SARS-CoV-2 by assessing its molecular interaction with PfCRT and MPro through molecular docking study. Methods: The protein target PfCRT and MPro were obtained from Protein Data Bank. Nigericin and the control ligand (chloroquine and N3) were obtained from PubChem. The pharmacokinetic analysis was done using SwissADME. Specific molecular docking was conducted using PyRx 0.9 and was visualized using LigPlot and PyMOL. Results: Nigericin has a large molecular weight, leading to the non-fulfillment of the Lipinski rule for oral administration. Through molecular docking study, the binding affinity of the Nigericin-PfCRT complex was -8.1 kcal/mol, and Nigericin-MPro was -8.6 kcal/mol. These binding affinities were stronger than the control ligand. The interaction between Nigericin-PfCRT and Nigericin-MPro share a similar pocket-site and amino acid residues as the control ligands. Conclusion: Nigericin has potential antimalarial and anti-coronavirus effects through molecular docking perspective by assessing the binding affinity and similarity of amino acid residues compared to control. Administration of systemic route can be an option in giving nigericin.

BIODEGRADATION of BIOPLASTICS, INJECTED MOLDED POLYHYDROXYALKANOATES, by A BACTERIUM ISOLATED from VERMICOMPOST

According to the Argentinian Wildlife Foundation census on the coast of Buenos Aires province, 80% of the wastes were petrochemicals plastics and microplastics. Since last year, due to the influence of the COVID-19 pandemic, the use of plastics has increased, especially in containers for prepared food and single-use plastics. For this reason, the world market for bioplastics is growing steadily. The aim of this work was to evaluate the biodegradation of injected molded bioplastics in vermicompost using a bacterium isolated with extracellular enzymatic activity for the depolymerization of polyhydroxyalkanoates (PHAs). Vermicompost (Californian red worm) was sieved through 5 mm opening size. Phylogenetic analysis: the sequence of the 16S rDNA from the isolated Actinomycetes was compared with the EMBL and GenBank databases. The phylogenetic tree was constructed. The morphological characteristics were performed in ISP media and the biochemical tests were carried out according to the Bergeýs manual. Biodegradation analysis: injected molded PHAs samples consisted in rectangular (1.00 ± 0.05 cm width and 3.00 ± 0.05 cm length, thickness: 200 μm) and circular samples (diameter 2 cm, thickness 0.2 cm). Biodegradation by extracellular depolymerase activity was measured at 650 nm by turbidity decrease and by halo formation around colonies (ISP media, 12 days, 30 °C). PHAs surfaces were observed using a microscope. 28 Actinomycetes were isolated with PHAs biodegradation capacity, with different types of growth, colony morphology and extracellular enzyme production. Based on the biodegradation halo area, isolates were classified into three groups: low, medium and high enzymatic activity. From the last group, the one with the highest degradative activity under different environmental conditions was selected. The bacterium was identified as Streptomyces omiyaensis by phylogenetic studies, 16S rDNA sequencing, morphological characterization and biochemical tests and it was determined as GRAS. The strain was deposited in the AGRAL FAUBA culture collection as S. omiyaensis SSM5670. The PHAs samples in vermicompost inoculated with S. omiyaensis SSM5670 showed the deterioration of their surfaces, with the presence of surface irregularities and roughness, until the total biodegradation of the samples. The inoculation of vermicompost with an Actinomycetes isolate with extracellular PHAs degradation activity, would improve the bioplastics degradation, which would be critical given that the global production capacity of bioplastics has been estimated to increase to approximately 2.44 million tonnes in 2022.

Repositioning Ivermectin for Covid-19 treatment: Molecular mechanisms of action against SARS-CoV-2 replication.

Ivermectin (IVM) is an FDA approved macrocyclic lactone compound traditionally used to treat parasitic infestations and has shown to have antiviral potential from previous in-vitro studies. Currently, IVM is commercially available as a veterinary drug but have also been applied in humans to treat onchocerciasis (river blindness - a parasitic worm infection) and strongyloidiasis (a roundworm/nematode infection). In light of the recent pandemic, the repurposing of IVM to combat SARS-CoV-2 has acquired significant attention. Recently, IVM has been proven effective in numerous in-silico and molecular biology experiments against the infection in mammalian cells and human cohort studies. One promising study had reported a marked reduction of 93% of released virion and 99.98% unreleased virion levels upon administration of IVM to Vero-hSLAM cells. IVM's mode of action centres around the inhibition of the cytoplasmic-nuclear shuttling of viral proteins by disrupting the Importin heterodimer complex (IMPα/ß1) and downregulating STAT3, thereby effectively reducing the cytokine storm. Furthermore, the ability of IVM to block the active sites of viral 3CLpro and S protein, disrupts important machinery such as viral replication and attachment. This review compiles all the molecular evidence to date, in review of the antiviral characteristics exhibited by IVM. Thereafter, we discuss IVM's mechanism and highlight the clinical advantages that could potentially contribute towards disabling the viral replication of SARS-CoV-2. In summary, the collective review of recent efforts suggests that IVM has a prophylactic effect and would be a strong candidate for clinical trials to treat SARS-CoV-2.

Antibiotic Biosynthesis Pathways from Endophytic Streptomyces SUK 48 through Metabolomics and Genomics Approaches.

Streptomyces sp. has been known to be a major antibiotic producer since the 1940s. As the number of cases related to resistance pathogens infection increases yearly, discovering the biosynthesis pathways of antibiotic has become important. In this study, we present the streamline of a project report summary; the genome data and metabolome data of newly isolated Streptomyces SUK 48 strain are also analyzed. The antibacterial activity of its crude extract is also determined. To obtain genome data, the genomic DNA of SUK 48 was extracted using a commercial kit (Promega) and sent for sequencing (Pac Biosciences technology platform, Menlo Park, CA, USA). The raw data were assembled and polished using Hierarchical Genome Assembly Process 4.0 (HGAP 4.0). The assembled data were structurally predicted using tRNAscan-SE and rnammer. Then, the data were analyzed using Kyoto Encyclopedia of Genes and Genomes (KEGG) database and antiSMASH analysis. Meanwhile, the metabolite profile of SUK 48 was determined using liquid chromatography-mass spectrophotometry (LC-MS) for both negative and positive modes. The results showed that the presence of kanamycin and gentamicin, as well as the other 11 antibiotics. Nevertheless, the biosynthesis pathways of aurantioclavine were also found. The cytotoxicity activity showed IC50 value was at 0.35 ± 1.35 mg/mL on the cell viability of HEK 293. In conclusion, Streptomyces sp. SUK 48 has proven to be a non-toxic antibiotic producer such as auranticlavine and gentamicin.

Scaffold Hopping of α-Rubromycin Enables Direct Access to FDA-Approved Cromoglicic Acid as a SARS-CoV-2 MPro Inhibitor.

The COVID-19 pandemic is still active around the globe despite the newly introduced vaccines. Hence, finding effective medications or repurposing available ones could offer great help during this serious situation. During our anti-COVID-19 investigation of microbial natural products (MNPs), we came across α-rubromycin, an antibiotic derived from Streptomyces collinus ATCC19743, which was able to suppress the catalytic activity (IC50 = 5.4 µM and Ki = 3.22 µM) of one of the viral key enzymes (i.e., MPro). However, it showed high cytotoxicity toward normal human fibroblasts (CC50 = 16.7 µM). To reduce the cytotoxicity of this microbial metabolite, we utilized a number of in silico tools (ensemble docking, molecular dynamics simulation, binding free energy calculation) to propose a novel scaffold having the main pharmacophoric features to inhibit MPro with better drug-like properties and reduced/minimal toxicity. Nevertheless, reaching this novel scaffold synthetically is a time-consuming process, particularly at this critical time. Instead, this scaffold was used as a template to explore similar molecules among the FDA-approved medications that share its main pharmacophoric features with the aid of pharmacophore-based virtual screening software. As a result, cromoglicic acid (aka cromolyn) was found to be the best hit, which, upon in vitro MPro testing, was 4.5 times more potent (IC50 = 1.1 µM and Ki = 0.68 µM) than α-rubromycin, with minimal cytotoxicity toward normal human fibroblasts (CC50 > 100 µM). This report highlights the potential of MNPs in providing unprecedented scaffolds with a wide range of therapeutic efficacy. It also revealed the importance of cheminformatics tools in speeding up the drug discovery process, which is extremely important in such a critical situation.

Multi-Omics-Guided Discovery of Omicsynins Produced by Streptomyces sp. 1647: Pseudo-Tetrapeptides Active Against Influenza A Viruses and Coronavirus HCoV-229E.

Many microorganisms have mechanisms that protect cells against attack from viruses. The fermentation components of Streptomyces sp. 1647 exhibit potent anti-influenza A virus (IAV) activity. This strain was isolated from soil in southern China in the 1970s, but the chemical nature of its antiviral substance(s) has remained unknown until now. We used an integrated multi-omics strategy to identify the antiviral agents from this streptomycete. The antibiotics and Secondary Metabolite Analysis Shell (antiSMASH) analysis of its genome sequence revealed 38 biosynthetic gene clusters (BGCs) for secondary metabolites, and the target BGCs possibly responsible for the production of antiviral components were narrowed down to three BGCs by bioactivity-guided comparative transcriptomics analysis. Through bioinformatics analysis and genetic manipulation of the regulators and a biosynthetic gene, cluster 36 was identified as the BGC responsible for the biosynthesis of the antiviral compounds. Bioactivity-based molecular networking analysis of mass spectrometric data from different recombinant strains illustrated that the antiviral compounds were a class of structural analogues. Finally, 18 pseudo-tetrapeptides with an internal ureido linkage, omicsynins A1-A6, B1-B6, and C1-C6, were identified and/or isolated from fermentation broth. Among them, 11 compounds (omicsynins A1, A2, A6, B1-B3, B5, B6, C1, C2, and C6) are new compounds. Omicsynins B1-B4 exhibited potent antiviral activity against IAV with the 50% inhibitory concentration (IC50) of approximately 1 µmol∙L-1 and a selectivity index (SI) ranging from 100 to 300. Omicsynins B1-B4 also showed significant antiviral activity against human coronavirus HCoV-229E. By integrating multi-omics data, we discovered a number of novel antiviral pseudo-tetrapeptides produced by Streptomyces sp. 1647, indicating that the secondary metabolites of microorganisms are a valuable source of novel antivirals.