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Molecules (Basel, Switzerland) May 2024Prediction of the antibacterial activity of new chemical compounds is an important task, due to the growing problem of bacterial drug resistance. Generalized linear...
Prediction of the antibacterial activity of new chemical compounds is an important task, due to the growing problem of bacterial drug resistance. Generalized linear models (GLMs) were created using 85 amidrazone derivatives based on the results of antimicrobial activity tests, determined as the minimum inhibitory concentration (MIC) against Gram-positive bacteria: , , , , and . For the analysis of compounds characterized by experimentally measured MIC values, we included physicochemical properties (e.g., molecular weight, number of hydrogen donors and acceptors, topological polar surface area, compound percentages of carbon, nitrogen, and oxygen, melting points, and lipophilicity) as potential predictors. The presence of R1 and R2 substituents, as well as interactions between melting temperature and R1 or R2 substituents, were also considered. The set of potential predictors also included possible biological effects (e.g., antibacterial, antituberculotic) of tested compounds calculated with the PASS (Prediction of Activity Spectra for Substances) program. Using GLMs with least absolute shrinkage and selection (LASSO), least-angle regression, and stepwise selection, statistically significant models with the optimal value of the adjusted determination coefficient and of seven fit criteria were chosen, e.g., Akaike's information criterion. The most often selected variables were as follows: molecular weight, PASS_antieczematic, PASS_anti-inflam, squared melting temperature, PASS_antitumor, and experimental lipophilicity. Additionally, relevant to the bacterial strain, the interactions between melting temperature and R1 or R2 substituents were selected, indicating that the relationship between MIC and melting temperature depends on the type of R1 or R2 substituent.
Topics: Anti-Bacterial Agents; Microbial Sensitivity Tests; Gram-Positive Bacteria; Structure-Activity Relationship; Molecular Structure
PubMed: 38792231
DOI: 10.3390/molecules29102369 -
Biology Apr 2024(Mtb) ranks as the most lethal human pathogen, able to fend off repeated attacks by the immune system or medications. PE_PGRS proteins are hallmarks of the...
(Mtb) ranks as the most lethal human pathogen, able to fend off repeated attacks by the immune system or medications. PE_PGRS proteins are hallmarks of the pathogenicity of Mtb and contribute to its antigenic diversity, virulence, and persistence during infection. is a nonpathogenic mycobacterium that naturally lacks PE_PGRS and is used as a model to express Mtb proteins. PE_PGRS has the capability to evade host immune responses and enhance the intracellular survival of . Despite the intense investigations into PE_PGRS proteins, their role in tuberculosis remains elusive. We engineered the recombinant strain Ms-PE_PGRS38. The result shows that PE_PGRS38 is expressed in the cell wall of . PE_PGRS38 contributes to biofilm formation, confers permeability to the cell wall, and shows variable responses to exogenous stresses. PE_PGRS38 downregulated TLR4/NF-κB signaling in RAW264.7 macrophages and lung tissues of infected mice. In addition, PE_PGRS38 decreased NLRP3-dependent IL-1β release and limited pathogen-mediated inflammasome activity during infection. Moreover, PE_PGRS38 inhibited the apoptosis of RAW264.7 cells by downregulating the expression of apoptotic markers including Bax, cytochrome c, caspase-3, and caspase-9. In a nutshell, our findings demonstrate that PE_PGRS38 is a virulence factor for Mtb that enables recombinant to survive by resisting and evading the host's immune responses during infection.
PubMed: 38785795
DOI: 10.3390/biology13050313 -
Tuberculosis (Edinburgh, Scotland) Jul 2024Targeted gene deletion in mycobacteria remain complicated, requiring expertise and multiple steps. Here we present a single-step, easy to understand and perform method...
Targeted gene deletion in mycobacteria remain complicated, requiring expertise and multiple steps. Here we present a single-step, easy to understand and perform method for targeted gene deletion. Using this method, we successfully deleted several genes in both M. smegmatis and M. abscessus. We believe this method will facilitate molecular research of mycobacteria and make it accessible to a greater number of researchers throughout the world.
Topics: Gene Deletion; Mycobacterium smegmatis; Mycobacterium abscessus; Genes, Bacterial; Humans; Bacterial Proteins
PubMed: 38781657
DOI: 10.1016/j.tube.2024.102520 -
DNA Repair Jul 2024MutT proteins belong to the Nudix hydrolase superfamily that includes a diverse group of Mg requiring enzymes. These proteins use a generalized substrate, nucleoside...
MutT proteins belong to the Nudix hydrolase superfamily that includes a diverse group of Mg requiring enzymes. These proteins use a generalized substrate, nucleoside diphosphate linked to a chemical group X (NDP-X), to produce nucleoside monophosphate (NMP) and the moiety X linked with phosphate (XP). E. coli MutT (EcoMutT) and mycobacterial MutT1 (MsmMutT1) belong to the Nudix hydrolase superfamily that utilize 8-oxo-(d)GTP (referring to both 8-oxo-GTP or 8-oxo-dGTP). However, predominant products of their activities are different. While EcoMutT produces 8-oxo-(d)GMP, MsmMutT1 gives rise to 8-oxo-(d)GDP. Here, we show that the altered cleavage specificities of the two proteins are largely a consequence of the variation at the equivalent of Gly37 (G37) in EcoMutT to Lys (K65) in the MsmMutT1. Remarkably, mutations of G37K (EcoMutT) and K65G (MsmMutT1) switch their cleavage specificities to produce 8-oxo-(d)GDP, and 8-oxo-(d)GMP, respectively. Further, a time course analysis using 8-oxo-GTP suggests that MsmMutT1(K65G) hydrolyses 8-oxo-(d)GTP to 8-oxo-(d)GMP in a two-step reaction via 8-oxo-(d)GDP intermediate. Expectedly, unlike EcoMutT (G37K) and MsmMutT1, EcoMutT and MsmMutT1 (K65G) rescue an E. coli ΔmutT strain, better by decreasing A to C mutations.
Topics: Escherichia coli Proteins; Mycobacterium smegmatis; Substrate Specificity; Deoxyguanine Nucleotides; Escherichia coli; Bacterial Proteins; Amino Acid Substitution; Pyrophosphatases; Phosphoric Monoester Hydrolases; Guanosine Triphosphate
PubMed: 38776712
DOI: 10.1016/j.dnarep.2024.103693 -
Nature Communications May 2024Lipid biosynthesis in the pathogen Mycobacterium tuberculosis depends on biotin for posttranslational modification of key enzymes. However, the mycobacterial biotin...
Lipid biosynthesis in the pathogen Mycobacterium tuberculosis depends on biotin for posttranslational modification of key enzymes. However, the mycobacterial biotin synthetic pathway is not fully understood. Here, we show that rv1590, a gene of previously unknown function, is required by M. tuberculosis to synthesize biotin. Chemical-generic interaction experiments mapped the function of rv1590 to the conversion of dethiobiotin to biotin, which is catalyzed by biotin synthases (BioB). Biochemical studies confirmed that in contrast to BioB of Escherichia coli, BioB of M. tuberculosis requires Rv1590 (which we named "biotin synthase auxiliary protein" or BsaP), for activity. We found homologs of bsaP associated with bioB in many actinobacterial genomes, and confirmed that BioB of Mycobacterium smegmatis also requires BsaP. Structural comparisons of BsaP-associated biotin synthases with BsaP-independent biotin synthases suggest that the need for BsaP is determined by the [2Fe-2S] cluster that inserts sulfur into dethiobiotin. Our findings open new opportunities to seek BioB inhibitors to treat infections with M. tuberculosis and other pathogens.
Topics: Biotin; Mycobacterium tuberculosis; Bacterial Proteins; Sulfurtransferases; Mycobacterium smegmatis; Escherichia coli
PubMed: 38755122
DOI: 10.1038/s41467-024-48448-1 -
Nucleic Acids Research May 2024In the canonical DNA mismatch repair (MMR) mechanism in bacteria, if a nucleotide is incorrectly mis-paired with the template strand during replication, the resulting...
In the canonical DNA mismatch repair (MMR) mechanism in bacteria, if a nucleotide is incorrectly mis-paired with the template strand during replication, the resulting repair of this mis-pair can result in the degradation and re-synthesis of hundreds or thousands of nucleotides on the newly-replicated strand (long-patch repair). While mycobacteria, which include important pathogens such as Mycobacterium tuberculosis, lack the otherwise highly-conserved enzymes required for the canonical MMR reaction, it was found that disruption of a mycobacterial mismatch-sensitive endonuclease NucS results in a hyper-mutative phenotype, leading to the idea that NucS might be involved in a cryptic, independently-evolved DNA MMR mechanism, perhaps mediated by homologous recombination (HR) with a sister chromatid. Using oligonucleotide recombination, which allows us to introduce mismatches specifically into the genomes of a model for M. tuberculosis, Mycobacterium smegmatis, we find that NucS participates in a direct repair of DNA mismatches where the patch of excised nucleotides is largely confined to within ∼5-6 bp of the mis-paired nucleotides, which is inconsistent with mechanistic models of canonical mycobacterial HR or other double-strand break (DSB) repair reactions. The results presented provide evidence of a novel NucS-associated mycobacterial MMR mechanism occurring in vivo to regulate genetic mutations in mycobacteria.
PubMed: 38747340
DOI: 10.1093/nar/gkae402 -
BioRxiv : the Preprint Server For... Apr 2024Cell growth in mycobacteria involves cell wall expansion that is restricted to the cell poles. The DivIVA homolog Wag31 is required for this process, but the molecular...
Cell growth in mycobacteria involves cell wall expansion that is restricted to the cell poles. The DivIVA homolog Wag31 is required for this process, but the molecular mechanism and protein partners of Wag31 have not been described. In this study of , we identify a connection between and trehalose monomycolate (TMM) transporter in a suppressor screen, and show that Wag31 and polar regulator PlrA are required for MmpL3's polar localization. In addition, the localization of PlrA and MmpL3 are responsive to nutrient and energy deprivation and inhibition of peptidoglycan metabolism. We show that inhibition of MmpL3 causes delocalized cell wall metabolism, but does not delocalize MmpL3 itself. We found that cells with an MmpL3 C-terminal truncation, which is defective for localization, have only minor defects in polar growth, but are impaired in their ability to downregulate cell wall metabolism under stress. Our work suggests that, in addition to its established function in TMM transport, MmpL3 has a second function in regulating global cell wall metabolism in response to stress. Our data are consistent with a model in which the presence of TMMs in the periplasm stimulates polar elongation, and in which the connection between Wag31, PlrA and the C-terminus of MmpL3 is involved in detecting and responding to stress in order to coordinate synthesis of the different layers of the mycobacterial cell wall in changing conditions.
PubMed: 38746181
DOI: 10.1101/2024.04.29.591792 -
Nature Communications May 2024Proteolysis-targeting chimeras (PROTACs) represent a new therapeutic modality involving selectively directing disease-causing proteins for degradation through...
Proteolysis-targeting chimeras (PROTACs) represent a new therapeutic modality involving selectively directing disease-causing proteins for degradation through proteolytic systems. Our ability to exploit targeted protein degradation (TPD) for antibiotic development remains nascent due to our limited understanding of which bacterial proteins are amenable to a TPD strategy. Here, we use a genetic system to model chemically-induced proximity and degradation to screen essential proteins in Mycobacterium smegmatis (Msm), a model for the human pathogen M. tuberculosis (Mtb). By integrating experimental screening of 72 protein candidates and machine learning, we find that drug-induced proximity to the bacterial ClpC1P1P2 proteolytic complex leads to the degradation of many endogenous proteins, especially those with disordered termini. Additionally, TPD of essential Msm proteins inhibits bacterial growth and potentiates the effects of existing antimicrobial compounds. Together, our results provide biological principles to select and evaluate attractive targets for future Mtb PROTAC development, as both standalone antibiotics and potentiators of existing antibiotic efficacy.
Topics: Proteolysis; Mycobacterium smegmatis; Bacterial Proteins; Anti-Bacterial Agents; Mycobacterium tuberculosis; Humans; Microbial Sensitivity Tests; Machine Learning
PubMed: 38744895
DOI: 10.1038/s41467-024-48506-8 -
Chembiochem : a European Journal of... May 2024Higher fungi of the genus Armillaria belonging to the phylum Basidiomycota produce bioactive sesquiterpenoid aryl esters called melleolides. A bioactivity-guided...
Higher fungi of the genus Armillaria belonging to the phylum Basidiomycota produce bioactive sesquiterpenoid aryl esters called melleolides. A bioactivity-guided discovery process led to the identification of the new melleolide 5'‑methoxyarmillane (1) in organic extracts from the mycelium of Armillaria ostoyae. Remarkably, supplementation of rapeseed oil to the culture medium potato dextrose broth increased the production of 1 by a factor of six during the course of the 35 days fermentation. Compound 1 was isolated and its structure elucidated by UHPLC-QTOF-HR-MS/MS and NMR spectroscopy. It showed toxicity against Madin-Darby canine kidney II (MDCK II, IC50 19.2 mg/mL, 44.1 mM) and human lung cancer Calu-3 cells (IC50 15.2 mg/mL, 34.9 mM) as well as moderate bioactivity against Mycobacterium tuberculosis (MIC 8 mg/mL, 18.4 mM) and Mycobacterium smegmatis (MIC 16 mg/mL, 36.8 mM), but not against Staphylococcus aureus, Escherichia coli, Candida albicans, and Septoria tritici. No inhibitory effects of 1 against the influenza viruses H3N2, H1N1pdm, B/Malaysia, and B/Massachusetts were observed.
PubMed: 38738599
DOI: 10.1002/cbic.202400168 -
Journal of Ethnopharmacology Sep 2024Popularly known as "penicilina" and "terramicina", Alternanthera brasiliana (L.) Kuntze belongs to the Amaranthaceae family and stands out for its ethnomedicinal uses in... (Review)
Review
ETHNOPHARMACOLOGICAL RELEVANCE
Popularly known as "penicilina" and "terramicina", Alternanthera brasiliana (L.) Kuntze belongs to the Amaranthaceae family and stands out for its ethnomedicinal uses in the treatment of infections caused by pathogenic microorganisms in some countries.
AIM OF THE STUDY
The present study aimed to carry out a literature review and analyze whether the scientific evidence really validates the numerous indications for the use of A. brasiliana in traditional medicine for the treatment of infectious diseases. Phytochemical and toxicological studies related to this species were also analyzed.
MATERIAL AND METHODS
Scientific documents were retrieved from Google Scholar, PubMed®, ScienceDirect®, SciELO, SpringerLink®, Scopus®, and Web of Science™ databases. The literature was reviewed from the first report on the antimicrobial activity of A. brasiliana in 1994 until April 2024.
RESULTS
According to the scientific documents analyzed, it was observed that A. brasiliana is widely used as a natural antibiotic for the treatment of infectious diseases in Brazil, mainly in the states of Rio Grande do Sul, Mato Grosso, and Minas Gerais. Its ethnomedicinal uses have also been reported in other countries such as Colombia and India. The leaves (78%) of A. brasiliana are the main parts used in the preparation of herbal medicines by traditional communities. Several A. brasiliana extracts showed low activity when evaluated against pathogens, including gram-positive bacteria, gram-negative bacteria, parasitic protozoa, and fungi. Only two studies reported that extracts from this plant showed high activity against the herpes simplex virus, Mycobacterium smegmatis, and Candida albicans. Phytochemicals belonging to the classes of phenolic compounds and flavonoid (52%), saturated and unsaturated fatty acids (33%), steroids and phytosterols (8%), terpenoids (5%), and fatty alcohol esters (2%) were identified in A. brasiliana. Toxicity (in vivo) and cytotoxicity (in vitro) studies of polar and non-polar extracts obtained from A. brasiliana leaves indicated that this plant is biologically safe.
CONCLUSION
Despite being widely used as a natural antibiotic by traditional communities, scientific investigations related to the antimicrobial potential of A. brasiliana extracts have indicated inactivity against several pathogens.
Topics: Humans; Medicine, Traditional; Phytochemicals; Amaranthaceae; Plant Extracts; Animals; Communicable Diseases; Ethnopharmacology; Anti-Bacterial Agents; Phytotherapy; Brazil
PubMed: 38723917
DOI: 10.1016/j.jep.2024.118304