1-Deoxy-d-Xylulose 5-Phosphate Reductoisomerase (IspC) from Mycobacterium tuberculosis: towards Understanding Mycobacterial Resistance to Fosmidomycin

ABSTRACT 1-Deoxy-d-xylulose 5-phosphate reductoisomerase (IspC) catalyzes the first committed step in the mevalonate-independent isopentenyl diphosphate biosynthetic pathway and is a potential drug target in some pathogenic bacteria. The antibiotic fosmidomycin has been shown to inhibit IspC in a number of organisms and is active against most gram-negative bacteria but not gram positives, including Mycobacterium tuberculosis, even though the mevalonate-independent pathway is the sole isopentenyl diphosphate biosynthetic pathway in this organism. Therefore, the enzymatic properties of recombinant IspC from M. tuberculosis were characterized. Rv2870c from M. tuberculosis converts 1-deoxy-d-xylulose 5-phosphate to 2-C-methyl-d-erythritol 4-phosphate in the presence of NADPH. The enzymatic activity is dependent on the presence of Mg2+ ions and exhibits optimal activity between pH 7.5 and 7.9; the Km for 1-deoxyxylulose 5-phosphate was calculated to be 47.1 μM, and the Km for NADPH was 29.7 μM. The specificity constant of Rv2780c in the forward direction is 1.5 × 106 M−1 min−1, and the reaction is inhibited by fosmidomycin, with a 50% inhibitory concentration of 310 nM. In addition, Rv2870c complements an inactivated chromosomal copy of IspC in Salmonella enterica, and the complemented strain is sensitive to fosmidomycin. Thus, M. tuberculosis resistance to fosmidomycin is not due to intrinsic properties of Rv2870c, and the enzyme appears to be a valid drug target in this pathogen.

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Antimicrobial and antibiofilm properties of essential oils from Piper marginatum Jacq.

Research Society and Development ◽

10.33448/rsd-v10i11.19967 ◽

2021 ◽

Vol 10 (11) ◽

pp. e514101119967

Author(s):

Ana Lúcia Mendes dos Santos ◽

Filipe Augusto Matos Araújo ◽

Érika da Silva Matisui ◽

Luiz Antonio Mendonça Alves da Costa ◽

Alexandre José Macêdo ◽

...

Keyword(s):

Essential Oils ◽

Biofilm Formation ◽

Pathogenic Bacteria ◽

Inhibitory Concentration ◽

Folk Medicine ◽

Gram Negative Bacteria ◽

Biofilm Inhibition ◽

Future Developments ◽

Phytochemical Constituents ◽

Amazonian Region

A low shrub growing in the Amazonian region, Piper marginatum Jacq. has been related to the treatment of a disease variety in folk medicine, however, still lacking scientific support. This study aimed to describe the composition of essential oils obtained from leaves (EOL) and branches (EOB) of P. marginatum and their antimicrobial effects on six relevant pathogenic bacteria. A combination of GC-FID and GC-MS was used to identify the phytochemical constituents. As antimicrobial assays, the oils were screened at the minimum inhibitory concentration (MIC) of 3 µg/ml for planktonic and biofilm inhibition. EOL revealed the presence of trans–nerolidol, o–cymene, spathulenol, elemicin, and α–copaene, while EOB composition was mainly of myristicin, trans-caryophyllene, trans-nerolidol, caryophyllene oxide, α–copaene, γ–muurolene and spathulenol. The strongest inhibition of planktonic growth was achieved against Pseudomonas aeruginosa (EOB) and Escherichia coli (EOB). Overall, Gram negative bacteria were more sensitive to both EOB/EOL showing less ability of growth and biofilm formation. The Gram-positive strains seemed to react to the essential oils by massive adhesion. Our results corroborate the relevance of Piperaceae and indicate the possible use of P. marginatum in future developments of antimicrobials.

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Antimicrobial Activity of Fractions and Compounds from Calophyllum brasiliense (Clusiaceae/Guttiferae)

Zeitschrift für Naturforschung C ◽

10.1515/znc-2004-9-1009 ◽

2004 ◽

Vol 59 (9-10) ◽

pp. 657-662 ◽

Cited By ~ 30

Author(s):

Juliana B. Pretto ◽

Valdir Cechinel-Filho ◽

Vânia F. Noldin ◽

Mara R. K. Sartori ◽

Daniela E. B Isaias ◽

...

Keyword(s):

Antimicrobial Activity ◽

Pathogenic Bacteria ◽

Protocatechuic Acid ◽

Inhibitory Concentration ◽

Gram Negative Bacteria ◽

Gram Positive ◽

Gram Positive Bacteria ◽

Methanolic Extracts ◽

Calophyllum Brasiliense

Abstract Calophyllum brasiliense (Clusiaceae/Guttiferae) is a native Brazilian medicinal plant traditionally used against several diseases, including infectious pathologies. Crude methanolic extracts (CME) and two fractions, denoted non-polar (soluble in chloroform) and polar (nonsoluble in chloroform), were prepared from different parts of the plant (roots, stems, leaves, flowers and fruits) and studied. The following compounds were isolated and tested against pathogenic bacteria and yeasts by determination of the minimal inhibitory concentration (MIC): brasiliensic acid (1), gallic acid (2), epicatechin (3), protocatechuic acid (4), friedelin (5) and 1,5-dihydroxyxanthone (6). The results indicated that all the parts of the plant exhibited antimicrobial activity against Gram-positive bacteria, which are selectively inhibited by components of C. brasiliense. No activity was observed against Gram-negative bacteria and yeasts tested. Regarding the isolated compounds, substance 4 showed antimicrobial activity against all the tested microorganisms, whereas compound 6 exhibited antimicrobial activity only against Gram-positive bacteria. The results from the current study confirm and justify the popular use of this plant to treat infectious processes.

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Discovery of a Natural Product That Binds to the Mycobacterium tuberculosis Protein Rv1466 Using Native Mass Spectrometry

Molecules ◽

10.3390/molecules25102384 ◽

2020 ◽

Vol 25 (10) ◽

pp. 2384

Author(s):

Ali R. Elnaas ◽

Darren Grice ◽

Jianying Han ◽

Yunjiang Feng ◽

Angela Di Capua ◽

...

Keyword(s):

Mass Spectrometry ◽

Mycobacterium Tuberculosis ◽

Drug Discovery ◽

Drug Target ◽

Inhibitory Concentration ◽

Native Mass Spectrometry ◽

Cellular Activity ◽

Future Drug ◽

Mycobacterial Protein

Elucidation of the mechanism of action of compounds with cellular bioactivity is important for progressing compounds into future drug development. In recent years, phenotype-based drug discovery has become the dominant approach to drug discovery over target-based drug discovery, which relies on the knowledge of a specific drug target of a disease. Still, when targeting an infectious disease via a high throughput phenotypic assay it is highly advantageous to identifying the compound’s cellular activity. A fraction derived from the plant Polyalthia sp. showed activity against Mycobacterium tuberculosis at 62.5 μge/μL. A known compound, altholactone, was identified from this fraction that showed activity towards M. tuberculosis at an minimum inhibitory concentration (MIC) of 64 μM. Retrospective analysis of a target-based screen against a TB proteome panel using native mass spectrometry established that the active fraction was bound to the mycobacterial protein Rv1466 with an estimated pseudo-Kd of 42.0 ± 6.1 µM. Our findings established Rv1466 as the potential molecular target of altholactone, which is responsible for the observed in vivo toxicity towards M. tuberculosis.

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Inhibiting Mycobacterium tuberculosis CoaBC by targeting an allosteric site

Nature Communications ◽

10.1038/s41467-020-20224-x ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Vitor Mendes ◽

Simon R. Green ◽

Joanna C. Evans ◽

Jeannine Hess ◽

Michal Blaszczyk ◽

...

Keyword(s):

Mycobacterium Tuberculosis ◽

Mycobacterium Smegmatis ◽

Drug Target ◽

Biosynthetic Pathway ◽

Model Organism ◽

Allosteric Site ◽

Cellular Processes ◽

Coa Thioesters ◽

Multiple Pathogens ◽

Substantial Interest

AbstractCoenzyme A (CoA) is a fundamental co-factor for all life, involved in numerous metabolic pathways and cellular processes, and its biosynthetic pathway has raised substantial interest as a drug target against multiple pathogens including Mycobacterium tuberculosis. The biosynthesis of CoA is performed in five steps, with the second and third steps being catalysed in the vast majority of prokaryotes, including M. tuberculosis, by a single bifunctional protein, CoaBC. Depletion of CoaBC was found to be bactericidal in M. tuberculosis. Here we report the first structure of a full-length CoaBC, from the model organism Mycobacterium smegmatis, describe how it is organised as a dodecamer and regulated by CoA thioesters. A high-throughput biochemical screen focusing on CoaB identified two inhibitors with different chemical scaffolds. Hit expansion led to the discovery of potent and selective inhibitors of M. tuberculosis CoaB, which we show to bind to a cryptic allosteric site within CoaB.

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Isoprenoid biosynthetic pathways as anti-infective drug targets

Biochemical Society Transactions ◽

10.1042/bst0330785 ◽

2005 ◽

Vol 33 (4) ◽

pp. 785-791 ◽

Cited By ~ 79

Author(s):

F. Rohdich ◽

A. Bacher ◽

W. Eisenreich

Keyword(s):

Helicobacter Pylori ◽

Plasmodium Falciparum ◽

Mycobacterium Tuberculosis ◽

Drug Targets ◽

Biosynthetic Pathway ◽

Mevalonate Pathway ◽

Biosynthetic Pathways ◽

Isopentenyl Diphosphate ◽

Human Pathogens ◽

Dimethylallyl Diphosphate

IPP (isopentenyl diphosphate) and DMAPP (dimethylallyl diphosphate) serve as the universal precursors for the biosynthesis of isoprenoids. Besides the well-known mevalonate pathway, the existence of a second biosynthetic pathway conducive to IPP and DMAPP formation through 1-deoxy-D-xylulose 5-phosphate and 2C-methyl-D-erythritol 4-phosphate was discovered approx. 10 years ago in plants and certain eubacteria. It is now known that this pathway is widely distributed in the bacterial kingdom including major human pathogens, such as Mycobacterium tuberculosis and Helicobacter pylori. The pathway is also essential in the malaria vector Plasmodium falciparum. During the last few years, the genes, enzymes, intermediates and mechanisms of the biosynthetic route have been elucidated by a combination of comparative genomics, enzymology, advanced NMR technology and crystallography. The results provide the basis for the development of novel anti-infective drugs.

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Utility of Muropeptide Ligase for Identification of Inhibitors of the Cell Wall Biosynthesis Enzyme MurF

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.50.1.230-236.2006 ◽

2006 ◽

Vol 50 (1) ◽

pp. 230-236 ◽

Cited By ~ 22

Author(s):

Ellen Z. Baum ◽

Steven M. Crespo-Carbone ◽

Darren Abbanat ◽

Barbara Foleno ◽

Amy Maden ◽

...

Keyword(s):

Cell Wall ◽

Drug Target ◽

High Performance ◽

Inhibitory Concentration ◽

Enzyme Inhibitors ◽

Binding Assay ◽

Substrate Inhibition ◽

Cell Wall Biosynthesis ◽

Gram Negative Bacteria ◽

Key Enzyme

ABSTRACT MurF is a key enzyme in the biosynthesis of the bacterial cell wall in both gram-positive and gram-negative bacteria. This enzyme has not been extensively exploited as a drug target, possibly due to the difficulty in obtaining one of the substrates, UDP-MurNAc-l-Ala-γ-d-Glu-meso-diaminopimelate, which is usually purified from bacteria. We have identified putative inhibitors of Escherichia coli MurF by a binding assay, thus bypassing the need for substrate. Inhibition of enzymatic activity was demonstrated in a high-performance liquid chromatography-based secondary assay with UDP-MurNAc-l-Ala-γ-d-Glu-diaminopimelate substrate prepared in a novel way by using muropeptide ligase enzyme to add UDP-MurNAc to synthetic l-Ala-γ-d-Glu-diaminopimelate; the substrate specificity of muropeptide ligase for peptides containing l-Lys in place of diaminopimelate was also investigated. Using the muropeptide ligase-generated MurF substrate, a thiazolylaminopyrimidine series of MurF enzyme inhibitors with 50% inhibitory concentration values as low as 2.5 μM was identified.

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Effect of leaves Extracts of Duranta repens on growth and activity of some types of Pathogenic Bacteria and Some types of Fungi

Baghdad Science Journal ◽

10.21123/bsj.6.1.29-42 ◽

2009 ◽

Vol 6 (1) ◽

pp. 29-42 ◽

Cited By ~ 1

Author(s):

Baghdad Science Journal

Keyword(s):

Pathogenic Bacteria ◽

Inhibitory Concentration ◽

Minimum Bactericidal Concentration ◽

Inhibition Zone ◽

Diameter Growth ◽

Gram Negative Bacteria ◽

Organic Extract ◽

Gram Negative ◽

Gram Positive Bacteria ◽

Mic Value

A study were conducted to examinate the effect of organic and aqueous (Hot, Cold) Extracts from leaves of Duranta repens on the growth and activities of the following types of Bacteria:- Staphylococcus aureus,Streptococcus pyogens ,Escherichia coli,Klebsilla pneumonia, in addition to the yeast Candida albicans and the fungi Aspergullis niger ,Aspergulls flavus.The result showed that gram Positive Bacteria is more sensitive to the extracts than gram negative bacteria with Minimum inhibitory concentration (MIC) value (50,25,50,100)% and Minimum Bactericidal Concentration (MBC) value (100,50,200,100)% for all types Bacteria respectively . The most active extract against A.niger ,A,flavus was cold and hot aqueous extract from the leaves with diameter growth of colony value of ( 0.93,0.37)cm for A.niger in 20 % concentration compared with organic extract (0.26)cm, and the inhibition zone value of cold and hot extract to A.flavus (0.90,0.80)cm respectively compared with organic extract (7.056)cm.

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Inhibiting Mycobacterium tuberculosis CoaBC by targeting a new allosteric site

10.1101/870154 ◽

2019 ◽

Author(s):

Vitor Mendes ◽

Simon R. Green ◽

Joanna C. Evans ◽

Jeannine Hess ◽

Michal Blaszczyk ◽

...

Keyword(s):

Mycobacterium Tuberculosis ◽

Mycobacterium Smegmatis ◽

Drug Target ◽

Biosynthetic Pathway ◽

Model Organism ◽

Allosteric Site ◽

Cellular Processes ◽

Coa Thioesters ◽

Multiple Pathogens ◽

Substantial Interest

AbstractCoenzyme A (CoA) is a fundamental co-factor for all life, involved in numerous metabolic pathways and cellular processes, and its biosynthetic pathway has raised substantial interest as a drug target against multiple pathogens including Mycobacterium tuberculosis. The biosynthesis of CoA is performed in five steps, with the second and third steps being catalysed in the vast majority of prokaryotes, including M. tuberculosis, by a single bifunctional protein, CoaBC. Depletion of CoaBC was found to be bactericidal in M. tuberculosis. Here we report the first structure of a full-length CoaBC, from the model organism Mycobacterium smegmatis, describe how it is organised as a dodecamer and regulated by CoA thioesters. A high-throughput biochemical screen focusing on CoaB identified two inhibitors with different chemical scaffolds. Hit expansion led to the discovery of potent inhibitors of M. tuberculosis CoaB, which we show to bind to a novel cryptic allosteric site within CoaB.

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Efektivitas Ekstrak Kloroform Caulerpa racemosa Dalam Menghambat Pertumbuhan Bakteri Patogen Penyebab Infeksi Saluran Pernapasan Akut (ISPA)

JURNAL BIOLOGI PAPUA ◽

10.31957/jbp.103 ◽

2018 ◽

Vol 9 (1) ◽

pp. 14-17

Author(s):

Sriyati Sampulawa ◽

Ali Awan ◽

Dominggus Rumahlatu

Keyword(s):

Antibacterial Activity ◽

Green Algae ◽

Respiratory Infection ◽

Acute Respiratory Infection ◽

Pathogenic Bacteria ◽

Inhibitory Concentration ◽

Extraction Process ◽

Gram Negative Bacteria ◽

Caulerpa Racemosa ◽

Antibacterial Compounds

Acute respiratory infection is a serious health problem in the world and in Indonesia. Acute respiratory infection is caused by a variant of the bacteria and resistance to antibiotics. The Latest researches on antibacterial compounds based on natural ingredients have been conducted. One of them is derived from green algae. This study aims to determine the antibacterial activity of green algae Caulerpa racemosa extract in inhibiting the growth of pathogenic bacteria causing acute respiratory infection. This study includes an extraction process using chloroform. Antibacterial testing was done by using a concentration of 0.5%, 1%, 5%, 10%, 20%, 40%, 60% and 80%, in order to obtain the minimal Inhibitory Concentration. The results showed that C. racemosa extract was able to inhibit the growth of test bacteria Streptococcus mitis, Bacillus anthrachis, and B. cereus, with the best activity at concentration of 0.5% and 80%. Meanwhile the extract did not have the activity to inhibit the Gram-negative bacteria. Phytochemical test showed that chloroform of C. racemosa extract contain steroids and terpenoids compounds capable of inhibiting the growth of testing bacteria. Key words: antibacterial activity, C. racemosa, pathogenic bacteria, Acute respiratory infection

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Crystal structures and kinetic analyses ofN-acetylmannosamine-6-phosphate 2-epimerases fromFusobacterium nucleatumandVibrio cholerae

Acta Crystallographica Section F Structural Biology Communications ◽

10.1107/s2053230x18008543 ◽

2018 ◽

Vol 74 (7) ◽

pp. 431-440 ◽

Cited By ~ 4

Author(s):

Lavanyaa Manjunath ◽

Sai Rohit Guntupalli ◽

Michael J. Currie ◽

Rachel A. North ◽

Renwick C. J. Dobson ◽

...

Keyword(s):

Sialic Acid ◽

Drug Target ◽

Pathogenic Bacteria ◽

Fusobacterium Nucleatum ◽

Sialic Acids ◽

Gram Negative Bacteria ◽

Catabolic Pathway ◽

Gram Negative ◽

Gram Positive Bacteria ◽

Tim Barrel

Sialic acids are nine-carbon sugars that are found abundantly on the cell surfaces of mammals as glycoprotein or glycolipid complexes. Several Gram-negative and Gram-positive bacteria have the ability to scavenge and catabolize sialic acids to use as a carbon source. This gives them an advantage in colonizing sialic acid-rich environments. The genes of the sialic acid catabolic pathway are generally present as the operonnanAKE. The third gene in the operon encodes the enzymeN-acetylmannosamine-6-phosphate 2-epimerase (NanE), which catalyzes the conversion ofN-acetylmannosamine 6-phosphate toN-acetylglucosamine 6-phosphate, thus committing it to enter glycolysis. The NanE enzyme belongs to the isomerase class of enzymes possessing the triose phosphate isomerase (TIM) barrel fold. Here, comparative structural and functional characterizations of the NanE epimerases from two pathogenic Gram-negative bacteria,Fusobacterium nucleatum(Fn) andVibrio cholerae(Vc), have been carried out. Structures of NanE from Vc (VcNanE) with and without ligand bound have been determined to 1.7 and 2.7 Å resolution, respectively. The structure of NanE from Fn (FnNanE) has been determined to 2.2 Å resolution. The enzymes show kinetic parameters that are consistent with those ofClostridium perfringensNanE. These studies allowed an evaluation of whether NanE may be a good drug target against these pathogenic bacteria.

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