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Screening and Molecular Docking of Novel Benzothiazole Derivatives as Potential Antimicrobial Agents. Antibiotics (Basel) 2020; 9:antibiotics9050221. [PMID: 32365587 PMCID: PMC7277330 DOI: 10.3390/antibiotics9050221] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/26/2020] [Accepted: 04/27/2020] [Indexed: 02/06/2023] Open
Abstract
The burden of antibiotic resistance necessitates a continued search for new antimicrobials. We evaluated the antimicrobial activities of novel benzothiazoles synthesized by our group. Antibacterial activity was evaluated in vitro in Staphylococcus aureus, Bacillus subtilis, and Escherichia coli, while the antifungal activity was tested in Candida albicans and Aspergillus niger, and expressed as the minimum inhibitory concentration (MIC; µg/mL). MIC values of benzothiazole compounds ranged from 25 to 200 µg/mL. Compounds 3 and 4 gave high antibacterial and moderate antifungal activities, while 10 and 12 showed moderate activity against all tested organisms. In addition, some benzothiazole compounds significantly suppressed the activity of Escherichia coli dihydroorotase and inhibited the dimorphic transition of Candida albicans. Moreover, the active benzothiazole compounds induced DNA and protein leakage in Aspergillus niger spores. Molecular interactions of benzothiazole derivatives with dihydroorotase revealed the formation of hydrogen bonds with the active site residues LEU222 or ASN44. Strong hydrophobic interactions of the bulky thiazole and naphthalene rings at the entrance to the active site might interfere with the access of substrates to their binding sites, which results in dihydroorotase inhibition. Thus, inhibition of dihydroorotase might contribute to the observed antimicrobial actions of these compounds.
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Chaudhary R, Balhara M, Jangir DK, Dangi M, Dangi M, Chhillar AK. In Silico Protein Interaction Network Analysis of Virulence Proteins Associated with Invasive Aspergillosis for Drug Discovery. Curr Top Med Chem 2019; 19:146-155. [PMID: 30465504 DOI: 10.2174/1568026619666181120150633] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Revised: 10/05/2018] [Accepted: 11/04/2018] [Indexed: 01/08/2023]
Abstract
BACKGROUND Protein-Protein interaction (PPI) network analysis of virulence proteins of Aspergillus fumigatus is a prevailing strategy to understand the mechanism behind the virulence of A. fumigatus. The identification of major hub proteins and targeting the hub protein as a new antifungal drug target will help in treating the invasive aspergillosis. MATERIALS & METHOD In the present study, the PPI network of 96 virulence (drug target) proteins of A. fumigatus were investigated which resulted in 103 nodes and 430 edges. Topological enrichment analysis of the PPI network was also carried out by using STRING database and Network analyzer a cytoscape plugin app. The key enriched KEGG pathway and protein domains were analyzed by STRING. CONCLUSION Manual curation of PPI data identified three proteins (PyrABCN-43, AroM-34, and Glt1- 34) of A. fumigatus possessing the highest interacting partners. Top 10% hub proteins were also identified from the network using cytohubba on the basis of seven algorithms, i.e. betweenness, radiality, closeness, degree, bottleneck, MCC and EPC. Homology model and the active pocket of top three hub proteins were also predicted.
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Affiliation(s)
- Renu Chaudhary
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak-124001, Haryana, India
| | - Meenakshi Balhara
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak-124001, Haryana, India
| | - Deepak Kumar Jangir
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak-124001, Haryana, India
| | - Mehak Dangi
- Centre for Bioinformatics, Maharshi Dayanand University, Rohtak-124001, Haryana, India
| | - Mrridula Dangi
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak-124001, Haryana, India
| | - Anil K Chhillar
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak-124001, Haryana, India
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Abstract
In bacteria, more than half of the genes in the genome are organized in operons. In contrast, in eukaryotes, functionally related genes are usually dispersed across the genome. There are, however, numerous examples of functional clusters of nonhomologous genes for metabolic pathways in fungi and plants. Despite superficial similarities with operons (physical clustering, coordinate regulation), these clusters have not usually originated by horizontal gene transfer from bacteria, and (unlike operons) the genes are typically transcribed separately rather than as a single polycistronic message. This clustering phenomenon raises intriguing questions about the origins of clustered metabolic pathways in eukaryotes and the significance of clustering for pathway function. Here we review metabolic gene clusters from fungi and plants, highlight commonalities and differences, and consider how these clusters form and are regulated. We also identify opportunities for future research in the areas of large-scale genomics, synthetic biology, and experimental evolution.
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Affiliation(s)
- Hans-Wilhelm Nützmann
- Department of Metabolic Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom; .,Current affiliation: Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom;
| | - Claudio Scazzocchio
- Department of Microbiology, Imperial College, London SW7 2AZ, United Kingdom; .,Institute for Integrative Biology of the Cell, 91190 Gif-sur-Yvette, France
| | - Anne Osbourn
- Department of Metabolic Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom;
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Villarino M, De Cal A, Melgarejo P, Larena I, Espeso EA. The development of genetic and molecular markers to register and commercialize Penicillium rubens (formerly Penicillium oxalicum) strain 212 as a biocontrol agent. Microb Biotechnol 2016; 9:89-99. [PMID: 26467970 PMCID: PMC4720407 DOI: 10.1111/1751-7915.12325] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 09/07/2015] [Accepted: 09/08/2015] [Indexed: 11/29/2022] Open
Abstract
Penicillium oxalicum strain 212 (PO212) is an effective biocontrol agent (BCA) against a large number of economically important fungal plant pathogens. For successful registration as a BCA in Europe, PO212 must be accurately identified. In this report, we describe the use of classical genetic and molecular markers to characterize and identify PO212 in order to understand its ecological role in the environment or host. We successfully generated pyrimidine (pyr-) auxotrophic mutants. In addition we also designed specific oligonucleotides for the pyrF gene at their untranslated regions for rapid and reliable identification and classification of strains of P. oxalicum and P. rubens, formerly P. chrysogenum. Using these DNA-based technologies, we found that PO212 is a strain of P. rubens, and is not a strain of P. oxalicum. This work presents PO212 as the unique P. rubens strain to be described as a BCA and the information contained here serves for its registration and commercialization in Europe.
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Affiliation(s)
- Maria Villarino
- SGIT-INIA, Departamento de Protección Vegetal, Madrid, Spain
- CIB-CSIC, Departamento de Biología Celular y Molecular, Madrid, Spain
| | | | | | | | - Eduardo A Espeso
- CIB-CSIC, Departamento de Biología Celular y Molecular, Madrid, Spain
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Barba M, Glansdorff N, Labedan B. Evolution of Cyclic Amidohydrolases: A Highly Diversified Superfamily. J Mol Evol 2013; 77:70-80. [DOI: 10.1007/s00239-013-9580-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 08/16/2013] [Indexed: 11/29/2022]
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Lee DH, Lim JA, Lee J, Roh E, Jung K, Choi M, Oh C, Ryu S, Yun J, Heu S. Characterization of genes required for the pathogenicity of Pectobacterium carotovorum subsp. carotovorum Pcc21 in Chinese cabbage. MICROBIOLOGY-SGM 2013; 159:1487-1496. [PMID: 23676432 PMCID: PMC3749726 DOI: 10.1099/mic.0.067280-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Pectobacterium carotovorum subsp. carotovorum is a well-known plant pathogen that causes severe soft rot disease in various crops, resulting in considerable economic loss. To identify pathogenicity-related factors, Chinese cabbage was inoculated with 5314 transposon mutants of P. carotovorum subsp. carotovorum Pcc21 derived using Tn5 transposon mutagenesis. A total of 35 reduced-virulence or avirulent mutants were isolated, and 14 loci were identified. The 14 loci could be functionally grouped into nutrient utilization (pyrD, purH, purD, leuA and serB), production of plant cell-wall-degrading enzymes (PCWDEs) (expI, expR and PCC21_023220), motility (flgA, fliA and flhB), biofilm formation (expI, expR and qseC), susceptibility to antibacterial plant chemicals (tolC) and unknown function (ECA2640). Among the 14 genes identified, qseC, tolC and PCC21_023220 are novel pathogenicity factors of P. carotovorum subsp. carotovorum involved in biofilm formation, phytochemical resistance and PCWDE production, respectively.
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Affiliation(s)
- Dong Hwan Lee
- Division of Microbial Safety, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Republic of Korea
| | - Jeong-A Lim
- Division of Microbial Safety, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Republic of Korea
| | - Juneok Lee
- Division of Microbial Safety, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Republic of Korea
| | - Eunjung Roh
- Division of Microbial Safety, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Republic of Korea
| | - Kyusuk Jung
- Division of Microbial Safety, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Republic of Korea
| | - Minseon Choi
- Department of Horticultural Biotechnology and Institute of Life Science & Resources, Kyung Hee University, Yongin 441-701, Republic of Korea
| | - Changsik Oh
- Department of Horticultural Biotechnology and Institute of Life Science & Resources, Kyung Hee University, Yongin 441-701, Republic of Korea
| | - Sangryeol Ryu
- Department of Agricultural Biotechnology, Center for Agricultural Biomaterials, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea
| | - Jongchul Yun
- Division of Microbial Safety, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Republic of Korea
| | - Sunggi Heu
- Division of Microbial Safety, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Republic of Korea
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Hamari Z, Amillis S, Drevet C, Apostolaki A, Vágvölgyi C, Diallinas G, Scazzocchio C. Convergent evolution and orphan genes in the Fur4p-like family and characterization of a general nucleoside transporter inAspergillus nidulans. Mol Microbiol 2009; 73:43-57. [DOI: 10.1111/j.1365-2958.2009.06738.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Kim GJ, Lee DE, Kim HS. Characterization and evaluation of a distinct fusion ability in the functionally related cyclic amidohydrolase family enzymes. BIOTECHNOL BIOPROC E 2002. [DOI: 10.1007/bf02932913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Kim GJ, Lee DE, Kim HS. High-level expression and one-step purification of cyclic amidohydrolase family enzymes. Protein Expr Purif 2001; 23:128-33. [PMID: 11570854 DOI: 10.1006/prep.2001.1484] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The cyclic amidohydrolase family enzymes, including hydantoinase, dihydropyrimidinase, allantoinase and dihydroorotase, are metal-dependent hydrolases and play a crucial role in the metabolism of purine and pyrimidine in prokaryotic and eukaryotic cells. With the increasing demand for the elucidation of enzyme structures and functions, along with industrial applications, the research on the family enzymes has recently been proliferating, but the related enzymes had been purified conventionally by multistep purification procedures. Here, we reported the expression in Escherichia coli cells of maltose-binding protein-fused family enzymes and their one-step purification. The expression levels of the fusion proteins account for 20-35% of the total protein in E. coli, allowing approximately 2-3 mg of the purified proteins by affinity chromatography to be obtained per 0.3 L of bacterial culture. As more promising results, their nascent biochemical properties, after the cleavage of the fusion proteins with Factor Xa, in terms of oligomeric structure, optimal pH, specific activity, and kinetic property, were also conserved as those from the native enzymes. The availability of the family enzymes to fusion strategy shows potential as a convenient procedure to recombinant protein purification and accelerates the structure-function study of the related family enzymes.
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Affiliation(s)
- G J Kim
- Department of Molecular Science and Technology, Ajou University, San5, Woncheon-dong, Paldal-gu, Suwon, 442-749, Korea
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Kim GJ, Lee DE, Kim HS. Functional expression and characterization of the two cyclic amidohydrolase enzymes, allantoinase and a novel phenylhydantoinase, from Escherichia coli. J Bacteriol 2000; 182:7021-8. [PMID: 11092864 PMCID: PMC94829 DOI: 10.1128/jb.182.24.7021-7028.2000] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A superfamily of cyclic amidohydrolases, including dihydropyrimidinase, allantoinase, hydantoinase, and dihydroorotase, all of which are involved in the metabolism of purine and pyrimidine rings, was recently proposed based on the rigidly conserved structural domains in identical positions of the related enzymes. With these conserved domains, two putative cyclic amidohydrolase genes from Escherichia coli, flanked by related genes, were identified and characterized. From the genome sequence of E. coli, the allB gene and a putative open reading frame, tentatively designated as a hyuA (for hydantoin-utilizing enzyme) gene, were predicted to express hydrolases. In contrast to allB, high-level expression of hyuA in E. coli of a single protein was unsuccessful even under various induction conditions. We expressed HyuA as a maltose binding protein fusion protein and AllB in its native form and then purified each of them by conventional procedures. allB was found to encode a tetrameric allantoinase (453 amino acids) which specifically hydrolyzes the purine metabolite allantoin to allantoic acid. Another open reading frame, hyuA, located near 64.4 min on the physical map and known as a UUG start, coded for D-stereospecific phenylhydantoinase (465 amino acids) which is a homotetramer. As a novel enzyme belonging to a cyclic amidohydrolase superfamily, E. coli phenylhydantoinase exhibited a distinct activity toward the hydantoin derivative with an aromatic side chain at the 5' position but did not readily hydrolyze the simple cyclic ureides. The deduced amino acid sequence of the novel phenylhydantoinase shared a significant homology (>45%) with those of allantoinase and dihydropyrimidinase, but its functional role still remains to be elucidated. Despite the unclear physiological function of HyuA, its presence, along with the allantoin-utilizing AllB, strongly suggested that the cyclic ureides might be utilized as nutrient sources in E. coli.
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Affiliation(s)
- G J Kim
- Department of Molecular Science and Technology, Ajou University, Suwon 442-749, Korea
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Aleksenko A, Liu W, Gojkovic Z, Nielsen J, Piskur J. Structural and transcriptional analysis of the pyrABCN, pyrD and pyrF genes in Aspergillus nidulans and the evolutionary origin of fungal dihydroorotases. Erratum. Mol Microbiol 2000. [DOI: 10.1046/j.1365-2958.2000.01903.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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