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Abd El-Haleem A, Ammar U, Masci D, El-Ansary S, Abdel Rahman D, Abou-Elazm F, El-Dydamony N. Discovery of Benzopyrone-Based Candidates as Potential Antimicrobial and Photochemotherapeutic Agents through Inhibition of DNA Gyrase Enzyme B: Design, Synthesis, In Vitro and In Silico Evaluation. Pharmaceuticals (Basel) 2024; 17:1197. [PMID: 39338359 PMCID: PMC11434840 DOI: 10.3390/ph17091197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 08/16/2024] [Accepted: 09/03/2024] [Indexed: 09/30/2024] Open
Abstract
Bacterial DNA gyrase is considered one of the validated targets for antibacterial drug discovery. Benzopyrones have been reported as promising derivatives that inhibit bacterial DNA gyrase B through competitive binding into the ATP binding site of the B subunit. In this study, we designed and synthesized twenty-two benzopyrone-based derivatives with different chemical features to assess their antimicrobial and photosensitizing activities. The antimicrobial activity was evaluated against B. subtilis, S. aureus, E. coli, and C. albicans. Compounds 6a and 6b (rigid tetracyclic-based derivatives), 7a-7f (flexible-linker containing benzopyrones), and 8a-8f (rigid tricyclic-based compounds) exhibited promising results against B. subtilis, S. aureus, and E. coli strains. Additionally, these compounds demonstrated photosensitizing activities against the B. subtilis strain. Both in silico molecular docking and in vitro DNA gyrase supercoiling inhibitory assays were performed to study their potential mechanisms of action. Compounds 8a-8f exhibited the most favorable binding interactions, engaging with key regions within the ATP binding site of the DNA gyrase B domain. Moreover, compound 8d displayed the most potent IC50 value (0.76 μM) compared to reference compounds (novobiocin = 0.41 μM and ciprofloxacin = 2.72 μM). These results establish a foundation for structure-based optimization targeting DNA gyrase inhibition with antibacterial activity.
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Affiliation(s)
- Akram Abd El-Haleem
- Pharmaceutical Chemistry Department, College of Pharmaceutical Sciences and Drug Manufacturing, Misr University for Science and Technology, Al-Motamayez District, 6th of October City P.O. Box 77, Egypt; (S.E.-A.); (N.E.-D.)
| | - Usama Ammar
- School of Applied Sciences, Edinburgh Napier University, Sighthill Campus, 9 Sighthill Court, Edinburgh EH11 4BN, UK
| | - Domiziana Masci
- Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Catholic University of the Sacred Heart, Largo Francesco Vito 1, 00168 Rome, Italy;
| | - Sohair El-Ansary
- Pharmaceutical Chemistry Department, College of Pharmaceutical Sciences and Drug Manufacturing, Misr University for Science and Technology, Al-Motamayez District, 6th of October City P.O. Box 77, Egypt; (S.E.-A.); (N.E.-D.)
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo 11562, Egypt
| | - Doaa Abdel Rahman
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo 11562, Egypt
| | - Fatma Abou-Elazm
- Department of Microbiology and Immunology, College of Pharmaceutical Sciences and Drug Manufacturing, Misr University for Science and Technology, Al-Motamayez District, 6th of October City P.O. Box 77, Egypt;
| | - Nehad El-Dydamony
- Pharmaceutical Chemistry Department, College of Pharmaceutical Sciences and Drug Manufacturing, Misr University for Science and Technology, Al-Motamayez District, 6th of October City P.O. Box 77, Egypt; (S.E.-A.); (N.E.-D.)
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Zhang X, Song Y, Zhang Z, Lu C, Shen Y. New bioactive secondary metabolites from the soil-derived Streptomyces sp. S045 and their anti-bacterial and anti-type III secretion system activities. Nat Prod Res 2024:1-7. [PMID: 38247396 DOI: 10.1080/14786419.2024.2306601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 01/11/2024] [Indexed: 01/23/2024]
Abstract
A total of seven compounds were isolated from the ISP3 agar cultures of a soil-derived Streptomyces sp. S045 strain. Their structures were determined based on 1D, 2D NMR spectroscopic data, HR ESI mass spectroscopy, X-ray diffraction analysis and comparison with the reported data. The new compounds were identified to be (S)-4-(1-hydroxyethyl)quinoline-2-carboxamide (1) and methyl 4-(hydroxymethyl)-2-(4-methylpentyl)-4,5-dihydrofuran-3-carboxylate (3), respectively. Their anti-bacterial and anti-type III secretion system (T3SS) activities were evaluated.
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Affiliation(s)
- Xiaochun Zhang
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yuliang Song
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Zhiqiang Zhang
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Chunhua Lu
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yuemao Shen
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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3
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Qandeel BM, Mowafy S, Abouzid K, Farag NA. Lead generation of UPPS inhibitors targeting MRSA: Using 3D-QSAR pharmacophore modeling, virtual screening, molecular docking, and molecular dynamic simulations. BMC Chem 2024; 18:14. [PMID: 38245752 PMCID: PMC10800075 DOI: 10.1186/s13065-023-01110-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 12/21/2023] [Indexed: 01/22/2024] Open
Abstract
Undecaprenyl Pyrophosphate Synthase (UPPS) is a vital target enzyme in the early stages of bacterial cell wall biosynthesis. UPPS inhibitors have antibacterial activity against resistant strains such as MRSA and VRE. In this study, we used several consecutive computer-based protocols to identify novel UPPS inhibitors. The 3D QSAR pharmacophore model generation (HypoGen algorithm) protocol was used to generate a valid predictive pharmacophore model using a set of UPPS inhibitors with known reported activity. The developed model consists of four pharmacophoric features: one hydrogen bond acceptor, two hydrophobic, and one aromatic ring. It had a correlation coefficient of 0.86 and a null cost difference of 191.39, reflecting its high predictive power. Hypo1 was proven to be statistically significant using Fischer's randomization at a 95% confidence level. The validated pharmacophore model was used for the virtual screening of several databases. The resulting hits were filtered using SMART and Lipinski filters. The hits were docked into the binding site of the UPPS protein, affording 70 hits with higher docking affinities than the reference compound (6TC, - 21.17 kcal/mol). The top five hits were selected through extensive docking analysis and visual inspection based on docking affinities, fit values, and key residue interactions with the UPPS receptor. Moreover, molecular dynamic simulations of the top hits were performed to confirm the stability of the protein-ligand complexes, yielding five promising novel UPPS inhibitors.
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Affiliation(s)
- Basma M Qandeel
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Misr International University, Km28 Cairo-Ismailia Road, Ahmed Orabi District, Cairo, Egypt.
| | - Samar Mowafy
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Misr International University, Km28 Cairo-Ismailia Road, Ahmed Orabi District, Cairo, Egypt
| | - Khaled Abouzid
- Department of Pharmaceutical Chemistry, College of Pharmacy, Ain-Shams University, Abbasia, 11566, Egypt
| | - Nahla A Farag
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Misr International University, Km28 Cairo-Ismailia Road, Ahmed Orabi District, Cairo, Egypt.
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Korona-Głowniak I, Nitek W, Tejchman W, Żesławska E. Influence of chlorine and methyl substituents and their position on the antimicrobial activities and crystal structures of 4-methyl-1,6-diphenylpyrimidine-2(1H)-selenone derivatives. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2021; 77:649-658. [PMID: 34607988 DOI: 10.1107/s205322962100975x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 09/19/2021] [Indexed: 11/10/2022]
Abstract
Derivatives of 4-methyl-1,6-diphenylpyrimidine-2(1H)-selenone show very strong antimicrobial activity. In order to extend the current knowledge about the features responsible for the biological activity, crystal structure analyses are presented for 4-methyl-1-(2-methylphenyl)-6-phenylpyrimidine-2(1H)-selenone (1), 4-methyl-1-(3-methylphenyl)-6-phenylpyrimidine-2(1H)-selenone (2), 4-methyl-1-(4-methylphenyl)-6-phenylpyrimidine-2(1H)-selenone (3) (all C18H16N2Se) and 1-(4-chlorophenyl)-4-methyl-6-phenylpyrimidine-2(1H)-selenone (4) (C17H13ClN2Se). Furthermore, the antibacterial and antifungal activities of these compounds were evaluated. All the presented derivatives crystallize in the space group P21/c with one molecule in the asymmetric unit. The molecular geometries differ slightly in the mutual orientation of the rings. The packing of molecules in the crystals is dominated by C-H...N and C-H...Se intermolecular interactions. Additionally, in the crystal structure of 4, C-H...Cl intermolecular interactions are observed. The introduction of a methyl or chlorine substituent improves the biological activity, while its position significantly affects biological activity only in case of the chlorine substituent.
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Affiliation(s)
- Izabela Korona-Głowniak
- Medical University of Lublin, Department of Pharmaceutical Microbiology, Chodźki 1, 20-093 Lublin, Poland
| | - Wojciech Nitek
- Jagiellonian University, Faculty of Chemistry, Gronostajowa 2, 30-387 Kraków, Poland
| | - Waldemar Tejchman
- Pedagogical University, Institute of Biology, Podchorążych 2, 30-084 Kraków, Poland
| | - Ewa Żesławska
- Pedagogical University, Institute of Biology, Podchorążych 2, 30-084 Kraków, Poland
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Das A, Das A, Banik BK. Influence of dipole moments on the medicinal activities of diverse organic compounds. J INDIAN CHEM SOC 2021. [DOI: 10.1016/j.jics.2021.100005] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Affiliation(s)
- Shovan Mondal
- Department of Chemistry, Syamsundar College, Shyamsundar, India
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Chakkyarath V, Shanmugam A, Natarajan J. Prioritization of potential drug targets and antigenic vaccine candidates against Klebsiella aerogenes using the computational subtractive proteome-driven approach. JOURNAL OF PROTEINS AND PROTEOMICS 2021; 12:201-211. [PMID: 34305354 PMCID: PMC8284688 DOI: 10.1007/s42485-021-00068-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 06/14/2021] [Accepted: 07/05/2021] [Indexed: 02/07/2023]
Abstract
Klebsiella aerogenes is a multidrug-resistant Gram-negative bacterium that causes nosocomial infections. The organism showed resistance to most of the conventional antibiotics available. Because of the high resistance of the species, the treatment of K. aerogenes is difficult. These species are resistant to third-generation cephalosporins due to the production of chromosomal beta-lactams with cephalosporin activity. The lack of better treatment and the development of therapeutic resistance in hospitals hinders better/new broad-spectrum-based treatment against this pathogen. This study identifies potential drug targets/vaccine candidates through a computational subtractive proteome-driven approach. This method is used to predict proteins that are not homologous to humans and human symbiotic intestinal flora. The resultant proteome of K. aerogenes was further searched for proteins, which are essential, virulent, and determinants of antibiotic/drug resistance. Subsequently, their druggability properties were also studied. The data set was reduced based on its presence in the pathogen-specific metabolic pathways. The subtractive proteome analysis predicted 13 proteins as potential drug targets for K. aerogenes. Furthermore, these target proteins were annotated based on their spectrum of activity, cellular localization, and antigenicity properties, which ensured that they are potent candidates for broad-spectrum antibiotic and vaccine design. The results open up new opportunities for designing and manufacturing powerful antigenic vaccines against K. aerogenes and the detection and release of new and active drugs against K. aerogenes without altering the gut microbiome. Supplementary Information The online version contains supplementary material available at 10.1007/s42485-021-00068-9.
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Affiliation(s)
- Vijina Chakkyarath
- grid.411677.20000 0000 8735 2850Data Mining and Text Mining Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, 641046 India
| | - Anusuya Shanmugam
- grid.444708.b0000 0004 1799 6895Department of Pharmaceutical Engineering, Vinayaka Mission’s Kirupananda Variyar Engineering College, Vinayaka Mission’s Research Foundation (Deemed to be University), Salem, Tamil Nadu 636308 India
| | - Jeyakumar Natarajan
- grid.411677.20000 0000 8735 2850Data Mining and Text Mining Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, 641046 India
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8
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Khulbe K, Karmakar K, Ghosh S, Chandra K, Chakravortty D, Mugesh G. Nanoceria-Based Phospholipase-Mimetic Cell Membrane Disruptive Antibiofilm Agents. ACS APPLIED BIO MATERIALS 2020; 3:4316-4328. [PMID: 35025431 DOI: 10.1021/acsabm.0c00363] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Kritika Khulbe
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Kapudeep Karmakar
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
- Regional Research Station, Terai Zone, Uttar Banga Krishi Viswavidyalaya-ICAR, Coochbehar 736165, West Bengal, India
| | - Sourav Ghosh
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Kasturi Chandra
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Dipshikha Chakravortty
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
- Center for Biosystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Govindasamy Mugesh
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
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9
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Methionine Limitation Impairs Pathogen Expansion and Biofilm Formation Capacity. Appl Environ Microbiol 2019; 85:AEM.00177-19. [PMID: 30824455 DOI: 10.1128/aem.00177-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 02/23/2019] [Indexed: 02/01/2023] Open
Abstract
Multidrug-resistant bacterial pathogens are becoming increasingly prevalent, and novel strategies to treat bacterial infections caused by these organisms are desperately needed. Bacterial central metabolism is crucial for catabolic processes and provides precursors for anabolic pathways, such as the biosynthesis of essential biomolecules like amino acids or vitamins. However, most essential pathways are not regarded as good targets for antibiotic therapy since their products might be acquired from the environment. This issue raises doubts about the essentiality of such targets during infection. A putative target in bacterial anabolism is the methionine biosynthesis pathway. In contrast to humans, almost all bacteria carry methionine biosynthesis pathways which have often been suggested as putative targets for novel anti-infectives. While the growth of methionine auxotrophic strains can be stimulated by exogenous methionine, the extracellular concentrations required by most bacterial species are unknown. Furthermore, several phenotypic characteristics of methionine auxotrophs are only partly reversed by exogenous methionine. We investigated methionine auxotrophic mutants of Staphylococcus aureus, Pseudomonas aeruginosa, and Escherichia coli (all differing in methionine biosynthesis enzymes) and found that each needed concentrations of exogenous methionine far exceeding that reported for human serum (∼30 µM). Accordingly, these methionine auxotrophs showed a reduced ability to proliferate in human serum. Additionally, S. aureus and P. aeruginosa methionine auxotrophs were significantly impaired in their ability to form and maintain biofilms. Altogether, our data show intrinsic defects of methionine auxotrophs. This result suggests that the pathway should be considered for further studies validating the therapeutic potential of inhibitors.IMPORTANCE New antibiotics that attack novel targets are needed to circumvent widespread resistance to conventional drugs. Bacterial anabolic pathways, such as the enzymes for biosynthesis of the essential amino acid methionine, have been proposed as potential targets. However, the eligibility of enzymes in these pathways as drug targets is unclear because metabolites might be acquired from the environment to overcome inhibition. We investigated the nutritional needs of methionine auxotrophs of the pathogens Staphylococcus aureus, Pseudomonas aeruginosa, and Escherichia coli We found that each auxotrophic strain retained a growth disadvantage at methionine concentrations mimicking those available in vivo and showed that biofilm biomass was strongly influenced by endogenous methionine biosynthesis. Our experiments suggest that inhibition of the methionine biosynthesis pathway has deleterious effects even in the presence of external methionine. Therefore, additional efforts to validate the effects of methionine biosynthesis inhibitors in vivo are warranted.
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Putta VPRK, Gujjarappa R, Tyagi U, Pujar PP, Malakar CC. A metal- and base-free domino protocol for the synthesis of 1,3-benzoselenazines, 1,3-benzothiazines and related scaffolds. Org Biomol Chem 2019; 17:2516-2528. [PMID: 30758005 DOI: 10.1039/c8ob03058h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Efficient protocols have been described for the synthesis of 1,3-benzoselenazines, 1,3-benzothiazines, 2-aryl thiazin-4-ones and diaryl[b,f][1,5]diazocine-6,12(5H,11H)-diones. These transformations were successfully driven towards the product formation under mild acid catalyzed reaction conditions at room temperature using 2-amino aryl/hetero-aryl alkyl alcohols and amides as substrates. The merits of the present methods also rely on the easy access of rarely explored bioactive scaffolds like 1,3-benzoselenazine derivatives, for which well-documented methods are rarely known in the literature. A broad range of substrates with both electron-rich and electron-deficient groups were well-tolerated under the developed conditions to furnish the desired products in yields up to 98%. The scope of the devised method is not only restricted to the synthesis of 1,3-benzoselenazines, but it was also further extended towards the synthesis of 1,3-benzothiazines, 1,3-benzothiazinones and the corresponding eight membered N-heterocycles such as diaryl[b,f][1,5]diazocine-6,12(5H,11H)-diones.
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12
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Žalubovskis R, Winum JY. Inhibitors of Selected Bacterial Metalloenzymes. Curr Med Chem 2018; 26:2690-2714. [PMID: 29611472 DOI: 10.2174/0929867325666180403154018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 03/14/2018] [Accepted: 03/19/2018] [Indexed: 12/26/2022]
Abstract
The utilization of bacterial metalloenzymes, especially ones not having mammalian (human) counterparts, has drawn attention to develop novel antibacterial agents to overcome drug resistance and especially multidrug resistance. In this review, we focus on the recent achievements on the development of inhibitors of bacterial enzymes peptide deformylase (PDF), metallo-β-lactamase (MBL), methionine aminopeptidase (MetAP) and UDP-3-O-acyl- N-acetylglucosamine deacetylase (LpxC). The state of the art of the design and investigation of inhibitors of bacterial metalloenzymes is presented, and challenges are outlined and discussed.
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Affiliation(s)
- Raivis Žalubovskis
- Latvian Institute of Organic Synthesis, Riga, Latvia.,Institute of Technology of Organic Chemistry, Faculty of Materials Science and Applied Chemistry, Riga Technical University, Latvia
| | - Jean-Yves Winum
- Institut des Biomolecules Max Mousseron, Universite de Montpellier, France
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Keri RS, Pandule SS, Budagumpi S, Nagaraja BM. Quinoxaline and quinoxaline-1,4-di-N
-oxides: An emerging class of antimycobacterials. Arch Pharm (Weinheim) 2018; 351:e1700325. [DOI: 10.1002/ardp.201700325] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 02/27/2018] [Accepted: 03/06/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Rangappa S. Keri
- Centre for Nano and Material Sciences, Jain University; Jain Global Campus; Bangalore India
| | | | - Srinivasa Budagumpi
- Centre for Nano and Material Sciences, Jain University; Jain Global Campus; Bangalore India
| | - Bhari M. Nagaraja
- Centre for Nano and Material Sciences, Jain University; Jain Global Campus; Bangalore India
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Abstract
Antibiotics have saved millions of lives over the past decades. However, the accumulation of so many antibiotic resistance genes by some clinically relevant pathogens has begun to lead to untreatable infections worldwide. The current antibiotic resistance crisis will require greater efforts by governments and the scientific community to increase the research and development of new antibacterial drugs with new mechanisms of action. A major challenge is the identification of novel microbial targets, essential for in vivo growth or pathogenicity, whose inhibitors can overcome the currently circulating resistome of human pathogens. In this article, we focus on the potential high value of bacterial transcriptional regulators as targets for the development of new antibiotics, discussing in depth the molecular role of these regulatory proteins in bacterial physiology and pathogenesis. Recent advances in the search for novel compounds that inhibit the biological activity of relevant transcriptional regulators in pathogenic bacteria are reviewed.
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15
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Mandewale MC, Patil UC, Shedge SV, Dappadwad UR, Yamgar RS. A review on quinoline hydrazone derivatives as a new class of potent antitubercular and anticancer agents. BENI-SUEF UNIVERSITY JOURNAL OF BASIC AND APPLIED SCIENCES 2017. [DOI: 10.1016/j.bjbas.2017.07.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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16
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Antifungal toxicity of linear geranylphenol. Influence of oxigenate substituents. Food Chem Toxicol 2017; 109:827-835. [DOI: 10.1016/j.fct.2017.05.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 05/12/2017] [Accepted: 05/13/2017] [Indexed: 01/06/2023]
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17
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van Teeseling MCF, de Pedro MA, Cava F. Determinants of Bacterial Morphology: From Fundamentals to Possibilities for Antimicrobial Targeting. Front Microbiol 2017; 8:1264. [PMID: 28740487 PMCID: PMC5502672 DOI: 10.3389/fmicb.2017.01264] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 06/23/2017] [Indexed: 12/11/2022] Open
Abstract
Bacterial morphology is extremely diverse. Specific shapes are the consequence of adaptive pressures optimizing bacterial fitness. Shape affects critical biological functions, including nutrient acquisition, motility, dispersion, stress resistance and interactions with other organisms. Although the characteristic shape of a bacterial species remains unchanged for vast numbers of generations, periodical variations occur throughout the cell (division) and life cycles, and these variations can be influenced by environmental conditions. Bacterial morphology is ultimately dictated by the net-like peptidoglycan (PG) sacculus. The species-specific shape of the PG sacculus at any time in the cell cycle is the product of multiple determinants. Some morphological determinants act as a cytoskeleton to guide biosynthetic complexes spatiotemporally, whereas others modify the PG sacculus after biosynthesis. Accumulating evidence supports critical roles of morphogenetic processes in bacteria-host interactions, including pathogenesis. Here, we review the molecular determinants underlying morphology, discuss the evidence linking bacterial morphology to niche adaptation and pathogenesis, and examine the potential of morphological determinants as antimicrobial targets.
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Affiliation(s)
- Muriel C F van Teeseling
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå UniversityUmeå, Sweden
| | - Miguel A de Pedro
- Centro de Biología Molecular "Severo Ochoa" - Consejo Superior de Investigaciones Científicas, Universidad Autónoma de MadridMadrid, Spain
| | - Felipe Cava
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå UniversityUmeå, Sweden
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18
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Shukla R, Shukla H, Sonkar A, Pandey T, Tripathi T. Structure-based screening and molecular dynamics simulations offer novel natural compounds as potential inhibitors of Mycobacterium tuberculosis isocitrate lyase. J Biomol Struct Dyn 2017; 36:2045-2057. [DOI: 10.1080/07391102.2017.1341337] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Rohit Shukla
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Harish Shukla
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Amit Sonkar
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Tripti Pandey
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Timir Tripathi
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
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Staegemann MH, Gitter B, Dernedde J, Kuehne C, Haag R, Wiehe A. Mannose-Functionalized Hyperbranched Polyglycerol Loaded with Zinc Porphyrin: Investigation of the Multivalency Effect in Antibacterial Photodynamic Therapy. Chemistry 2017; 23:3918-3930. [PMID: 28029199 DOI: 10.1002/chem.201605236] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Indexed: 02/03/2023]
Abstract
The antibacterial photodynamic activity of hyperbranched polyglycerol (hPG) loaded with zinc porphyrin photosensitizers and mannose units was investigated. hPG, with a MW of 19.5 kDa, was functionalized with about 15 molecules of the photosensitizer {5,10,15-tris(3-hydroxyphenyl)-20-[4-(prop-2-yn-1-ylamino)tetrafluorophenyl]porphyrinato}-zinc(II) by using copper(I)-catalyzed 1,3-dipolar cycloaddition (CuAAC). These nanoparticle conjugates were functionalized systematically with increasing loadings of mannose in the range of approximately 20 to 110 groups. With higher mannose loadings (ca. 58-110 groups) the water-insoluble zinc porphyrin photosensitizer could thus be transferred into a water-soluble form. Targeting of the conjugates was proven in binding studies to the mannose-specific lectin concanavalin A (Con A) by using surface plasmon resonance (SPR). The antibacterial phototoxicity of the conjugates on Staphylococcus aureus (as a typical Gram-positive germ) was investigated in phosphate-buffered saline (PBS). It was shown that conjugates with approximately 70-110 mannose units exhibit significant antibacterial activity, whereas conjugates with approximately 20-60 units did not induce bacterial killing at all. These results give an insight into the multivalency effect in combination with photodynamic therapy (PDT). On addition of serum to the bacterial cultures, a quenching of this antibacterial phototoxicity was observed. In fluorescence studies with the conjugates in the presence of increasing bovine serum albumin (BSA) concentrations, protein-conjugate associations could be identified as a plausible cause for this quenching.
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Affiliation(s)
- Michael H Staegemann
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustr. 3, 14195, Berlin, Germany
| | - Burkhard Gitter
- Biolitec research GmbH, Otto-Schott-Str. 15, 07745, Jena, Germany
| | - Jens Dernedde
- Charité-Universitätsmedizin Berlin, Institut für Laboratoriumsmedizin, Klinische Chemie und Pathobiochemie, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Christian Kuehne
- Charité-Universitätsmedizin Berlin, Institut für Laboratoriumsmedizin, Klinische Chemie und Pathobiochemie, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Rainer Haag
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustr. 3, 14195, Berlin, Germany
| | - Arno Wiehe
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustr. 3, 14195, Berlin, Germany.,Biolitec research GmbH, Otto-Schott-Str. 15, 07745, Jena, Germany
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20
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Debnath M, Sasmal S, Haldar D. Fabrication of egg shell-like nanovesicles from a thiocoumarin-based ε-amino ester: a potential carrier. J Mater Chem B 2017; 5:5450-5457. [DOI: 10.1039/c7tb00025a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A thiocoumarin-based ε-amino ester has been designed and synthesized and used to fabricate egg shell-like nanovesicles for sustained release of sulfamethoxazole antibiotic.
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Affiliation(s)
- Mintu Debnath
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Kolkata
- Mohanpur
- India
| | - Supriya Sasmal
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Kolkata
- Mohanpur
- India
| | - Debasish Haldar
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Kolkata
- Mohanpur
- India
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21
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Competitive Growth Enhances Conditional Growth Mutant Sensitivity to Antibiotics and Exposes a Two-Component System as an Emerging Antibacterial Target in Burkholderia cenocepacia. Antimicrob Agents Chemother 2016; 61:AAC.00790-16. [PMID: 27799222 DOI: 10.1128/aac.00790-16] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 10/26/2016] [Indexed: 01/08/2023] Open
Abstract
Chemogenetic approaches to profile an antibiotic mode of action are based on detecting differential sensitivities of engineered bacterial strains in which the antibacterial target (usually encoded by an essential gene) or an associated process is regulated. We previously developed an essential-gene knockdown mutant library in the multidrug-resistant Burkholderia cenocepacia by transposon delivery of a rhamnose-inducible promoter. In this work, we used Illumina sequencing of multiplex-PCR-amplified transposon junctions to track individual mutants during pooled growth in the presence of antibiotics. We found that competition from nontarget mutants magnified the hypersensitivity of a clone underexpressing gyrB to novobiocin by 8-fold compared with hypersensitivity measured during clonal growth. Additional profiling of various antibiotics against a pilot library representing most categories of essential genes revealed a two-component system with unknown function, which, upon depletion of the response regulator, sensitized B. cenocepacia to novobiocin, ciprofloxacin, tetracycline, chloramphenicol, kanamycin, meropenem, and carbonyl cyanide 3-chlorophenylhydrazone, but not to colistin, hydrogen peroxide, and dimethyl sulfoxide. We named the gene cluster esaSR for enhanced sensitivity to antibiotics sensor and response regulator. Mutational analysis and efflux activity assays revealed that while esaS is not essential and is involved in antibiotic-induced efflux, esaR is an essential gene and regulates efflux independently of antibiotic-mediated induction. Furthermore, microscopic analysis of cells stained with propidium iodide provided evidence that depletion of EsaR has a profound effect on the integrity of cell membranes. In summary, we unraveled a previously uncharacterized two-component system that can be targeted to reduce antibiotic resistance in B. cenocepacia.
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22
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Linker-switch approach towards new ATP binding site inhibitors of DNA gyrase B. Eur J Med Chem 2016; 125:500-514. [PMID: 27689732 DOI: 10.1016/j.ejmech.2016.09.040] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 08/18/2016] [Accepted: 09/13/2016] [Indexed: 12/30/2022]
Abstract
Due to increasing emergence of bacterial resistance, compounds with new mechanisms of action are of paramount importance. One of modestly researched therapeutic targets in the field of antibacterial discovery is DNA gyrase B. In the present work we synthesized a focused library of potential DNA gyrase B inhibitors composed of two key pharmacophoric moieties linked by three types of sp3-rich linkers to obtain three structural classes of compounds. Using molecular docking, molecular dynamics and analysis of conserved waters in the binding site, we identified a favourable binding mode for piperidin-4-yl and 4-cyclohexyl pyrrole-2-carboxamides while predicting unfavourable interactions with the active site for piperazine pyrrole-2-carboxamides. Biological evaluation of prepared compounds on isolated enzyme DNA gyrase B confirmed our predictions and afforded multiple moderately potent inhibitors of DNA gyrase B. Namely trans-4-(4,5-dibromo-1H-pyrrole-2-carboxamide)cyclohexyl)glycine and 4-(4-(3,4-dichloro-5-methyl-1H-pyrrole-2-carboxamido)piperidin-1-yl)-4-oxobutanoic acid with an IC50 value of 16 and 0.5 μM respectively.
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23
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Czarny TL, Brown ED. A Small-Molecule Screening Platform for the Discovery of Inhibitors of Undecaprenyl Diphosphate Synthase. ACS Infect Dis 2016; 2:489-99. [PMID: 27626101 DOI: 10.1021/acsinfecdis.6b00044] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The bacterial cell wall has long been a celebrated target for antibacterial drug discovery due to its critical nature in bacteria and absence in mammalian systems. At the heart of the cell wall biosynthetic pathway lies undecaprenyl phosphate (Und-P), the lipid-linked carrier upon which the bacterial cell wall is built. This study exploits recent insights into the link between late-stage wall teichoic acid inhibition and Und-P production, in Gram-positive organisms, to develop a cell-based small-molecule screening platform that enriches for inhibitors of undecaprenyl diphosphate synthase (UppS). Screening a chemical collection of 142,000 small molecules resulted in the identification of 6 new inhibitors of UppS. To date, inhibitors of UppS have generally shown off-target effects on membrane potential due to their physical-chemical characteristics. We demonstrate that MAC-0547630, one of the six inhibitors identified, exhibits selective, nanomolar inhibition against UppS without off-target effects on membrane potential. Such characteristics make it a unique chemical probe for exploring the inhibition of UppS in bacterial cell systems.
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Affiliation(s)
- Tomasz L. Czarny
- Department
of Biochemistry and Biomedical Sciences and ‡Michael G. DeGroote Institute of
Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Eric D. Brown
- Department
of Biochemistry and Biomedical Sciences and ‡Michael G. DeGroote Institute of
Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
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24
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Hoagland DT, Liu J, Lee RB, Lee RE. New agents for the treatment of drug-resistant Mycobacterium tuberculosis. Adv Drug Deliv Rev 2016; 102:55-72. [PMID: 27151308 PMCID: PMC4903924 DOI: 10.1016/j.addr.2016.04.026] [Citation(s) in RCA: 230] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 04/20/2016] [Accepted: 04/22/2016] [Indexed: 02/06/2023]
Abstract
Inadequate dosing and incomplete treatment regimens, coupled with the ability of the tuberculosis bacilli to cause latent infections that are tolerant of currently used drugs, have fueled the rise of multidrug-resistant tuberculosis (MDR-TB). Treatment of MDR-TB infections is a major clinical challenge that has few viable or effective solutions; therefore patients face a poor prognosis and years of treatment. This review focuses on emerging drug classes that have the potential for treating MDR-TB and highlights their particular strengths as leads including their mode of action, in vivo efficacy, and key medicinal chemistry properties. Examples include the newly approved drugs bedaquiline and delaminid, and other agents in clinical and late preclinical development pipeline for the treatment of MDR-TB. Herein, we discuss the challenges to developing drugs to treat tuberculosis and how the field has adapted to these difficulties, with an emphasis on drug discovery approaches that might produce more effective agents and treatment regimens.
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Affiliation(s)
- Daniel T Hoagland
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Pharmaceutical Sciences Graduate Program, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Jiuyu Liu
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Robin B Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Richard E Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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25
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Bai H, Lv F, Liu L, Wang S. Supramolecular Antibiotic Switches: A Potential Strategy for Combating Drug Resistance. Chemistry 2016; 22:11114-21. [DOI: 10.1002/chem.201600877] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Haotian Bai
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Organic Solids; Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 P. R. China
| | - Fengting Lv
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Organic Solids; Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 P. R. China
| | - Libing Liu
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Organic Solids; Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 P. R. China
| | - Shu Wang
- Beijing National Laboratory for Molecular Sciences; Key Laboratory of Organic Solids; Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 P. R. China
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26
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Acosta P, Insuasty B, Ortiz A, Abonia R, Sortino M, Zacchino SA, Quiroga J. Solvent-free microwave-assisted synthesis of novel pyrazolo[4′,3′:5,6]pyrido[2,3-d]pyrimidines with potential antifungal activity. ARAB J CHEM 2016. [DOI: 10.1016/j.arabjc.2015.03.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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27
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Qiao Y, Huang Y, Feng F, Chen ZG. Efficient enzymatic synthesis and antibacterial activity of andrographolide glycoside. Process Biochem 2016. [DOI: 10.1016/j.procbio.2016.02.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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28
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Brown ED, Wright GD. Antibacterial drug discovery in the resistance era. Nature 2016; 529:336-43. [PMID: 26791724 DOI: 10.1038/nature17042] [Citation(s) in RCA: 1373] [Impact Index Per Article: 171.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 11/16/2015] [Indexed: 01/07/2023]
Abstract
The looming antibiotic-resistance crisis has penetrated the consciousness of clinicians, researchers, policymakers, politicians and the public at large. The evolution and widespread distribution of antibiotic-resistance elements in bacterial pathogens has made diseases that were once easily treatable deadly again. Unfortunately, accompanying the rise in global resistance is a failure in antibacterial drug discovery. Lessons from the history of antibiotic discovery and fresh understanding of antibiotic action and the cell biology of microorganisms have the potential to deliver twenty-first century medicines that are able to control infection in the resistance era.
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Affiliation(s)
- Eric D Brown
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8S 4L8, Canada.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4L8, Canada
| | - Gerard D Wright
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8S 4L8, Canada.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4L8, Canada
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29
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Dastan D, Salehi P, Aliahmadi A, Gohari AR, Maroofi H, Ardalan A. New coumarin derivatives from Ferula pseudalliacea with antibacterial activity. Nat Prod Res 2016; 30:2747-2753. [DOI: 10.1080/14786419.2016.1149705] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Dara Dastan
- Department of Pharmacognosy and Pharmaceutical Biotechnology, School of Pharmacy, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Peyman Salehi
- Department of Phytochemistry, Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, G. C., Evin, Tehran, Iran
| | - Atousa Aliahmadi
- Department of Biology, Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, G. C., Evin, Tehran, Iran
| | - Ahmad Reza Gohari
- Faculty of Pharmacy, Medicinal Plants Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Hossein Maroofi
- Research Center of Agriculture and Natural Resources, Sanandaj, Iran
| | - Afshan Ardalan
- Department of Phytochemistry, Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, G. C., Evin, Tehran, Iran
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30
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Liu X, Lei Z, Liu D, Wang Z. Development of a sandwiched microarray platform for studying the interactions of antibiotics with Staphylococcus aureus. Anal Chim Acta 2016; 917:93-100. [PMID: 27026605 DOI: 10.1016/j.aca.2016.02.038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 02/25/2016] [Accepted: 02/27/2016] [Indexed: 11/18/2022]
Abstract
It still confronts an outstanding challenge to screen efficient antibacterial drugs from millions of potential antibiotic candidates. In this regard, a sandwiched microarray platform has been developed to culture live bacteria and carry out high-throughput screening antibacterial drugs. The optimized lectin-hydrogel microarray can be used as an efficient bacterial capturing and culturing platform, which is beneficial to identify spots and collect data. At the same time, a matching drug-laden polyacrylamide microarray with Luria-Bertani (LB) culture medium can be generated automatically and accurately by using a standard non-contacting procedure. A large number of microscale culture chambers (more than 100 individual samples) between two microarrays can be formed by linking two aligned hydrogel spots using LB culture medium, where live bacteria can be co-cultured with drug candidates. Using Staphylococcus aureus (S. aureus) and four well-known antibiotics (amoxicillin, vancomycin, streptomycin and chloramphenicol) as model system, the MIC (minimum inhibitory concentration) values of the antibiotics can be determined by the drug induced change of bacterial growth, and the results demonstrate that the MIC values of amoxicillin, vancomycin and streptomycin are 1.7 μg mL(-1), 3.3 μg mL(-1) and 10.3 μg mL(-1), respectively.
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Affiliation(s)
- Xia Liu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun 130022, PR China
| | - Zhen Lei
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun 130022, PR China; University of Chinese Academy of Sciences, Beijing 100039, PR China
| | - Dianjun Liu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun 130022, PR China
| | - Zhenxin Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun 130022, PR China.
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31
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Yang H, Liu X, Li Q, Li L, Zhang JR, Tang Y. Total synthesis and preliminary SAR study of (±)-merochlorins A and B. Org Biomol Chem 2016; 14:198-205. [DOI: 10.1039/c5ob01946j] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A modular synthesis of merochlorins A and B, two naturally occurring antibiotics, has been achieved from the readily available building blocks in a highly concise manner.
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Affiliation(s)
- Hongzhi Yang
- The Comprehensive AIDS Research Center
- and Department of Pharmacology & Pharmaceutical Sciences
- School of Medicine
- Tsinghua University
- Beijing 100084
| | - Xue Liu
- Department of Basic Medical Sciences
- School of Medicine
- Tsinghua University
- Beijing 100084
- China
| | - Qingong Li
- The Comprehensive AIDS Research Center
- and Department of Pharmacology & Pharmaceutical Sciences
- School of Medicine
- Tsinghua University
- Beijing 100084
| | - Longbo Li
- The Comprehensive AIDS Research Center
- and Department of Pharmacology & Pharmaceutical Sciences
- School of Medicine
- Tsinghua University
- Beijing 100084
| | - Jing-Ren Zhang
- Department of Basic Medical Sciences
- School of Medicine
- Tsinghua University
- Beijing 100084
- China
| | - Yefeng Tang
- The Comprehensive AIDS Research Center
- and Department of Pharmacology & Pharmaceutical Sciences
- School of Medicine
- Tsinghua University
- Beijing 100084
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32
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Pramanik A, Paikar A, Das T, Maji K, Haldar D. Self-assembled peptide microspheres for sustainable release of sulfamethoxazole. RSC Adv 2016. [DOI: 10.1039/c6ra07095g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Porous peptide microspheres have been used for the loading and sustained release of the bacteriostatic antibiotic sulfamethoxazole.
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Affiliation(s)
- Apurba Pramanik
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Kolkata
- Mohanpur
- India
| | - Arpita Paikar
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Kolkata
- Mohanpur
- India
| | - Tanmay Das
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Kolkata
- Mohanpur
- India
| | - Krishnendu Maji
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Kolkata
- Mohanpur
- India
| | - Debasish Haldar
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Kolkata
- Mohanpur
- India
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33
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Acosta P, Butassi E, Insuasty B, Ortiz A, Abonia R, Zacchino SA, Quiroga J. Microwave-Assisted Synthesis of Novel Pyrazolo[3,4-g][1,8]naphthyridin-5-amine with Potential Antifungal and Antitumor Activity. Molecules 2015; 20:8499-520. [PMID: 25985354 PMCID: PMC6273193 DOI: 10.3390/molecules20058499] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 05/05/2015] [Accepted: 05/06/2015] [Indexed: 12/26/2022] Open
Abstract
The microwave assisted reaction between heterocyclic o-aminonitriles 1 and cyclic ketones 2 catalyzed by zinc chloride led to new series of pyrazolo[3,4-b][1,8]naphthyridin-5-amines 3 in good yields. This procedure provides several advantages such as being environmentally friendly, high yields, simple work-up procedure, broad scope of applicability and the protocol provides an alternative for the synthesis of pyrazolonaphthyridines. The whole series showed antifungal activities against Candida albicans and Cryptococcus neoformans standardized strains, being compounds with a 4-p-tolyl substituent of the naphthyridin scheleton (3a, 3d and 3g), the most active ones mainly against C. albicans, which appear to be related to their comparative hydrophobicity. Among them, 3d, containing a cyclohexyl fused ring, showed the best activity. The anti-Candida activity was corroborated by testing the three most active compounds against clinical isolates of albicans and non-albicans Candida strains. These compounds were also screened by the US National Cancer Institute (NCI) for their ability to inhibit 60 different human tumor cell lines. Compounds 3a and 3e showed remarkable antitumor activity against cancer cell lines, with the most important GI50 values ranging from 0.62 to 2.18 μM.
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Affiliation(s)
- Paola Acosta
- Heterocyclic Compounds Research Group, Department of Chemistry, Universidad del Valle, A.A. 25360 Cali, Colombia.
| | - Estefanía Butassi
- Farmacognosia, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, CP 2000 Rosario, Argentina.
| | - Braulio Insuasty
- Heterocyclic Compounds Research Group, Department of Chemistry, Universidad del Valle, A.A. 25360 Cali, Colombia.
| | - Alejandro Ortiz
- Heterocyclic Compounds Research Group, Department of Chemistry, Universidad del Valle, A.A. 25360 Cali, Colombia.
| | - Rodrigo Abonia
- Heterocyclic Compounds Research Group, Department of Chemistry, Universidad del Valle, A.A. 25360 Cali, Colombia.
| | - Susana A Zacchino
- Farmacognosia, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, CP 2000 Rosario, Argentina.
| | - Jairo Quiroga
- Heterocyclic Compounds Research Group, Department of Chemistry, Universidad del Valle, A.A. 25360 Cali, Colombia.
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34
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Perdih A, Hrast M, Pureber K, Barreteau H, Grdadolnik SG, Kocjan D, Gobec S, Solmajer T, Wolber G. Furan-based benzene mono- and dicarboxylic acid derivatives as multiple inhibitors of the bacterial Mur ligases (MurC-MurF): experimental and computational characterization. J Comput Aided Mol Des 2015; 29:541-60. [PMID: 25851408 DOI: 10.1007/s10822-015-9843-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 03/28/2015] [Indexed: 01/05/2023]
Abstract
Bacterial resistance to the available antibiotic agents underlines an urgent need for the discovery of novel antibacterial agents. Members of the bacterial Mur ligase family MurC-MurF involved in the intracellular stages of the bacterial peptidoglycan biosynthesis have recently emerged as a collection of attractive targets for novel antibacterial drug design. In this study, we have first extended the knowledge of the class of furan-based benzene-1,3-dicarboxylic acid derivatives by first showing a multiple MurC-MurF ligase inhibition for representatives of the extended series of this class. Steady-state kinetics studies on the MurD enzyme were performed for compound 1, suggesting a competitive inhibition with respect to ATP. To the best of our knowledge, compound 1 represents the first ATP-competitive MurD inhibitor reported to date with concurrent multiple inhibition of all four Mur ligases (MurC-MurF). Subsequent molecular dynamic (MD) simulations coupled with interaction energy calculations were performed for two alternative in silico models of compound 1 in the UMA/D-Glu- and ATP-binding sites of MurD, identifying binding in the ATP-binding site as energetically more favorable in comparison to the UMA/D-Glu-binding site, which was in agreement with steady-state kinetic data. In the final stage, based on the obtained MD data novel furan-based benzene monocarboxylic acid derivatives 8-11, exhibiting multiple Mur ligase (MurC-MurF) inhibition with predominantly superior ligase inhibition over the original series, were discovered and for compound 10 it was shown to possess promising antibacterial activity against S. aureus. These compounds represent novel leads that could by further optimization pave the way to novel antibacterial agents.
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Affiliation(s)
- Andrej Perdih
- National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia,
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35
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Keri RS, Patil SA, Budagumpi S, Nagaraja BM. Triazole: A Promising Antitubercular Agent. Chem Biol Drug Des 2015; 86:410-23. [PMID: 25643871 DOI: 10.1111/cbdd.12527] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 12/19/2014] [Accepted: 01/06/2015] [Indexed: 01/04/2023]
Abstract
Tuberculosis is a contagious disease with comparatively high mortality worldwide. The statistics shows that around three million people throughout the world die annually from tuberculosis and there are around eight million new cases each year, of which developing countries showed major share. Therefore, the discovery and development of effective antituberculosis drugs with novel mechanism of action have become an insistent task for infectious diseases research programs. The literature reveals that, heterocyclic moieties have drawn attention of the chemists, pharmacologists, microbiologists, and other researchers owing to its indomitable biological potential as anti-infective agents. Among heterocyclic compounds, triazole (1,2,3-triazole/1,2,4-triazole) nucleus is one of the most important and well-known heterocycles, which is a common and integral feature of a variety of natural products and medicinal agents. Triazole core is considered as a privileged structure in medicinal chemistry and is widely used as 'parental' compounds to synthesize molecules with medical benefits, especially with infection-related activities. In the present review, we have collated published reports on this versatile core to provide an insight so that its complete therapeutic potential can be utilized for the treatment of tuberculosis. This review also explores triazole as a potential targeted core moiety against tuberculosis and various research ongoing worldwide. It is hoped that this review will be helpful for new thoughts in the quest for rational designs of more active and less toxic triazole-based antituberculosis drugs.
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Affiliation(s)
- Rangappa S Keri
- Centre for Nano and Material Sciences, Jain University, Jain Global Campus, Bangalore, Karnataka, 562112, India
| | - Siddappa A Patil
- Centre for Nano and Material Sciences, Jain University, Jain Global Campus, Bangalore, Karnataka, 562112, India
| | - Srinivasa Budagumpi
- Centre for Nano and Material Sciences, Jain University, Jain Global Campus, Bangalore, Karnataka, 562112, India
| | - Bhari Mallanna Nagaraja
- Centre for Nano and Material Sciences, Jain University, Jain Global Campus, Bangalore, Karnataka, 562112, India
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36
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Xu ZX, Tan YX, Fu HR, Liu J, Zhang J. Homochiral Metal–Organic Frameworks with Enantiopure Proline Units for the Catalytic Synthesis of β-Lactams. Inorg Chem 2014; 53:12199-204. [DOI: 10.1021/ic501849g] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Zhong-Xuan Xu
- State
Key Laboratory of Structural Chemistry, Fujian Institute of Research
on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, People’s Republic of China
- Department
of Chemistry, Zunyi Normal College, Zunyi, 563002, People’s Republic of China
| | - Yan-Xi Tan
- State
Key Laboratory of Structural Chemistry, Fujian Institute of Research
on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, People’s Republic of China
| | - Hong-Ru Fu
- State
Key Laboratory of Structural Chemistry, Fujian Institute of Research
on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, People’s Republic of China
| | - Juan Liu
- State
Key Laboratory of Structural Chemistry, Fujian Institute of Research
on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, People’s Republic of China
| | - Jian Zhang
- State
Key Laboratory of Structural Chemistry, Fujian Institute of Research
on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, People’s Republic of China
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37
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Borrero NV, Bai F, Perez C, Duong BQ, Rocca JR, Jin S, Huigens RW. Phenazine antibiotic inspired discovery of potent bromophenazine antibacterial agents against Staphylococcus aureus and Staphylococcus epidermidis. Org Biomol Chem 2014; 12:881-6. [PMID: 24389824 DOI: 10.1039/c3ob42416b] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nearly all clinically used antibiotics have been (1) discovered from microorganisms (2) using phenotype screens to identify inhibitors of bacterial growth. The effectiveness of these antibiotics is attributed to their endogenous roles as bacterial warfare agents against competing microorganisms. Unfortunately, every class of clinically used antibiotic has been met with drug resistant bacteria. In fact, the emergence of resistant bacterial infections coupled to the dismal pipeline of new antibacterial agents has resulted in a global health care crisis. There is an urgent need for innovative antibacterial strategies and treatment options to effectively combat drug resistant bacterial pathogens. Here, we describe the implementation of a Pseudomonas competition strategy, using redox-active phenazines, to identify novel antibacterial leads against Staphylococcus aureus and Staphylococcus epidermidis. In this report, we describe the chemical synthesis and evaluation of a diverse 27-membered phenazine library. Using this microbial warfare inspired approach, we have identified several bromophenazines with potent antibacterial activities against S. aureus and S. epidermidis. The most potent bromophenazine analogue from this focused library demonstrated a minimum inhibitory concentration (MIC) of 0.78-1.56 μM, or 0.31-0.62 μg mL(-1), against S. aureus and S. epidermidis and proved to be 32- to 64-fold more potent than the phenazine antibiotic pyocyanin in head-to-head MIC experiments. In addition to the discovery of potent antibacterial agents against S. aureus and S. epidermidis, we also report a detailed structure-activity relationship for this class of bromophenazine small molecules.
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Keri RS, Patil SA. Quinoline: A promising antitubercular target. Biomed Pharmacother 2014; 68:1161-75. [DOI: 10.1016/j.biopha.2014.10.007] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Accepted: 10/16/2014] [Indexed: 10/24/2022] Open
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Brahmachari S, Mandal SK, Das PK. Fabrication of SWCNT-Ag nanoparticle hybrid included self-assemblies for antibacterial applications. PLoS One 2014; 9:e106775. [PMID: 25191756 PMCID: PMC4159779 DOI: 10.1371/journal.pone.0106775] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 08/03/2014] [Indexed: 01/08/2023] Open
Abstract
The present article reports the development of soft nanohybrids comprising of single walled carbon nanotube (SWCNT) included silver nanoparticles (AgNPs) having superior antibacterial property. In this regard aqueous dispersing agent of carbon nanotube (CNT) containing a silver ion reducing unit was synthesised by the inclusion of tryptophan and tyrosine within the backbone of the amphiphile. The dispersions were characterized spectroscopically and microscopically using TEM, AFM and Raman spectroscopy. The nanotube-nanoparticle conjugates were prepared by the in situ photoreduction of AgNO3. The phenolate residue and the indole moieties of tyrosine and tryptophan, respectively reduces the sliver ion as well as acts as stabilizing agents for the synthesized AgNPs. The nanohybrids were characterized using TEM and AFM. The antibacterial activity of the nanohybrids was studied against Gram-positive (Bacillus subtilis and Micrococcus luteus) and Gram-negative bacteria (Escherichia coli and Klebsiella aerogenes). The SWCNT dispersions showed moderate killing ability (40-60%) against Gram-positive bacteria however no antibacterial activity was observed against the Gram negative ones. Interestingly, the developed SWCNT-amphiphile-AgNP nanohybrids exhibited significant killing ability (∼90%) against all bacteria. Importantly, the cell viability of these newly developed self-assemblies was checked towards chinese hamster ovarian cells and high cell viability was observed after 24 h of incubation. This specific killing of bacterial cells may have been achieved due to the presence of higher -SH containing proteins in the cell walls of the bacteria. The developed nanohybrids were subsequently infused into tissue engineering scaffold agar-gelatin films and the films similarly showed bactericidal activity towards both kinds of bacterial strains while allowing normal growth of eukaryotic cells on the surface of the films.
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Affiliation(s)
- Sayanti Brahmachari
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Kolkata, India
| | - Subhra Kanti Mandal
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Kolkata, India
| | - Prasanta Kumar Das
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Kolkata, India
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Kouidmi I, Levesque RC, Paradis-Bleau C. The biology of Mur ligases as an antibacterial target. Mol Microbiol 2014; 94:242-53. [DOI: 10.1111/mmi.12758] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/14/2014] [Indexed: 01/19/2023]
Affiliation(s)
- Imène Kouidmi
- Department of Microbiology, Infectiology and Immunology; Université de Montreal; Montreal Quebec Canada
| | - Roger C. Levesque
- Institut de biologie intégrative et des systèmes; Université Laval; Montreal Quebec Canada
| | - Catherine Paradis-Bleau
- Department of Microbiology, Infectiology and Immunology; Université de Montreal; Montreal Quebec Canada
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41
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Wong SSW, Samaranayake LP, Seneviratne CJ. In pursuit of the ideal antifungal agent for Candida infections: high-throughput screening of small molecules. Drug Discov Today 2014; 19:1721-1730. [PMID: 24952336 DOI: 10.1016/j.drudis.2014.06.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 05/23/2014] [Accepted: 06/12/2014] [Indexed: 01/22/2023]
Abstract
Candida infections have created a great burden on the public healthcare sector. The situation is worsened by recent epidemiological changes. Furthermore, the current arsenal of antifungal agents is limited and associated with undesirable drawbacks. Therefore, new antifungal agents that surpass the existing ones are urgently needed. High-throughput screening of small molecule libraries enables rapid hit identification and, possibly, increases hit rate. Moreover, the identified hits could be associated with unrecognized or multiple drug targets, which would provide novel insights into the biological processes of the pathogen. Hence, it is proposed that high-throughput screening of small molecules is particularly important in the pursuit of the ideal antifungal agents for Candida infections.
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Affiliation(s)
- Sarah S W Wong
- Faculty of Dentistry, University of Hong Kong, Hong Kong
| | | | - Chaminda J Seneviratne
- Faculty of Dentistry, University of Hong Kong, Hong Kong; Oral Sciences, Faculty of Dentistry, National University of Singapore, Singapore.
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Perdih A, Hrast M, Barreteau H, Gobec S, Wolber G, Solmajer T. Benzene-1,3-dicarboxylic acid 2,5-dimethylpyrrole derivatives as multiple inhibitors of bacterial Mur ligases (MurC-MurF). Bioorg Med Chem 2014; 22:4124-34. [PMID: 24953950 DOI: 10.1016/j.bmc.2014.05.058] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 05/23/2014] [Indexed: 12/24/2022]
Abstract
Enzymes catalyzing the biosynthesis of bacterial peptidoglycan represent traditionally a collection of highly selective targets for novel antibacterial drug design. Four members of the bacterial Mur ligase family-MurC, MurD, MurE and MurF-are involved in the intracellular steps of peptidoglycan biosynthesis, catalyzing the synthesis of the peptide moiety of the Park's nucleotide. In our previous virtual screening campaign, a chemical class of benzene-1,3-dicarboxylic acid 2,5-dimethylpyrrole derivatives exhibiting dual MurD/MurE inhibition properties was discovered. In the present study we further investigated this class of compounds by performing inhibition assays on all four Mur ligases (MurC-MurF). Furthermore, molecular dynamics (MD) simulation studies of one of the initially discovered compound 1 were performed to explore its geometry as well as its energetic behavior based on the Linear Interaction Energy (LIE) method. Further in silico virtual screening (VS) experiments based on the parent active compound 1 were conducted to optimize the discovered series. Selected hits were assayed against all Escherichia coli MurC-MurF enzymes in biochemical inhibition assays and molecules 10-14 containing benzene-1,3-dicarboxylic acid 2,5-dimethylpyrrole coupled with five member-ring rhodanine moiety were found to be multiple inhibitors of the whole MurC-MurF cascade of bacterial enzymes in the micromolar range. Steady-state kinetics studies suggested this class to act as competitive inhibitors of the MurD enzyme towards d-Glu. These compounds represent novel valuable starting point in the development of novel antibacterial agents.
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Affiliation(s)
- Andrej Perdih
- National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia; Institute of Pharmacy, Freie Universität Berlin, Königin Luise-Strasse 2+4, 14195 Berlin, Germany.
| | - Martina Hrast
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1001 Ljubljana, Slovenia
| | - Hélène Barreteau
- Enveloppes Bactériennes et Antibiotiques, IBBMC, UMR 8619 CNRS, Univ Paris-Sud, 91405 Orsay, France
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1001 Ljubljana, Slovenia
| | - Gerhard Wolber
- Institute of Pharmacy, Freie Universität Berlin, Königin Luise-Strasse 2+4, 14195 Berlin, Germany
| | - Tom Solmajer
- National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
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Perdih A, Hrast M, Barreteau H, Gobec S, Wolber G, Solmajer T. Inhibitor design strategy based on an enzyme structural flexibility: a case of bacterial MurD ligase. J Chem Inf Model 2014; 54:1451-66. [PMID: 24724969 DOI: 10.1021/ci500104m] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Increasing bacterial resistance to available antibiotics stimulated the discovery of novel efficacious antibacterial agents. The biosynthesis of the bacterial peptidoglycan, where the MurD enzyme is involved in the intracellular phase of the UDP-MurNAc-pentapeptide formation, represents a collection of highly selective targets for novel antibacterial drug design. In our previous computational studies, the C-terminal domain motion of the MurD ligase was investigated using Targeted Molecular Dynamic (TMD) simulation and the Off-Path Simulation (OPS) technique. In this study, we present a drug design strategy using multiple protein structures for the identification of novel MurD ligase inhibitors. Our main focus was the ATP-binding site of the MurD enzyme. In the first stage, three MurD protein conformations were selected based on the obtained OPS/TMD data as the initial criterion. Subsequently, a two-stage virtual screening approach was utilized combining derived structure-based pharmacophores with molecular docking calculations. Selected compounds were then assayed in the established enzyme binding assays, and compound 3 from the aminothiazole class was discovered to act as a dual MurC/MurD inhibitor in the micomolar range. A steady-state kinetic study was performed on the MurD enzyme to provide further information about the mechanistic aspects of its inhibition. In the final stage, all used conformations of the MurD enzyme with compound 3 were simulated in classical molecular dynamics (MD) simulations providing atomistic insights of the experimental results. Overall, the study depicts several challenges that need to be addressed when trying to hit a flexible moving target such as the presently studied bacterial MurD enzyme and show the possibilities of how computational tools can be proficiently used at all stages of the drug discovery process.
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Affiliation(s)
- Andrej Perdih
- National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
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Discovery of novel cell wall-active compounds using P ywaC, a sensitive reporter of cell wall stress, in the model gram-positive bacterium Bacillus subtilis. Antimicrob Agents Chemother 2014; 58:3261-9. [PMID: 24687489 DOI: 10.1128/aac.02352-14] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The emergence of antibiotic resistance in recent years has radically reduced the clinical efficacy of many antibacterial treatments and now poses a significant threat to public health. One of the earliest studied well-validated targets for antimicrobial discovery is the bacterial cell wall. The essential nature of this pathway, its conservation among bacterial pathogens, and its absence in human biology have made cell wall synthesis an attractive pathway for new antibiotic drug discovery. Herein, we describe a highly sensitive screening methodology for identifying chemical agents that perturb cell wall synthesis, using the model of the Gram-positive bacterium Bacillus subtilis. We report on a cell-based pilot screen of 26,000 small molecules to look for cell wall-active chemicals in real time using an autonomous luminescence gene cluster driven by the promoter of ywaC, which encodes a guanosine tetra(penta)phosphate synthetase that is expressed under cell wall stress. The promoter-reporter system was generally much more sensitive than growth inhibition testing and responded almost exclusively to cell wall-active antibiotics. Follow-up testing of the compounds from the pilot screen with secondary assays to verify the mechanism of action led to the discovery of 9 novel cell wall-active compounds.
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In vitro and in vivo anti-Helicobacter pylori activities of FEMY-R7 composed of fucoidan and evening primrose extract. Lab Anim Res 2014; 30:28-34. [PMID: 24707302 PMCID: PMC3973808 DOI: 10.5625/lar.2014.30.1.28] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 02/25/2014] [Accepted: 03/01/2014] [Indexed: 01/14/2023] Open
Abstract
Effects of FEMY-R7, composed of fucoidan and evening primrose extract, on the bacterial growth and intragastric infection of Helicobacter pylori as well as gastric secretion were investigated in comparison with a proton-pump inhibitor pantoprazole. For in vitro anti-bacterial activity test, H. pylori (1×10(8) CFU/mL) was incubated with a serially-diluted FEMY-R7 for 3 days. As a result, FEMY-R7 fully inhibited the bacterial growth at 100 µg/mL, which was determined to be a minimal inhibitory concentration. In addition, 6-hour incubation with H. pylori, FEMY-R7 inhibited urease activity in a concentration-dependent manner, showing a median inhibitory concentration of 1,500 µg/mL. In vivo elimination study, male C57BL/6 mice were infected with the bacteria by intragastric inoculation (5×10(9) CFU/mouse) 3 times at 2-day intervals, and simultaneously, orally treated twice a day with 10, 30 or 100 mg/kg FEMY-R7 for 7 days. In Campylobcter-like organism-detection test and bacterial identification, FEMY-R7 exerted a high bacteria-eliminating capacity at 30-100 mg/kg, comparably to 30 mg/kg pantoprazole. In contrast to a strong antacid activity of pantoprazole in a pylorus-ligation study, FEMY-R7 did not significantly affect gastric pH, free HCl, and total acidity, although it significantly decreased fluid volume at a low dose (10 mg/kg). The results indicate that FEMY-R7 eliminate H. pylori from gastric mucosa by directly killing the bacteria and preventing their adhesion and invasion, rather than by inhibiting gastric secretion or mucosal damage.
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Abstract
The increasing emergence of antimicrobial multiresistant bacteria is of great concern to public health. While these bacteria are becoming an ever more prominent cause of nosocomial and community-acquired infections worldwide, the antibiotic discovery pipeline has been stalled in the last few years with very few efforts in the research and development of novel antibacterial therapies. Some of the root causes that have hampered current antibiotic drug development are the lack of understanding of the mode of action (MOA) of novel antibiotic molecules and the poor characterization of the bacterial physiological response to antibiotics that ultimately causes resistance. Here, we review how bacterial genetic tools can be applied at the genomic level with the goal of profiling resistance to antibiotics and elucidating antibiotic MOAs. Specifically, we highlight how chemical genomic detection of the MOA of novel antibiotic molecules and antibiotic profiling by next-generation sequencing are leveraging basic antibiotic research to unprecedented levels with great opportunities for knowledge translation.
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Affiliation(s)
- Silvia T Cardona
- a Department of Microbiology , University of Manitoba , Winnipeg , Canada and.,b Department of Medical Microbiology & Infectious Disease , University of Manitoba , Winnipeg , Canada
| | - Carrie Selin
- a Department of Microbiology , University of Manitoba , Winnipeg , Canada and
| | - April S Gislason
- a Department of Microbiology , University of Manitoba , Winnipeg , Canada and
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Kakuchi R. Metal-Catalyzed Multicomponent Reactions for the Synthesis of Polymers. MULTI-COMPONENT AND SEQUENTIAL REACTIONS IN POLYMER SYNTHESIS 2014. [DOI: 10.1007/12_2014_300] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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48
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Zhao J, Zhao C, Liang G, Zhang M, Zheng J. Engineering antimicrobial peptides with improved antimicrobial and hemolytic activities. J Chem Inf Model 2013; 53:3280-96. [PMID: 24279498 DOI: 10.1021/ci400477e] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The rapid rise of antibiotic resistance in pathogens becomes a serious and growing threat to medicine and public health. Naturally occurring antimicrobial peptides (AMPs) are an important line of defense in the immune system against invading bacteria and microbial infection. In this work, we present a combined computational and experimental study of the biological activity and membrane interaction of the computationally designed Bac2A-based peptide library. We used the MARTINI coarse-grained molecular dynamics with adaptive biasing force method and the umbrella sampling technique to investigate the translocation of a total of 91 peptides with different amino acid substitutions through a mixed anionic POPE/POPG (3:1) bilayer and a neutral POPC bilayer, which mimic the bacterial inner membrane and the human red blood cell (hRBC) membrane, respectively. Potential of mean force (PMF, free energy profile) was obtained to measure the free energy barrier required to transfer the peptides from the bulk water phase to the water-membrane interface and to the bilayer interior. Different PMF profiles can indeed identify different membrane insertion scenarios by mapping out peptide-lipid energy landscapes, which are correlated with antimicrobial activity and hemolytic activity. Computationally designed peptides were further tested experimentally for their antimicrobial and hemolytic activities using bacteria growth inhibition assay and hemolysis assay. Comparison of PMF data with cell assay results reveals a good correlation of the peptides between predictive transmembrane activity and antimicrobial/hemolytic activity. Moreover, the most active mutants with the balanced substitutions of positively charged Arg and hydrophobic Trp residues at specific positions were discovered to achieve the improved antimicrobial activity while minimizing red blood cell lysis. Such substitutions provide more effective and cooperative interactions to distinguish the peptide interaction with different lipid bilayers. This work provides a useful computational tool to better understand the mechanism and energetics of membrane insertion of AMPs and to rationally design more effective AMPs.
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Affiliation(s)
- Jun Zhao
- Department of Chemical and Biomolecular Engineering, The University of Akron , Akron, Ohio 44325, United States
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Vosloo JA, Stander MA, Leussa ANN, Spathelf BM, Rautenbach M. Manipulation of the tyrothricin production profile of Bacillus aneurinolyticus. Microbiology (Reading) 2013; 159:2200-2211. [DOI: 10.1099/mic.0.068734-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Johan Arnold Vosloo
- BIOPEP Peptide Group, Department of Biochemistry, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Marietjie A. Stander
- Department of Biochemistry and LCMS-Central Analytical Facility, Science Faculty, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Adrienne N.-N. Leussa
- BIOPEP Peptide Group, Department of Biochemistry, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | | | - Marina Rautenbach
- BIOPEP Peptide Group, Department of Biochemistry, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
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50
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Khangarot RK, Kaliappan KP. Kinugasa Reaction: A Direct One-Pot Route to Highly Functionalized β-Lactams. European J Org Chem 2013. [DOI: 10.1002/ejoc.201300597] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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