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De Luca V, Giovannuzzi S, Capasso C, Supuran CT. Cloning, expression, and purification of an α-carbonic anhydrase from Toxoplasma gondii to unveil its kinetic parameters and anion inhibition profile. J Enzyme Inhib Med Chem 2024; 39:2346523. [PMID: 38847581 PMCID: PMC11163988 DOI: 10.1080/14756366.2024.2346523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 04/17/2024] [Indexed: 06/12/2024] Open
Abstract
Toxoplasmosis, induced by the intracellular parasite Toxoplasma gondii, holds considerable implications for global health. While treatment options primarily focusing on folate pathway enzymes have notable limitations, current research endeavours concentrate on pinpointing specific metabolic pathways vital for parasite survival. Carbonic anhydrases (CAs, EC 4.2.1.1) have emerged as potential drug targets due to their role in fundamental reactions critical for various protozoan metabolic processes. Within T. gondii, the Carbonic Anhydrase-Related Protein (TgCA_RP) plays a pivotal role in rhoptry biogenesis. Notably, α-CA (TcCA) from another protozoan, Trypanosoma cruzi, exhibited considerable susceptibility to classical CA inhibitors (CAIs) such as anions, sulphonamides, thiols, and hydroxamates. Here, the recombinant DNA technology was employed to synthesise and clone the identified gene in the T. gondii genome, which encodes an α-CA protein (Tg_CA), with the purpose of heterologously overexpressing its corresponding protein. Tg_CA kinetic constants were determined, and its inhibition patterns explored with inorganic metal-complexing compounds, which are relevant for rational compound design. The significance of this study lies in the potential development of innovative therapeutic strategies that disrupt the vital metabolic pathways crucial for T. gondii survival and virulence. This research may lead to the development of targeted treatments, offering new approaches to manage toxoplasmosis.
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Affiliation(s)
- Viviana De Luca
- Department of Biology, Agriculture and Food Sciences, National Research Council (CNR), Institute of Biosciences and Bioresources, Naples, Italy
| | - Simone Giovannuzzi
- Neurofarba Department, Pharmaceutical and Nutraceutical Section, University of Florence, Sesto Fiorentino, Italy
| | - Clemente Capasso
- Department of Biology, Agriculture and Food Sciences, National Research Council (CNR), Institute of Biosciences and Bioresources, Naples, Italy
| | - Claudiu T. Supuran
- Neurofarba Department, Pharmaceutical and Nutraceutical Section, University of Florence, Sesto Fiorentino, Italy
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2
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Bahadır S, Abdulla MF, Mostafa K, Kavas M, Hacıkamiloğlu S, Kurt O, Yıldırım K. Exploring the role of FAT genes in Solanaceae species through genome-wide analysis and genome editing. THE PLANT GENOME 2024:e20506. [PMID: 39253757 DOI: 10.1002/tpg2.20506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 07/08/2024] [Accepted: 08/04/2024] [Indexed: 09/11/2024]
Abstract
Plants produce numerous fatty acid derivatives, and some of these compounds have significant regulatory functions, such as governing effector-induced resistance, systemic resistance, and other defense pathways. This study systematically identified and characterized eight FAT genes (Acyl-acyl carrier protein thioesterases), four in the Solanum lycopersicum and four in the Solanum tuberosum genome. Phylogenetic analysis classified these genes into four distinct groups, exhibiting conserved domain structures across different plant species. Promoter analysis revealed various cis-acting elements, most of which are associated with stress responsiveness and growth and development. Micro-RNA (miRNA) analysis identified specific miRNAs, notably miRNA166, targeting different FAT genes in both species. Utilizing clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-mediated knockout, mutant lines for SlFATB1 and SlFATB3 were successfully generated and exhibited diverse mutation types. Biochemical evaluation of selected mutant lines revealed significant changes in fatty acid composition, with linoleic and linolenic acid content variations. The study also explored the impact of FAT gene knockout on tomato leaf architecture through scanning electron microscopy, providing insights into potential morphological alterations. Knocking out of FAT genes resulted in a significant reduction in both trichome and stoma density. These findings contribute to a comprehensive understanding of FAT genes in Solanaceous species, encompassing genetic, functional, and phenotypic aspects.
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Affiliation(s)
- Sibel Bahadır
- Faculty of Agriculture, Department of Agricultural Biotechnology, Ondokuz Mayis University, Samsun, Turkey
| | - Mohamed Farah Abdulla
- Faculty of Agriculture, Department of Agricultural Biotechnology, Ondokuz Mayis University, Samsun, Turkey
| | - Karam Mostafa
- Faculty of Agriculture, Department of Agricultural Biotechnology, Ondokuz Mayis University, Samsun, Turkey
- The Central Laboratory for Date Palm Research and Development, Agricultural Research Center (ARC), Giza, Egypt
| | - Musa Kavas
- Faculty of Agriculture, Department of Agricultural Biotechnology, Ondokuz Mayis University, Samsun, Turkey
| | - Safa Hacıkamiloğlu
- Faculty of Agriculture, Department of Field Crops, Ondokuz Mayis University, Samsun, Turkey
| | - Orhan Kurt
- Faculty of Agriculture, Department of Field Crops, Ondokuz Mayis University, Samsun, Turkey
| | - Kubilay Yıldırım
- Faculty of Science, Department of Molecular Biology and Genetics, Ondokuz Mayis University, Samsun, Turkey
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3
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Váczy KZ, Otto M, Gomba-Tóth A, Geiger A, Golen R, Hegyi-Kaló J, Cels T, Geml J, Zsófi Z, Hegyi ÁI. Botrytis cinerea causes different plant responses in grape ( Vitis vinifera) berries during noble and grey rot: diverse metabolism versus simple defence. FRONTIERS IN PLANT SCIENCE 2024; 15:1433161. [PMID: 39166245 PMCID: PMC11333459 DOI: 10.3389/fpls.2024.1433161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Accepted: 07/19/2024] [Indexed: 08/22/2024]
Abstract
The complexity of the interaction between the necrotrophic pathogen Botrytis cinerea and grape berries (Vitis vinifera spp.) can result in the formation of either the preferred noble rot (NR) or the loss-making grey rot (GR), depending on the prevailing climatic conditions. In this study, we focus on the functional gene set of V. vinifera by performing multidimensional scaling followed by differential expression and enrichment analyses. The aim of this study is to identify the differences in gene expression between grape berries in the phases of grey rot, noble rot, and developing rot (DR, in its early stages) phases. The grapevine transcriptome at the NR phase was found to exhibit significant differences from that at the DR and GR stages, which displayed strong similarities. Similarly, several plant defence-related pathways, including plant-pathogen interactions as hypersensitive plant responses were found to be enriched. The results of the analyses identified a potential plant stress response pathway (SGT1 activated hypersensitive response) that was found to be upregulated in the GR berry but downregulated in the NR berry. The study revealed a decrease in defence-related in V. vinifera genes during the NR stages, with a high degree of variability in functions, particularly in enriched pathways. This indicates that the plant is not actively defending itself against Botrytis cinerea, which is otherwise present on its surface with high biomass. This discrepancy underscores the notion that during the NR phase, the grapevine and the pathogenic fungi interact in a state of equilibrium. Conversely the initial stages of botrytis infection manifest as a virulent fungus-plant interaction, irrespective of whether the outcome is grey or noble rot.
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Affiliation(s)
- Kálmán Z. Váczy
- Food and Wine Research Institute, Eszterházy Károly Catholic University, Eger, Hungary
| | - Margot Otto
- Food and Wine Research Institute, Eszterházy Károly Catholic University, Eger, Hungary
- Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, Stellenbosch, South Africa
| | - Adrienn Gomba-Tóth
- Food and Wine Research Institute, Eszterházy Károly Catholic University, Eger, Hungary
| | - Adrienn Geiger
- Food and Wine Research Institute, Eszterházy Károly Catholic University, Eger, Hungary
| | - Richárd Golen
- Food and Wine Research Institute, Eszterházy Károly Catholic University, Eger, Hungary
| | - Júlia Hegyi-Kaló
- Food and Wine Research Institute, Eszterházy Károly Catholic University, Eger, Hungary
| | - Thomas Cels
- Food and Wine Research Institute, Eszterházy Károly Catholic University, Eger, Hungary
| | - József Geml
- Food and Wine Research Institute, Eszterházy Károly Catholic University, Eger, Hungary
- HUN-REN-EKKE Lendület Environmental Microbiome Research Group, Eszterházy Károly Catholic University, Eger, Hungary
| | - Zsolt Zsófi
- Institute for Viticulture and Enology, Eszterházy Károly Catholic University, Eger, Hungary
| | - Ádám István Hegyi
- Food and Wine Research Institute, Eszterházy Károly Catholic University, Eger, Hungary
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Junior DBC, Lacerda PS, de Pilla Varotti F, Leite FHA. Towards development of new antimalarial compounds through in silico and in vitro assays. Comput Biol Chem 2024; 111:108093. [PMID: 38772047 DOI: 10.1016/j.compbiolchem.2024.108093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/17/2024] [Accepted: 05/01/2024] [Indexed: 05/23/2024]
Abstract
Malaria is one of most widespread infectious disease in world. The antimalarial therapy presents a series of limitations, such as toxicity and the emergence of resistance, which makes the search for new drugs urgent. Thus, it becomes necessary to explore essential and exclusive therapeutic targets of the parasite to achieve selective inhibition. Enoyl-ACP reductase is an enzyme of the type II fatty acid biosynthetic pathway and is responsible for the rate-limiting step in the fatty acid elongation cycle. In this work, we use hierarchical virtual screening and drug repositioning strategies to prioritize compounds for phenotypic assays and molecular dynamics studies. The molecules were tested against chloroquine-resistant W2 strain of Plasmodium falciparum (EC50 between 330.05 and 13.92 µM). Nitrofurantoin was the best antimalarial activity at low micromolar range (EC50 = 13.92 µM). However, a hit compound against malaria must have a biological activity value below 1 µM. A large number of molecules present problems with permeability in biological membranes and reaching an effective concentration in their target's microenvironment. Nitrofurantoin derivatives with inclusions of groups which confer increased lipid solubility (methyl groups, halogens and substituted and unsubstituted aromatic rings) have been proposed. These derivatives were pulled through the lipid bilayer in molecular dynamics simulations. Molecules 14, 18 and 21 presented lower free energy values than nitrofurantoin when crossing the lipid bilayer.
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Affiliation(s)
| | - Pedro Sousa Lacerda
- Laboratório de Bioinformática e Modelagem Molecular, Universidade Federal da Bahia, Brazil
| | | | - Franco Henrique Andrade Leite
- Programa de pós-graduação em Biotecnologia, Universidade Estadual de Feira de Santana, Brazil; Programa de pós-graduação em Ciências Farmacêuticas, Universidade Estadual de Feira de Santana, Brazil; Laboratório de Modelagem Molecular, Universidade Estadual de Feira de Santana, Brazil.
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Huang H, Chang S, Cui T, Huang M, Qu J, Zhang H, Lu T, Zhang X, Zhou C, Feng Y. An inhibitory mechanism of AasS, an exogenous fatty acid scavenger: Implications for re-sensitization of FAS II antimicrobials. PLoS Pathog 2024; 20:e1012376. [PMID: 39008531 PMCID: PMC11271967 DOI: 10.1371/journal.ppat.1012376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 07/25/2024] [Accepted: 06/26/2024] [Indexed: 07/17/2024] Open
Abstract
Antimicrobial resistance is an ongoing "one health" challenge of global concern. The acyl-ACP synthetase (termed AasS) of the zoonotic pathogen Vibrio harveyi recycles exogenous fatty acid (eFA), bypassing the requirement of type II fatty acid synthesis (FAS II), a druggable pathway. A growing body of bacterial AasS-type isoenzymes compromises the clinical efficacy of FAS II-directed antimicrobials, like cerulenin. Very recently, an acyl adenylate mimic, C10-AMS, was proposed as a lead compound against AasS activity. However, the underlying mechanism remains poorly understood. Here we present two high-resolution cryo-EM structures of AasS liganded with C10-AMS inhibitor (2.33 Å) and C10-AMP intermediate (2.19 Å) in addition to its apo form (2.53 Å). Apart from our measurements for C10-AMS' Ki value of around 0.6 μM, structural and functional analyses explained how this inhibitor interacts with AasS enzyme. Unlike an open state of AasS, ready for C10-AMP formation, a closed conformation is trapped by the C10-AMS inhibitor. Tight binding of C10-AMS blocks fatty acyl substrate entry, and therefore inhibits AasS action. Additionally, this intermediate analog C10-AMS appears to be a mixed-type AasS inhibitor. In summary, our results provide the proof of principle that inhibiting salvage of eFA by AasS reverses the FAS II bypass. This facilitates the development of next-generation anti-bacterial therapeutics, esp. the dual therapy consisting of C10-AMS scaffold derivatives combined with certain FAS II inhibitors.
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Affiliation(s)
- Haomin Huang
- Key Laboratory of Multiple Organ Failure, Ministry of Education; Departments of Microbiology and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Shenghai Chang
- Center of Cryo-Electron Microscopy, Zhejiang University, Hangzhou, Zhejiang, China
| | - Tao Cui
- School of Life Sciences, Northwestern Polytechnical University, Xi’an, Shaanxi, China
| | - Man Huang
- Key Laboratory of Multiple Organ Failure, Ministry of Education; Departments of Microbiology and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jiuxin Qu
- Department of Clinical Laboratory, Shenzhen Third People’s Hospital, National Clinical Research Center for Infectious Diseases, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Huimin Zhang
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Ting Lu
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Xing Zhang
- Center of Cryo-Electron Microscopy, Zhejiang University, Hangzhou, Zhejiang, China
| | - Chun Zhou
- School of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Youjun Feng
- Key Laboratory of Multiple Organ Failure, Ministry of Education; Departments of Microbiology and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Department of Clinical Laboratory, Shenzhen Third People’s Hospital, National Clinical Research Center for Infectious Diseases, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, China
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6
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Kim G, Kim HJ, Kim K, Kim HJ, Yang J, Seo SW. Tunable translation-level CRISPR interference by dCas13 and engineered gRNA in bacteria. Nat Commun 2024; 15:5319. [PMID: 38909033 PMCID: PMC11193725 DOI: 10.1038/s41467-024-49642-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 06/13/2024] [Indexed: 06/24/2024] Open
Abstract
Although CRISPR-dCas13, the RNA-guided RNA-binding protein, was recently exploited as a translation-level gene expression modulator, it has still been difficult to precisely control the level due to the lack of detailed characterization. Here, we develop a synthetic tunable translation-level CRISPR interference (Tl-CRISPRi) system based on the engineered guide RNAs that enable precise and predictable down-regulation of mRNA translation. First, we optimize the Tl-CRISPRi system for specific and multiplexed repression of genes at the translation level. We also show that the Tl-CRISPRi system is more suitable for independently regulating each gene in a polycistronic operon than the transcription-level CRISPRi (Tx-CRISPRi) system. We further engineer the handle structure of guide RNA for tunable and predictable repression of various genes in Escherichia coli and Vibrio natriegens. This tunable Tl-CRISPRi system is applied to increase the production of 3-hydroxypropionic acid (3-HP) by 14.2-fold via redirecting the metabolic flux, indicating the usefulness of this system for the flux optimization in the microbial cell factories based on the RNA-targeting machinery.
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Affiliation(s)
- Giho Kim
- School of Chemical and Biological Engineering, Seoul National University, Seoul, Republic of Korea
| | - Ho Joon Kim
- School of Chemical and Biological Engineering, Seoul National University, Seoul, Republic of Korea
| | - Keonwoo Kim
- School of Chemical and Biological Engineering, Seoul National University, Seoul, Republic of Korea
| | - Hyeon Jin Kim
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, South Korea
| | - Jina Yang
- Department of Chemical Engineering, Jeju National University, Jeju-si, South Korea
| | - Sang Woo Seo
- School of Chemical and Biological Engineering, Seoul National University, Seoul, Republic of Korea.
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, South Korea.
- Institute of Chemical Processes, Seoul National University, Seoul, South Korea.
- Bio-MAX Institute, Seoul National University, Seoul, South Korea.
- Institute of Bio Engineering, Seoul National University, Seoul, South Korea.
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7
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Fivenson EM, Dubois L, Bernhardt TG. Co-ordinated assembly of the multilayered cell envelope of Gram-negative bacteria. Curr Opin Microbiol 2024; 79:102479. [PMID: 38718542 DOI: 10.1016/j.mib.2024.102479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/11/2024] [Accepted: 04/12/2024] [Indexed: 06/11/2024]
Abstract
Bacteria surround themselves with complex cell envelopes to maintain their integrity and protect against external insults. The envelope of Gram-negative organisms is multilayered, with two membranes sandwiching the periplasmic space that contains the peptidoglycan cell wall. Understanding how this complicated surface architecture is assembled during cell growth and division is a major fundamental problem in microbiology. Additionally, because the envelope is an important antibiotic target and determinant of intrinsic antibiotic resistance, understanding the mechanisms governing its assembly is relevant to therapeutic development. In the last several decades, most of the factors required to build the Gram-negative envelope have been identified. However, surprisingly, little is known about how the biogenesis of the different cell surface layers is co-ordinated. Here, we provide an overview of recent work that is beginning to uncover the links connecting the different envelope biosynthetic pathways and assembly machines to ensure uniform envelope growth.
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Affiliation(s)
- Elayne M Fivenson
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, United States
| | - Laurent Dubois
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, United States
| | - Thomas G Bernhardt
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, United States; Howard Hughes Medical Institute, Boston, United States.
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Li F, Deng J, Zhang Z, Wang C, Mao Y. FabV, the Unique Enoyl-Acyl Carrier Protein Reductase in Xanthomonas arboricola pv. juglandis Associated with Walnut Bacterial Blight, Is Essential for the Growth and Confers Triclosan Resistance to the Strain. PHYTOPATHOLOGY 2024; 114:780-791. [PMID: 37913555 DOI: 10.1094/phyto-08-23-0272-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
Walnut bacterial blight caused by Xanthomonas arboricola pv. juglandis (Xaj) is one of the most prevalent diseases of walnut (Juglans spp.), causing significant reductions in nut yield and important losses in economy. Enoyl-acyl carrier protein (ACP) reductase (ENR) is one of the key enzymes involved in the biosynthesis of bacterial fatty acids. In this study, we identified a single ENR-encoding gene, RS10040, in the genome of the XajDW3F3 strain. Sequence alignment analysis suggested RS10040 as a candidate fabV gene in Xaj. Expression of XajfabV restored the growth of the Escherichia coli fabI temperature-sensitive mutant under a nonpermissive growth condition. In vitro assays demonstrated that XajFabV catalyzed enoyl-ACPs of various chain lengths to acyl-ACPs, demonstrating its role in de novo fatty acid biosynthesis. Furthermore, we confirmed that XajfabV is an essential gene for growth, as no XajfabV deletion mutant could be obtained, although XajfabV in the chromosome could be deleted after compensating with a functional ENR-encoding gene via an exogenous plasmid. The fabV replacement mutants showed similar growth characteristic and fatty acid compositions. Our data further identified that fabV conferred Xaj with tolerance to various environmental stresses. Although XajFabV conferred Xaj with triclosan resistance, the resistance of Xaj was weaker than that found for Pseudomonas aeruginosa. Moreover, triclosan exhibited a control effect against infection of the ΔfabV/EcfabI to its host walnut. This study revealed the function of XajFabV and laid a theoretical foundation for the fatty acid synthesis mechanism of Xaj.
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Affiliation(s)
- Feng Li
- Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables/College of Life Science and Technology, Hubei Engineering University, Xiaogan 432000, China
| | - Jiangli Deng
- Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables/College of Life Science and Technology, Hubei Engineering University, Xiaogan 432000, China
| | - Zhilin Zhang
- Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables/College of Life Science and Technology, Hubei Engineering University, Xiaogan 432000, China
| | - Cheng Wang
- Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables/College of Life Science and Technology, Hubei Engineering University, Xiaogan 432000, China
| | - Yahui Mao
- Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables/College of Life Science and Technology, Hubei Engineering University, Xiaogan 432000, China
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Guo Q, Su J, Liao Y, Yu Y, Luo L, Weng X, Zhang W, Hu Z, Wang H, Beattie GA, Ma J. An atypical 3-ketoacyl ACP synthase III required for acyl homoserine lactone synthesis in Pseudomonas syringae pv. syringae B728a. Appl Environ Microbiol 2024; 90:e0225623. [PMID: 38415624 PMCID: PMC10952384 DOI: 10.1128/aem.02256-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 02/04/2024] [Indexed: 02/29/2024] Open
Abstract
The last step of the initiation phase of fatty acid biosynthesis in most bacteria is catalyzed by the 3-ketoacyl-acyl carrier protein (ACP) synthase III (FabH). Pseudomonas syringae pv. syringae strain B728a encodes two FabH homologs, Psyr_3467 and Psyr_3830, which we designated PssFabH1 and PssFabH2, respectively. Here, we explored the roles of these two 3-ketoacyl-ACP synthase (KAS) III proteins. We found that PssFabH1 is similar to the Escherichia coli FabH in using acetyl-acetyl-coenzyme A (CoA ) as a substrate in vitro, whereas PssFabH2 uses acyl-CoAs (C4-C10) or acyl-ACPs (C6-C10). Mutant analysis showed that neither KAS III protein is essential for the de novo fatty acid synthesis and cell growth. Loss of PssFabH1 reduced the production of an acyl homoserine lactone (AHL) quorum-sensing signal, and this production was partially restored by overexpressing FabH homologs from other bacteria. AHL production was also restored by inhibiting fatty acid elongation and providing exogenous butyric acid. Deletion of PssFabH1 supports the redirection of acyl-ACP toward biosurfactant synthesis, which in turn enhances swarming motility. Our study revealed that PssFabH1 is an atypical KAS III protein that represents a new KAS III clade that functions in providing a critical fatty acid precursor, butyryl-ACP, for AHL synthesis.IMPORTANCEAcyl homoserine lactones (AHLs) are important quorum-sensing compounds in Gram-negative bacteria. Although their formation requires acylated acyl carrier proteins (ACPs), how the acylated intermediate is shunted from cellular fatty acid synthesis to AHL synthesis is not known. Here, we provide in vivo evidence that Pseudomonas syringae strain B728a uses the enzyme PssFabH1 to provide the critical fatty acid precursor butyryl-ACP for AHL synthesis. Loss of PssFabH1 reduces the diversion of butyryl-ACP to AHL, enabling the accumulation of acyl-ACP for synthesis of biosurfactants that contribute to bacterial swarming motility. We report that PssFabH1 and PssFabH2 each encode a 3-ketoacyl-acyl carrier protein synthase (KAS) III in P. syringae B728a. Whereas PssFabH2 is able to function in redirecting intermediates from β-oxidation to fatty acid synthesis, PssFabH1 is an atypical KAS III protein that represents a new KAS III clade based on its sequence, non-involvement in cell growth, and novel role in AHL synthesis.
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Affiliation(s)
- Qiaoqiao Guo
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, China
| | - Jingtong Su
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, China
| | - Yuling Liao
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, China
| | - Yin Yu
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, China
| | - Lizhen Luo
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, China
| | - Xiaoshan Weng
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, China
| | - Wenbin Zhang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, China
| | - Zhe Hu
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, China
| | - Haihong Wang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, China
| | - Gwyn A. Beattie
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, Iowa, USA
| | - Jincheng Ma
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, China
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, Iowa, USA
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10
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Kugler A, Stensjö K. Machine learning predicts system-wide metabolic flux control in cyanobacteria. Metab Eng 2024; 82:171-182. [PMID: 38395194 DOI: 10.1016/j.ymben.2024.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 02/14/2024] [Accepted: 02/20/2024] [Indexed: 02/25/2024]
Abstract
Metabolic fluxes and their control mechanisms are fundamental in cellular metabolism, offering insights for the study of biological systems and biotechnological applications. However, quantitative and predictive understanding of controlling biochemical reactions in microbial cell factories, especially at the system level, is limited. In this work, we present ARCTICA, a computational framework that integrates constraint-based modelling with machine learning tools to address this challenge. Using the model cyanobacterium Synechocystis sp. PCC 6803 as chassis, we demonstrate that ARCTICA effectively simulates global-scale metabolic flux control. Key findings are that (i) the photosynthetic bioproduction is mainly governed by enzymes within the Calvin-Benson-Bassham (CBB) cycle, rather than by those involve in the biosynthesis of the end-product, (ii) the catalytic capacity of the CBB cycle limits the photosynthetic activity and downstream pathways and (iii) ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is a major, but not the most, limiting step within the CBB cycle. Predicted metabolic reactions qualitatively align with prior experimental observations, validating our modelling approach. ARCTICA serves as a valuable pipeline for understanding cellular physiology and predicting rate-limiting steps in genome-scale metabolic networks, and thus provides guidance for bioengineering of cyanobacteria.
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Affiliation(s)
- Amit Kugler
- Microbial Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Box 523, SE-751 20, Uppsala, Sweden
| | - Karin Stensjö
- Microbial Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Box 523, SE-751 20, Uppsala, Sweden.
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11
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Guo Q, Zhong C, Dong H, Cronan JE, Wang H. Diversity in fatty acid elongation enzymes: The FabB long-chain β-ketoacyl-ACP synthase I initiates fatty acid synthesis in Pseudomonas putida F1. J Biol Chem 2024; 300:105600. [PMID: 38335573 PMCID: PMC10869286 DOI: 10.1016/j.jbc.2023.105600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 02/12/2024] Open
Abstract
The condensation of acetyl-CoA with malonyl-acyl carrier protein (ACP) by β-ketoacyl-ACP synthase III (KAS III, FabH) and decarboxylation of malonyl-ACP by malonyl-ACP decarboxylase are the two pathways that initiate bacterial fatty acid synthesis (FAS) in Escherichia coli. In addition to these two routes, we report that Pseudomonas putida F1 β-ketoacyl-ACP synthase I (FabB), in addition to playing a key role in fatty acid elongation, also initiates FAS in vivo. We report that although two P. putida F1 fabH genes (PpfabH1 and PpfabH2) both encode functional KAS III enzymes, neither is essential for growth. PpFabH1 is a canonical KAS III similar to E. coli FabH whereas PpFabH2 catalyzes condensation of malonyl-ACP with short- and medium-chain length acyl-CoAs. Since these two KAS III enzymes are not essential for FAS in P. putida F1, we sought the P. putida initiation enzyme and unexpectedly found that it was FabB, the elongation enzyme of the oxygen-independent unsaturated fatty acid pathway. P. putida FabB decarboxylates malonyl-ACP and condenses the acetyl-ACP product with malonyl-ACP for initiation of FAS. These data show that P. putida FabB, unlike the paradigm E. coli FabB, can catalyze the initiation reaction in FAS.
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Affiliation(s)
- Qiaoqiao Guo
- National Key Laboratory of Green Pesticide, Integrative Microbiology Research Centre, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Canyao Zhong
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Huijuan Dong
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - John E Cronan
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA; Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
| | - Haihong Wang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China.
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12
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Kumatia EK, Zoiku FK, Asase A, Tung NH. In vitro and in silico anti-malarial activity and cytotoxicity of n-hexyl 1-O-rutinoside (a glycoside) isolated from Annickia polycarpa (DC.) Setten and Maas ex I.M. Turner (Annonaceae). JOURNAL OF ETHNOPHARMACOLOGY 2024; 319:117287. [PMID: 37827299 DOI: 10.1016/j.jep.2023.117287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/27/2023] [Accepted: 10/04/2023] [Indexed: 10/14/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Annickia polycarpa leaf is an effective anti-malarial agent. However, its chemical constituents have not been isolated and assayed against any pathogen. AIM OF THE STUDY To isolate and characterize anti-malarial compound(s) from the leaf of A. polycarpa. MATERIALS AND METHODS Bioassay-guided fractionation was employed to isolated the compound (AL1) from the chloroform fraction (ALCF) of the basified ethanol extract of A. polycarpa leaf (ALE). AL1 was characterized by LC-MS, 1D and 2D NMR spectroscopic analysis. Anti-malarial activity was evaluated against drug resistance Dd2 and drug sensitive 3D7 Plasmodium falciparum strains using the SYBR green assay. Cytotoxicity and mechanistic studies were determined using tetrazolium-based colorimetric assay and molecular docking respectively. RESULTS AL1 was characterized as n-hexyl 1-O-rutinoside. The IC50 values of ALE and ALCF against 3D7 and Dd2 P. falciparum strains ranges from 3.441 (0.3389) - 4.255 (0.2246) μg/mL. The IC50s obtained for n-hexyl 1-O-rutinoside and Artesunate (standard drug) were 7.71 (0.5473) and 0.001 (0.00008) nM against the 3D7 parasite strain respectively. Also, the efficacy of n-hexyl 1-O-rutinoside increased by 24.40% against the chloroquine resistance Dd2 P. falciparum strain whiles that of Artesunate decreased by 98.96%. Furthermore, ALE, ALCF and n-hexyl 1-O-rutinoside were weakly cytotoxic to human RBCs with high selectivity indices. N-hexyl 1-O-rutinoside inhibits P. falciparum chloroquine resistance transporter (PfCRT) and dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) better than chloroquine and pyrimethamine respectively. But, produced similar inhibition of P. falciparum 2-trans-enoyl -ACP-reductase (PfERN) as triclosan. CONCLUSION These results show that A. polycarpa leaf and n-hexyl 1-O-rutinoside possessed profound anti-malarial activity and are not cytotoxic. N-hexyl 1-O-rutinoside could therefore, be developed into a new anti-malarial medicine. This is the first study to report the anti-malarial activity of n-hexyl 1-O-rutinoside and its isolation from the genus Annickia.
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Affiliation(s)
- Emmanuel Kofi Kumatia
- Department of Phytochemistry, Centre for Plant Medicine Research, Mampong-Akwapim, Ghana; Department of Quality Management, Centre for Plant Medicine Research, Mampong-Akwapim, Ghana.
| | - Felix Kwame Zoiku
- Depaertment of Epidemiology, Nouguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana.
| | - Alex Asase
- Plant Development Department, Centre for Plant Medicine Research, Mampong-Akwapim, Ghana.
| | - Nguyen Huu Tung
- Faculty of Pharmacy, Phenikaa University, Hanoi 12116, Viet Nam.
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13
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Coandă M, Limban C, Nuță DC. Small Schiff Base Molecules-A Possible Strategy to Combat Biofilm-Related Infections. Antibiotics (Basel) 2024; 13:75. [PMID: 38247634 PMCID: PMC10812491 DOI: 10.3390/antibiotics13010075] [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: 12/13/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 01/23/2024] Open
Abstract
Microorganisms participating in the development of biofilms exhibit heightened resistance to antibiotic treatment, therefore infections involving biofilms have become a problem in recent years as they are more difficult to treat. Consequently, research efforts are directed towards identifying novel molecules that not only possess antimicrobial properties but also demonstrate efficacy against biofilms. While numerous investigations have focused on antimicrobial capabilities of Schiff bases, their potential as antibiofilm agents remains largely unexplored. Thus, the objective of this article is to present a comprehensive overview of the existing scientific literature pertaining to small molecules categorized as Schiff bases with antibiofilm properties. The survey involved querying four databases (Web of Science, ScienceDirect, Scopus and Reaxys). Relevant articles published in the last 10 years were selected and categorized based on the molecular structure into two groups: classical Schiff bases and oximes and hydrazones. Despite the majority of studies indicating a moderate antibiofilm potential of Schiff bases, certain compounds exhibited a noteworthy effect, underscoring the significance of considering this type of molecular modeling when seeking to develop new molecules with antibiofilm effects.
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Affiliation(s)
| | - Carmen Limban
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 6 Traian Vuia Str., 020950 Bucharest, Romania; (M.C.); (D.C.N.)
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14
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Loukili EH, Ouahabi S, Elbouzidi A, Taibi M, Yahyaoui MI, Asehraou A, Azougay A, Saleh A, Al Kamaly O, Parvez MK, El Guerrouj B, Touzani R, Ramdani M. Phytochemical Composition and Pharmacological Activities of Three Essential Oils Collected from Eastern Morocco (Origanum compactum, Salvia officinalis, and Syzygium aromaticum): A Comparative Study. PLANTS (BASEL, SWITZERLAND) 2023; 12:3376. [PMID: 37836118 PMCID: PMC10574104 DOI: 10.3390/plants12193376] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 10/15/2023]
Abstract
Throughout history, essential oils have been employed for their pleasing scents and potential therapeutic benefits. These oils have shown promise in various areas, including aromatherapy, personal care products, natural remedies, and even as alternatives to traditional cleaning agents or pest control solutions. The study aimed to explore the chemical makeup, antioxidant, and antibacterial properties of Origanum compactum Benth., Salvia officinalis L., and Syzygium aromaticum (L.) Merr. et Perry. Initially, the composition of the three essential oils, O. compactum (HO), S. officinalis (HS), and S. aromaticum (HC) was analyzed using GC-MS technology, revealing significant differences in the identified compounds. α-thujone emerged as the predominant volatile component in the oils, making up 78.04% of the composition, followed by eugenol, which constituted 72.66% and 11.22% of the HC and HO oils, respectively. To gauge antioxidant capabilities, tests involving DPPH scavenging capacity and total antioxidant capacity were conducted. Antioxidant activity was determined through the phosphomolybdate test and the DPPH• radical scavenging activity, with the HO essential oil displaying significant scavenging capacity (IC50 of 0.12 ± 0.02 mg/mL), similar to ascorbic acid (IC50 of 0.26 ± 0.24 mg/mL). Similarly, the TAC assay for HO oil revealed an IC50 of 1086.81 ± 0.32 µM AAE/mg. Additionally, the oils' effectiveness against four bacterial strains, namely Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, and Listeria monocytogenes, and five fungi, Geotrichum candidum, Aspergillus niger, Saccharomyces cerevisiae, Candida glabrata, and Candida albicans, was tested in vitro. The examined essential oils generally exhibited limited antimicrobial effects, with the exception of HC oil, which demonstrated an exceptionally impressive level of antifungal activity. In order to clarify the antioxidant, antibacterial, and antifungal effects of the identified plant compounds, we employed computational methods, specifically molecular docking. This technique involved studying the interactions between these compounds and established protein targets associated with antioxidant, antibacterial, and antifungal activities.
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Affiliation(s)
- El Hassania Loukili
- Laboratory of Applied Chemistry and Environment, Faculty of Sciences, Mohammed First University, Oujda 60000, Morocco; (S.O.); (R.T.); (M.R.)
- Centre de l’Oriental des Sciences et Technologies de l’Eau et de l’Environnement (COSTEE), Mohammed First University, Oujda 60000, Morocco;
| | - Safae Ouahabi
- Laboratory of Applied Chemistry and Environment, Faculty of Sciences, Mohammed First University, Oujda 60000, Morocco; (S.O.); (R.T.); (M.R.)
| | - Amine Elbouzidi
- Laboratoire d’Amélioration des Productions Agricoles, Biotechnologie et Environnement (LAPABE), Faculty of Sciences, Mohammed First University, Oujda 60000, Morocco;
| | - Mohamed Taibi
- Centre de l’Oriental des Sciences et Technologies de l’Eau et de l’Environnement (COSTEE), Mohammed First University, Oujda 60000, Morocco;
- Laboratoire d’Amélioration des Productions Agricoles, Biotechnologie et Environnement (LAPABE), Faculty of Sciences, Mohammed First University, Oujda 60000, Morocco;
| | - Meryem Idrissi Yahyaoui
- Laboratory of Bioresources, Biotechnology, Ethnopharmacology and Health, Faculty of Sciences, Mohammed First University, Oujda 60000, Morocco; (M.I.Y.); (A.A.)
| | - Abdeslam Asehraou
- Laboratory of Bioresources, Biotechnology, Ethnopharmacology and Health, Faculty of Sciences, Mohammed First University, Oujda 60000, Morocco; (M.I.Y.); (A.A.)
| | - Abdellah Azougay
- Laboratory of Applied Geosciences (LGA), Faculty of Sciences, Mohammed First University, Oujda 60000, Morocco;
| | - Asmaa Saleh
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia; (A.S.); (O.A.K.)
| | - Omkulthom Al Kamaly
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia; (A.S.); (O.A.K.)
| | - Mohammad Khalid Parvez
- Department of Pharmacognosy, College of Pharmacy King Saud University, P.O. Box 3660, Riyadh 11481, Saudi Arabia;
| | - Bouchra El Guerrouj
- Centre de l’Oriental des Sciences et Technologies de l’Eau et de l’Environnement (COSTEE), Mohammed First University, Oujda 60000, Morocco;
| | - Rachid Touzani
- Laboratory of Applied Chemistry and Environment, Faculty of Sciences, Mohammed First University, Oujda 60000, Morocco; (S.O.); (R.T.); (M.R.)
| | - Mohammed Ramdani
- Laboratory of Applied Chemistry and Environment, Faculty of Sciences, Mohammed First University, Oujda 60000, Morocco; (S.O.); (R.T.); (M.R.)
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15
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Shahzadi I, Aqeel M, Haider A, Naz S, Imran M, Nabgan W, Al-Shanini A, Shahzadi A, Alshahrani T, Ikram M. Hydrothermal Synthesis of Fe-Doped Cadmium Oxide Showed Bactericidal Behavior and Highly Efficient Visible Light Photocatalysis. ACS OMEGA 2023; 8:30681-30693. [PMID: 37636921 PMCID: PMC10448685 DOI: 10.1021/acsomega.3c04543] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 07/28/2023] [Indexed: 08/29/2023]
Abstract
Cationic dyes present in industrial effluents significantly reduce the effectiveness of remediation operations. Considering the terrible impact of these pollutants on environment and biodiversity, investigating strategies to remove potentially harmful compounds from water is becoming an increasingly intriguing issue. In this work, we employed a simple hydrothermal technique to synthesize Fe-doped CdO (2, 4, and 6 wt %) nanostructures and assessed their efficacy in degrading methylene blue (MB) dye and inhibiting the growth of Staphylococcus aureus and Escherichia coli, respectively. Structural, morphological, and optical characterization of produced nanomaterials was also performed using X-ray diffraction, TEM, and UV absorption spectra. The photocatalytic decomposition of MB was significantly enhanced (58.8%) by using Fe (6 wt %)-doped CdO catalysts for 80 min under irradiation. In addition, 2.05-5.05 mm inhibitory zones were seen against Gram-positive bacteria (S. aureus), whereas the range for Gram-negative bacteria (E. coli) was 1.65-2.75 mm. These nanostructures were shown to be very effective inhibitors of beta-lactamase, d-alanine-d-alanine ligase B, and fatty acid synthase inhibitor by in silico molecular docking investigations.
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Affiliation(s)
- Iram Shahzadi
- Punjab
University College of Pharmacy, Allama Iqbal Campus, University of the Punjab, Lahore 54000, Punjab, Pakistan
| | - Muhammad Aqeel
- Department
of Physics, The University of Gothenburg, Box 100 405 30 Gothenburg, Sweden
| | - Ali Haider
- Department
of Clinical Sciences, Faculty of Veterinary and Animal Sciences, Muhammad Nawaz Shareef University of Agriculture, Multan, 66000 Punjab, Pakistan
| | - Sadia Naz
- Tianjin
Institute of Industrial Biotechnology, Chinese
Academy of Sciences, Tianjin 300308, China
| | - Muhammad Imran
- Department
of Chemistry, Government College University
Faisalabad, Pakpattan
Road, Sahiwal, Punjab 57000, Pakistan
| | - Walid Nabgan
- Departament
d’Enginyeria Química, Universitat
Rovira I Virgili, Av Països Catalans 26,, Tarragona 43007, Spain
| | - Ali Al-Shanini
- College
of Petroleum and Engineering, Hadhramout
University, Hadhramout,
P.O. Box 50511, Mukalla 50511, Yemen
| | - Anum Shahzadi
- Faculty
of Pharmacy, The University of Lahore, Lahore, Punjab 54000, Pakistan
| | - Thamraa Alshahrani
- Department
of Physics, College of Sciences, Princess
Nourah bint Abdulrahman University (PNU), P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Muhammad Ikram
- Solar
Cell Applications Research Lab, Department of Physics, Government College University Lahore, Lahore, Punjab 54000, Pakistan
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16
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West AKR, Bailey CB. Crosstalk between primary and secondary metabolism: Interconnected fatty acid and polyketide biosynthesis in prokaryotes. Bioorg Med Chem Lett 2023; 91:129377. [PMID: 37328038 PMCID: PMC11239236 DOI: 10.1016/j.bmcl.2023.129377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 06/03/2023] [Accepted: 06/11/2023] [Indexed: 06/18/2023]
Abstract
In primary metabolism, fatty acid synthases (FASs) biosynthesize fatty acids via sequential Claisen-like condensations of malonyl-CoA followed by reductive processing. Likewise, polyketide synthases (PKSs) share biosynthetic logic with FAS which includes utilizing the same precursors and cofactors. However, PKS biosynthesize structurally diverse, complex secondary metabolites, many of which are pharmaceutically relevant. This digest covers examples of interconnected biosynthesis between primary and secondary metabolism in fatty acid and polyketide metabolism. Taken together, further understanding the biosynthetic linkage between polyketide biosynthesis and fatty acid biosynthesis may lead to improved discovery and production of novel drug leads from polyketide metabolites.
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Affiliation(s)
- Anna-Kay R West
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, TN 37996, USA
| | - Constance B Bailey
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, TN 37996, USA; School of Chemistry, The University of Sydney, Camperdown, New South Wales 2006, Australia.
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17
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Ouahabi S, Loukili EH, Elbouzidi A, Taibi M, Bouslamti M, Nafidi HA, Salamatullah AM, Saidi N, Bellaouchi R, Addi M, Ramdani M, Bourhia M, Hammouti B. Pharmacological Properties of Chemically Characterized Extracts from Mastic Tree: In Vitro and In Silico Assays. Life (Basel) 2023; 13:1393. [PMID: 37374175 DOI: 10.3390/life13061393] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/05/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
The mastic tree, scientifically known as Pistacia lentiscus, which belongs to the Anacardiaceae family, was used in this study. The aim of this research was to analyze the chemical composition of this plant and assess its antioxidant and antibacterial properties using both laboratory experiments and computer simulations through molecular docking, a method that predicts the binding strength of a small molecule to a protein. The soxhlet method (SE) was employed to extract substances from the leaves of P. lentiscus found in the eastern region of Morocco. Hexane and methanol were the solvents used for the extraction process. The n-hexane extract was subjected to gas chromatography-mass spectrometry (GC/MS) to identify its fatty acid content. The methanolic extract underwent high-performance liquid chromatography with a diode-array detector (HPLC-DAD) to determine the presence of phenolic compounds. Antioxidant activity was assessed using the DPPH spectrophotometric test. The findings revealed that the main components in the n-hexane extract were linoleic acid (40.97 ± 0.33%), oleic acid (23.69 ± 0.12%), and palmitic acid (22.83 ± 0.10%). Catechin (37.05 ± 0.15%) was identified as the predominant compound in the methanolic extract through HPLC analysis. The methanolic extract exhibited significant DPPH radical scavenging, with an IC50 value of 0.26 ± 0.14 mg/mL. The antibacterial activity was tested against Staphylococcus aureus, Listeria innocua, and Escherichia coli, while the antifungal activity was evaluated against Geotrichum candidum and Rhodotorula glutinis. The P. lentiscus extract demonstrated notable antimicrobial effects. Additionally, apart from molecular docking, other important factors, such as drug similarity, drug metabolism and distribution within the body, potential adverse effects, and impact on bodily systems, were considered for the substances derived from P. lentiscus. Scientific algorithms, such as Prediction of Activity Spectra for Substances (PASS), Absorption, Distribution, Metabolism, Excretion (ADME), and Pro-Tox II, were utilized for this assessment. The results obtained from this research support the traditional medicinal usage of P. lentiscus and suggest its potential for drug development.
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Affiliation(s)
- Safae Ouahabi
- Laboratory of Applied and Environmental Chemistry (LCAE), Faculty of Sciences, Mohammed First University, B.P. 717, Oujda 60000, Morocco
| | - El Hassania Loukili
- Laboratory of Applied and Environmental Chemistry (LCAE), Faculty of Sciences, Mohammed First University, B.P. 717, Oujda 60000, Morocco
| | - Amine Elbouzidi
- Laboratoire d'Amélioration des Productions Agricoles, Biotechnologie et Environnement (LAPABE), Faculté des Sciences, Université Mohammed Premier, Oujda 60000, Morocco
| | - Mohamed Taibi
- Laboratoire d'Amélioration des Productions Agricoles, Biotechnologie et Environnement (LAPABE), Faculté des Sciences, Université Mohammed Premier, Oujda 60000, Morocco
| | - Mohammed Bouslamti
- Laboratories of Natural Substances, Pharmacology, Environment, Modeling, Health and Quality of Life (SNAMOPEQ), Faculty of Sciences, Sidi Mohamed Ben Abdellah University, Fez 30000, Morocco
| | - Hiba-Allah Nafidi
- Department of Food Science, Faculty of Agricultural and Food Sciences, Laval University, Quebec City, QC G1V 0A6, Canada
| | - Ahmad Mohammad Salamatullah
- Department of Food Science & Nutrition, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
| | - Nezha Saidi
- Laboratory of Applied and Environmental Chemistry (LCAE), Faculty of Sciences, Mohammed First University, B.P. 717, Oujda 60000, Morocco
| | - Reda Bellaouchi
- Laboratory of Bioresources, Biotechnology, Ethnopharmacology and Health, Faculty of Sciences, Mohammed First University, Boulevard Mohamed VI, B.P. 717, Oujda 60000, Morocco
| | - Mohamed Addi
- Laboratoire d'Amélioration des Productions Agricoles, Biotechnologie et Environnement (LAPABE), Faculté des Sciences, Université Mohammed Premier, Oujda 60000, Morocco
| | - Mohamed Ramdani
- Laboratory of Applied and Environmental Chemistry (LCAE), Faculty of Sciences, Mohammed First University, B.P. 717, Oujda 60000, Morocco
| | - Mohammed Bourhia
- Department of Chemistry and Biochemistry, Faculty of Medicine and Pharmacy, Ibn Zohr University, Laayoune 70000, Morocco
| | - Belkheir Hammouti
- Laboratory of Applied and Environmental Chemistry (LCAE), Faculty of Sciences, Mohammed First University, B.P. 717, Oujda 60000, Morocco
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18
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Hasan S, Kayed K, Ghemrawi R, Bataineh NA, Mahgoub RE, Audeh R, Aldulaymi R, Atatreh N, Ghattas MA. Molecular Modelling Study and Antibacterial Evaluation of Diphenylmethane Derivatives as Potential FabI Inhibitors. Molecules 2023; 28:molecules28073000. [PMID: 37049763 PMCID: PMC10095751 DOI: 10.3390/molecules28073000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/10/2023] [Accepted: 03/23/2023] [Indexed: 03/30/2023] Open
Abstract
The need for new antibiotics has become a major worldwide challenge as bacterial strains keep developing resistance to the existing drugs at an alarming rate. Enoyl-acyl carrier protein reductases (FabI) play a crucial role in lipids and fatty acid biosynthesis, which are essential for the integrity of the bacterial cell membrane. Our study aimed to discover small FabI inhibitors in continuation to our previously found hit MN02. The process was initially started by conducting a similarity search to the NCI ligand database using MN02 as a query. Accordingly, ten compounds were chosen for the computational assessment and antimicrobial testing. Most of the compounds showed an antibacterial activity against Gram-positive strains, while RK10 exhibited broad-spectrum activity against both Gram-positive and Gram-negative bacteria. All tested compounds were then docked into the saFabI active site followed by 100 ns MD simulations (Molecular Dynamics) and MM-GBSA (Molecular Mechanics with Generalised Born and Surface Area Solvation) calculations in order to understand their fitting and estimate their binding energies. Interestingly, and in line with the experimental data, RK10 was able to exhibit the best fitting with the target catalytic pocket. To sum up, RK10 is a small compound with leadlike characteristics that can indeed act as a promising candidate for the future development of broad-spectrum antibacterial agents.
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Affiliation(s)
- Shaima Hasan
- College of Pharmacy, Al Ain University, Abu Dhabi 64141, United Arab Emirates
| | - Kawthar Kayed
- College of Pharmacy, Al Ain University, Abu Dhabi 64141, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi 64141, United Arab Emirates
| | - Rose Ghemrawi
- College of Pharmacy, Al Ain University, Abu Dhabi 64141, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi 64141, United Arab Emirates
| | - Nezar Al Bataineh
- College of Pharmacy, Al Ain University, Abu Dhabi 64141, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi 64141, United Arab Emirates
| | - Radwa E. Mahgoub
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi 64141, United Arab Emirates
| | - Rola Audeh
- College of Pharmacy, Al Ain University, Abu Dhabi 64141, United Arab Emirates
| | - Raghad Aldulaymi
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi 64141, United Arab Emirates
| | - Noor Atatreh
- College of Pharmacy, Al Ain University, Abu Dhabi 64141, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi 64141, United Arab Emirates
| | - Mohammad A. Ghattas
- College of Pharmacy, Al Ain University, Abu Dhabi 64141, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi 64141, United Arab Emirates
- Correspondence: ; Tel.: +971-26133275
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19
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Taibi M, Elbouzidi A, Ou-Yahia D, Dalli M, Bellaouchi R, Tikent A, Roubi M, Gseyra N, Asehraou A, Hano C, Addi M, El Guerrouj B, Chaabane K. Assessment of the Antioxidant and Antimicrobial Potential of Ptychotis verticillata Duby Essential Oil from Eastern Morocco: An In Vitro and In Silico Analysis. Antibiotics (Basel) 2023; 12:antibiotics12040655. [PMID: 37107017 PMCID: PMC10135233 DOI: 10.3390/antibiotics12040655] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/23/2023] [Accepted: 03/25/2023] [Indexed: 03/29/2023] Open
Abstract
Ptychotis verticillata Duby, referred to as Nûnkha in the local language, is a medicinal plant that is native to Morocco. This particular plant is a member of the Apiaceae family and has a longstanding history in traditional medicine and has been utilized for therapeutic purposes by practitioners for generations. The goal of this research is to uncover the phytochemical makeup of the essential oil extracted from P. verticillata, which is indigenous to the Touissite region in Eastern Morocco. The extraction of the essential oil of P. verticillata (PVEO) was accomplished through the use of hydro-distillation via a Clevenger apparatus. The chemical profile of the essential oil was then determined through analysis utilizing gas chromatography–mass spectrometry (GC/MS). The study findings indicated that the essential oil of P. verticillata is composed primarily of Carvacrol (37.05%), D-Limonene (22.97%), γ-Terpinene (15.97%), m-Cymene (12.14%) and Thymol (8.49%). The in vitro antioxidant potential of PVEO was evaluated using two methods: the 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical trapping assay and the ferric reducing antioxidant power (FRAP) method. The data demonstrated considerable radical scavenging and relative antioxidative power. Escherichia coli, Staphylococcus aureus, Listeria innocua, and Pseudomonas aeruginosa were the most susceptible bacterial strains tested, while Geotrichum candidum, Candida albicans, and Rhodotorula glutinis were the most resilient fungi strains. PVEO had broad-spectrum antifungal and antibacterial properties. To elucidate the antioxidative and antibacterial characteristics of the identified molecules, we applied the methodology of molecular docking, a computational approach that forecasts the binding of a small molecule to a protein. Additionally, we utilized the Prediction of Activity Spectra for Substances (PASS) algorithm; Absorption, Distribution, Metabolism, and Excretion (ADME); and Pro-Tox II (to predict the toxicity in silico) tests to demonstrate PVEO’s identified compounds’ drug-likeness, pharmacokinetic properties, the anticipated safety features after ingestion, and the potential pharmacological activity. Finally, our findings scientifically confirm the ethnomedicinal usage and usefulness of this plant, which may be a promising source for future pharmaceutical development.
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Affiliation(s)
- Mohamed Taibi
- Laboratoire d’Amélioration des Productions Agricoles, Biotechnologie et Environnement (LAPABE), Faculté des Sciences, Université Mohammed Premier, Oujda 60000, Morocco
- Centre de l’Oriental des Sciences et Technologies de l’Eau et de l’Environnement (COSTEE), Université Mohammed Premier, Oujda 60000, Morocco
| | - Amine Elbouzidi
- Laboratoire d’Amélioration des Productions Agricoles, Biotechnologie et Environnement (LAPABE), Faculté des Sciences, Université Mohammed Premier, Oujda 60000, Morocco
| | - Douaae Ou-Yahia
- Centre de l’Oriental des Sciences et Technologies de l’Eau et de l’Environnement (COSTEE), Université Mohammed Premier, Oujda 60000, Morocco
| | - Mohammed Dalli
- Laboratory of Bioresources, Biotechnology, Ethnopharmacology and Health, Faculty of Sciences, Mohammed First University, Boulevard Mohamed VI, B.P. 717, Oujda 60000, Morocco
- Laboratory of Microbiology, Faculty of Medicine and Pharmacy, University Mohammed The First, Oujda 60000, Morocco
| | - Reda Bellaouchi
- Laboratory of Bioresources, Biotechnology, Ethnopharmacology and Health, Faculty of Sciences, Mohammed First University, Boulevard Mohamed VI, B.P. 717, Oujda 60000, Morocco
| | - Aziz Tikent
- Laboratoire d’Amélioration des Productions Agricoles, Biotechnologie et Environnement (LAPABE), Faculté des Sciences, Université Mohammed Premier, Oujda 60000, Morocco
| | - Mohammed Roubi
- Laboratory of Bioresources, Biotechnology, Ethnopharmacology and Health, Faculty of Sciences, Mohammed First University, Boulevard Mohamed VI, B.P. 717, Oujda 60000, Morocco
| | - Nadia Gseyra
- Laboratory of Bioresources, Biotechnology, Ethnopharmacology and Health, Faculty of Sciences, Mohammed First University, Boulevard Mohamed VI, B.P. 717, Oujda 60000, Morocco
| | - Abdeslam Asehraou
- Laboratory of Bioresources, Biotechnology, Ethnopharmacology and Health, Faculty of Sciences, Mohammed First University, Boulevard Mohamed VI, B.P. 717, Oujda 60000, Morocco
| | - Christophe Hano
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRAE USC1328, University of Orleans, CEDEX 2, 45067 Orléans, France
- Correspondence: (C.H.); (M.A.)
| | - Mohamed Addi
- Laboratoire d’Amélioration des Productions Agricoles, Biotechnologie et Environnement (LAPABE), Faculté des Sciences, Université Mohammed Premier, Oujda 60000, Morocco
- Correspondence: (C.H.); (M.A.)
| | - Bouchra El Guerrouj
- Laboratoire d’Amélioration des Productions Agricoles, Biotechnologie et Environnement (LAPABE), Faculté des Sciences, Université Mohammed Premier, Oujda 60000, Morocco
- Centre de l’Oriental des Sciences et Technologies de l’Eau et de l’Environnement (COSTEE), Université Mohammed Premier, Oujda 60000, Morocco
| | - Khalid Chaabane
- Laboratoire d’Amélioration des Productions Agricoles, Biotechnologie et Environnement (LAPABE), Faculté des Sciences, Université Mohammed Premier, Oujda 60000, Morocco
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20
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Manhas A, Ghosh A, Verma Y, Das T, Jha PC. Identification of natural products against enoyl-acyl-carrier-protein reductase in malaria via combined pharmacophore modeling, molecular docking and simulations studies. J Biomol Struct Dyn 2023; 41:2002-2015. [PMID: 35043754 DOI: 10.1080/07391102.2022.2027819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Plasmodium falciparum is counted as one of the deadly species causing malaria. In that respect, enoyl acyl carrier protein reductase is recognized as one of the attractive druggable targets for the identification of antimalarials. Thus, from the structural proteome of ENR, common feature pharmacophores were constructed. To identify the representative models, all the hypotheses were subjected to validation methods, like, test set, enrichment factor, and Güner-Henry method, and the selected representative hypotheses were used to screen out the drug-like natural products. Further, the screened candidates were advanced to molecular docking calculations. Based on the docking score criteria and presence of essential interaction with Tyr277, seven candidates were shortlisted to conduct the HYDE and QSAR assessment. Further, the stability of these complexes was evaluated by employing molecular dynamics simulations, molecular mechanics-generalized born surface area approach-based free binding energy calculations with the residue-wise contribution of PfENR to the total binding free energy of the complex. On comparing the root mean square deviation, and fluctuation plots of the docked candidates with the reference, all the candidates displayed stable behavior, and the same outcome was depicted from the secondary structure element. However, from the free energy calculations, and residue-wise contribution conducted after dynamics, it was observed that out of seven, only five candidates sustain the binding with Tyr277 and cofactor of PfENR. Therefore, in the current work, the hybrid study of screening and stability lead to the identification of five structurally diverse candidates that can be employed for the design of novel antimalarials.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anu Manhas
- Department of Chemistry, Pandit Deendayal Energy University (former PDPU), Gandhinagar, Gujarat, India
| | - Amar Ghosh
- School of Applied Material Sciences, Central University of Gujarat, Gandhinagar, Gujarat, India
| | - Yogesh Verma
- School of Applied Material Sciences, Central University of Gujarat, Gandhinagar, Gujarat, India
| | - Tanay Das
- School of Applied Material Sciences, Central University of Gujarat, Gandhinagar, Gujarat, India
| | - Prakash C Jha
- School of Applied Material Sciences, Central University of Gujarat, Gandhinagar, Gujarat, India
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21
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Wang Y, Wang Y, Wu Y, Suo Y, Guo H, Yu Y, Yin R, Xi R, Wu J, Hua N, Zhang Y, Zhang S, Jin Z, He L, Ma G. Using the inner membrane of Escherichia coli as a scaffold to anchor enzymes for metabolic flux enhancement. Eng Life Sci 2023; 23:e2200034. [PMID: 36751472 PMCID: PMC9893748 DOI: 10.1002/elsc.202200034] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 11/21/2022] [Accepted: 11/23/2022] [Indexed: 01/11/2023] Open
Abstract
Clustering enzymes in the same metabolic pathway is a natural strategy to enhance productivity. Synthetic protein, RNA and DNA scaffolds have been designed to artificially cluster multiple enzymes in the cell, which require complex construction processes and possess limited slots for target enzymes. We utilized the Escherichia coli inner cell membrane as a native scaffold to cluster four fatty acid synthases (FAS) and achieved to improve the efficiency of fatty acid synthesis in vivo. The construction strategy is as simple as fusing target enzymes to the N-terminus or C-terminus of the membrane anchor protein (Lgt), and the number of anchored enzymes is not restricted. This novel device not only presents a similar efficiency in clustering multiple enzymes to that of other artificial scaffolds but also promotes the product secretion, driving the entire metabolic flux forward and further increasing the gross yield compared with that in a cytoplasmic scaffold system.
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Affiliation(s)
- You Wang
- Bio‐X‐Renji Hospital Research CenterRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghaiP.R. China
- Bio‐X InstitutesKey Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education)Shanghai Jiao Tong UniversityShanghaiP.R. China
- 2012 SJTU‐BioX‐Shanghai Team for The International Genetically Engineered Machine Competition (iGEM)Shanghai Jiao Tong UniversityShanghaiP.R. China
| | - Yushu Wang
- Bio‐X InstitutesKey Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education)Shanghai Jiao Tong UniversityShanghaiP.R. China
| | - Yuqi Wu
- Bio‐X InstitutesKey Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education)Shanghai Jiao Tong UniversityShanghaiP.R. China
- 2012 SJTU‐BioX‐Shanghai Team for The International Genetically Engineered Machine Competition (iGEM)Shanghai Jiao Tong UniversityShanghaiP.R. China
| | - Yang Suo
- Bio‐X InstitutesKey Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education)Shanghai Jiao Tong UniversityShanghaiP.R. China
- 2012 SJTU‐BioX‐Shanghai Team for The International Genetically Engineered Machine Competition (iGEM)Shanghai Jiao Tong UniversityShanghaiP.R. China
| | - Huaqing Guo
- Bio‐X InstitutesKey Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education)Shanghai Jiao Tong UniversityShanghaiP.R. China
- 2012 SJTU‐BioX‐Shanghai Team for The International Genetically Engineered Machine Competition (iGEM)Shanghai Jiao Tong UniversityShanghaiP.R. China
| | - Yineng Yu
- Bio‐X InstitutesKey Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education)Shanghai Jiao Tong UniversityShanghaiP.R. China
- 2012 SJTU‐BioX‐Shanghai Team for The International Genetically Engineered Machine Competition (iGEM)Shanghai Jiao Tong UniversityShanghaiP.R. China
| | - Ruonan Yin
- Bio‐X InstitutesKey Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education)Shanghai Jiao Tong UniversityShanghaiP.R. China
- 2012 SJTU‐BioX‐Shanghai Team for The International Genetically Engineered Machine Competition (iGEM)Shanghai Jiao Tong UniversityShanghaiP.R. China
| | - Rui Xi
- Bio‐X InstitutesKey Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education)Shanghai Jiao Tong UniversityShanghaiP.R. China
- 2012 SJTU‐BioX‐Shanghai Team for The International Genetically Engineered Machine Competition (iGEM)Shanghai Jiao Tong UniversityShanghaiP.R. China
| | - Jiajie Wu
- Bio‐X InstitutesKey Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education)Shanghai Jiao Tong UniversityShanghaiP.R. China
- 2012 SJTU‐BioX‐Shanghai Team for The International Genetically Engineered Machine Competition (iGEM)Shanghai Jiao Tong UniversityShanghaiP.R. China
| | - Nan Hua
- Bio‐X InstitutesKey Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education)Shanghai Jiao Tong UniversityShanghaiP.R. China
- 2012 SJTU‐BioX‐Shanghai Team for The International Genetically Engineered Machine Competition (iGEM)Shanghai Jiao Tong UniversityShanghaiP.R. China
| | - Yuehan Zhang
- Bio‐X InstitutesKey Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education)Shanghai Jiao Tong UniversityShanghaiP.R. China
- 2012 SJTU‐BioX‐Shanghai Team for The International Genetically Engineered Machine Competition (iGEM)Shanghai Jiao Tong UniversityShanghaiP.R. China
| | - Shaobo Zhang
- Bio‐X InstitutesKey Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education)Shanghai Jiao Tong UniversityShanghaiP.R. China
- 2012 SJTU‐BioX‐Shanghai Team for The International Genetically Engineered Machine Competition (iGEM)Shanghai Jiao Tong UniversityShanghaiP.R. China
| | - Zhenming Jin
- Bio‐X InstitutesKey Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education)Shanghai Jiao Tong UniversityShanghaiP.R. China
- 2012 SJTU‐BioX‐Shanghai Team for The International Genetically Engineered Machine Competition (iGEM)Shanghai Jiao Tong UniversityShanghaiP.R. China
| | - Lin He
- Bio‐X InstitutesKey Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education)Shanghai Jiao Tong UniversityShanghaiP.R. China
| | - Gang Ma
- Bio‐X‐Renji Hospital Research CenterRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghaiP.R. China
- Bio‐X InstitutesKey Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education)Shanghai Jiao Tong UniversityShanghaiP.R. China
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22
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Srivastava A, Kumar A, Biswas S, Kumar R, Srivastava V, Rajaram H, Mishra Y. Gamma (γ)-radiation stress response of the cyanobacterium Anabaena sp. PCC7120: Regulatory role of LexA and photophysiological changes. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 326:111529. [PMID: 36332765 DOI: 10.1016/j.plantsci.2022.111529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 10/28/2022] [Accepted: 10/30/2022] [Indexed: 06/16/2023]
Abstract
High radioresistance of the cyanobacterium, Anabaena sp. PCC7120 has been attributed to efficient DNA repair, protein recycling, and oxidative stress management. However, the regulatory network involved in these batteries of responses remains unexplored. In the present study, the role of a global regulator, LexA in modulating gamma (γ)-radiation stress response of Anabaena was investigated. Comparison of the cytosolic proteome profiles upon γ-radiation in recombinant Anabaena strains, AnpAM (vector-control) and AnlexA+ (LexA-overexpressing), revealed 41 differentially accumulated proteins, corresponding to 29 distinct proteins. LexA was found to be involved in the regulation of 27 of the corresponding genes based on the presence of AnLexA-Box, EMSA, and/or qRT-PCR studies. The majority of the regulated genes were found to be involved in C-assimilation either through photosynthesis or C-catabolism and oxidative stress alleviation. Photosynthesis, measured in terms of PSII photophysiological parameters and thylakoid membrane proteome was found to be affected by γ-radiation in both AnpAM and AnlexA+ cells, with LexA affecting them even under control growth conditions. Thus, LexA functioned as one of the transcriptional regulators involved in modulating γ-radiation stress response in Anabaena. This study could pave the way for a deeper understanding of the regulation of γ-radiation-responsive genes in cyanobacteria at large.
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Affiliation(s)
- Akanksha Srivastava
- Department of Botany, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Arvind Kumar
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Subhankar Biswas
- Department of Botany, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Rajender Kumar
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm 10691, Sweden
| | - Vaibhav Srivastava
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm 10691, Sweden
| | - Hema Rajaram
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai 400094, India.
| | - Yogesh Mishra
- Department of Botany, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
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23
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Walesch S, Birkelbach J, Jézéquel G, Haeckl FPJ, Hegemann JD, Hesterkamp T, Hirsch AKH, Hammann P, Müller R. Fighting antibiotic resistance-strategies and (pre)clinical developments to find new antibacterials. EMBO Rep 2022; 24:e56033. [PMID: 36533629 PMCID: PMC9827564 DOI: 10.15252/embr.202256033] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 12/23/2022] Open
Abstract
Antibacterial resistance is one of the greatest threats to human health. The development of new therapeutics against bacterial pathogens has slowed drastically since the approvals of the first antibiotics in the early and mid-20th century. Most of the currently investigated drug leads are modifications of approved antibacterials, many of which are derived from natural products. In this review, we highlight the challenges, advancements and current standing of the clinical and preclinical antibacterial research pipeline. Additionally, we present novel strategies for rejuvenating the discovery process and advocate for renewed and enthusiastic investment in the antibacterial discovery pipeline.
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Affiliation(s)
- Sebastian Walesch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)SaarbrückenGermany,Department of PharmacySaarland UniversitySaarbrückenGermany,Helmholtz Centre for Infection research (HZI)BraunschweigGermany,German Center for infection research (DZIF)BraunschweigGermany
| | - Joy Birkelbach
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)SaarbrückenGermany,Department of PharmacySaarland UniversitySaarbrückenGermany,Helmholtz Centre for Infection research (HZI)BraunschweigGermany,German Center for infection research (DZIF)BraunschweigGermany
| | - Gwenaëlle Jézéquel
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)SaarbrückenGermany,Helmholtz Centre for Infection research (HZI)BraunschweigGermany
| | - F P Jake Haeckl
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)SaarbrückenGermany,Department of PharmacySaarland UniversitySaarbrückenGermany,Helmholtz Centre for Infection research (HZI)BraunschweigGermany,German Center for infection research (DZIF)BraunschweigGermany
| | - Julian D Hegemann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)SaarbrückenGermany,Department of PharmacySaarland UniversitySaarbrückenGermany,Helmholtz Centre for Infection research (HZI)BraunschweigGermany,German Center for infection research (DZIF)BraunschweigGermany
| | - Thomas Hesterkamp
- Helmholtz Centre for Infection research (HZI)BraunschweigGermany,German Center for infection research (DZIF)BraunschweigGermany
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)SaarbrückenGermany,Department of PharmacySaarland UniversitySaarbrückenGermany,Helmholtz Centre for Infection research (HZI)BraunschweigGermany,German Center for infection research (DZIF)BraunschweigGermany,Helmholtz International Lab for Anti‐InfectivesSaarbrückenGermany
| | - Peter Hammann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)SaarbrückenGermany,Department of PharmacySaarland UniversitySaarbrückenGermany,Helmholtz Centre for Infection research (HZI)BraunschweigGermany,German Center for infection research (DZIF)BraunschweigGermany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)SaarbrückenGermany,Department of PharmacySaarland UniversitySaarbrückenGermany,Helmholtz Centre for Infection research (HZI)BraunschweigGermany,German Center for infection research (DZIF)BraunschweigGermany,Helmholtz International Lab for Anti‐InfectivesSaarbrückenGermany
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24
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Maltarollo VG, Shevchenko E, Lima IDDM, Cino EA, Ferreira GM, Poso A, Kronenberger T. Do Go Chasing Waterfalls: Enoyl Reductase (FabI) in Complex with Inhibitors Stabilizes the Tetrameric Structure and Opens Water Channels. J Chem Inf Model 2022; 62:5746-5761. [PMID: 36343333 DOI: 10.1021/acs.jcim.2c01178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The enzyme enoyl-ACP reductase (FabI) is the limiting step of the membrane's fatty acid biosynthesis in bacteria and a druggable target for novel antibacterial agents. The FabI active form is a homotetramer, which displays the highest affinity to inhibitors. Herein, molecular dynamics studies were carried out using the structure of FabI in complex with known inhibitors to investigate their effects on tetramerization. Our results suggest that multimerization is essential for the integrity of the catalytic site and that inhibitor binding enables the multimerization by stabilizing the substrate binding loop (SBL, L:195-200) coupled with changes in the H4/5 (QR interface). We also observed that AFN-1252 (naphtpyridinone derivative) promotes unique conformational changes affecting monomer-monomer interfaces. These changes are induced by AFN-1252 interaction with key residues in the binding sites (Ala95, Tyr146, and Tyr156). In addition, the analysis of water trajectories indicated that AFN-1252 complexes allow more water molecules to enter the binding site than triclosan and MUT056399 complexes. FabI-AFN-1252 simulations show accumulation of water molecules near the Tyr146/147 pocket, which can become a hotspot to the design of novel FabI inhibitors.
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Affiliation(s)
- Vinicius Gonçalves Maltarollo
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), 31270-901 Belo Horizonte, Minas Gerais, Brazil
| | - Ekaterina Shevchenko
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.,Department of Oncology and Pneumonology, Internal Medicine VIII, University Hospital Tübingen, Otfried-Müller-Straße 10, DE72076 Tübingen, Germany.,Tübingen Center for Academic Drug Discovery & Development (TüCAD2), 72076 Tübingen, Germany
| | - Igor Daniel de Miranda Lima
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, Brazil
| | - Elio A Cino
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, Brazil
| | - Glaucio Monteiro Ferreira
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Av Prof Lineu Prestes 580, 05508-000 São Paulo, Brazil
| | - Antti Poso
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.,Department of Oncology and Pneumonology, Internal Medicine VIII, University Hospital Tübingen, Otfried-Müller-Straße 10, DE72076 Tübingen, Germany.,Tübingen Center for Academic Drug Discovery & Development (TüCAD2), 72076 Tübingen, Germany.,School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Thales Kronenberger
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.,Department of Oncology and Pneumonology, Internal Medicine VIII, University Hospital Tübingen, Otfried-Müller-Straße 10, DE72076 Tübingen, Germany.,Tübingen Center for Academic Drug Discovery & Development (TüCAD2), 72076 Tübingen, Germany.,School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211 Kuopio, Finland
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25
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Marciano S, Dey D, Listov D, Fleishman SJ, Sonn-Segev A, Mertens H, Busch F, Kim Y, Harvey SR, Wysocki VH, Schreiber G. Protein quaternary structures in solution are a mixture of multiple forms. Chem Sci 2022; 13:11680-11695. [PMID: 36320402 PMCID: PMC9555727 DOI: 10.1039/d2sc02794a] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 09/21/2022] [Indexed: 11/21/2022] Open
Abstract
Over half the proteins in the E. coli cytoplasm form homo or hetero-oligomeric structures. Experimentally determined structures are often considered in determining a protein's oligomeric state, but static structures miss the dynamic equilibrium between different quaternary forms. The problem is exacerbated in homo-oligomers, where the oligomeric states are challenging to characterize. Here, we re-evaluated the oligomeric state of 17 different bacterial proteins across a broad range of protein concentrations and solutions by native mass spectrometry (MS), mass photometry (MP), size exclusion chromatography (SEC), and small-angle X-ray scattering (SAXS), finding that most exhibit several oligomeric states. Surprisingly, some proteins did not show mass-action driven equilibrium between the oligomeric states. For approximately half the proteins, the predicted oligomeric forms described in publicly available databases underestimated the complexity of protein quaternary structures in solution. Conversely, AlphaFold multimer provided an accurate description of the potential multimeric states for most proteins, suggesting that it could help resolve uncertainties on the solution state of many proteins.
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Affiliation(s)
- Shir Marciano
- Department of Biomolecular Sciences, Weizmann Institute of Science Rehovot Israel
| | - Debabrata Dey
- Department of Biomolecular Sciences, Weizmann Institute of Science Rehovot Israel
| | - Dina Listov
- Department of Biomolecular Sciences, Weizmann Institute of Science Rehovot Israel
| | - Sarel J Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science Rehovot Israel
| | - Adar Sonn-Segev
- Refeyn Ltd 1 Electric Avenue, Ferry Hinksey Road Oxford OX2 0BY UK
| | - Haydyn Mertens
- Hamburg Outstation, European Molecular Biology Laboratory Notkestrasse 85 Hamburg 22607 Germany
| | - Florian Busch
- Department of Chemistry and Biochemistry, Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University Columbus OH 43210 USA
| | - Yongseok Kim
- Department of Chemistry and Biochemistry, Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University Columbus OH 43210 USA
| | - Sophie R Harvey
- Department of Chemistry and Biochemistry, Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University Columbus OH 43210 USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University Columbus OH 43210 USA
| | - Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science Rehovot Israel
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26
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Hopf FSM, Roth CD, de Souza EV, Galina L, Czeczot AM, Machado P, Basso LA, Bizarro CV. Bacterial Enoyl-Reductases: The Ever-Growing List of Fabs, Their Mechanisms and Inhibition. Front Microbiol 2022; 13:891610. [PMID: 35814645 PMCID: PMC9260719 DOI: 10.3389/fmicb.2022.891610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 05/27/2022] [Indexed: 11/13/2022] Open
Abstract
Enoyl-ACP reductases (ENRs) are enzymes that catalyze the last step of the elongation cycle during fatty acid synthesis. In recent years, new bacterial ENR types were discovered, some of them with structures and mechanisms that differ from the canonical bacterial FabI enzymes. Here, we briefly review the diversity of structural and catalytic properties of the canonical FabI and the new FabK, FabV, FabL, and novel ENRs identified in a soil metagenome study. We also highlight recent efforts to use the newly discovered Fabs as targets for drug development and consider the complex evolutionary history of this diverse set of bacterial ENRs.
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Affiliation(s)
- Fernanda S. M. Hopf
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Candida D. Roth
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| | - Eduardo V. de Souza
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Luiza Galina
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
- Programa de Pós-Graduação em Medicina e Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Alexia M. Czeczot
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
- Programa de Pós-Graduação em Medicina e Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Pablo Machado
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Luiz A. Basso
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
- Programa de Pós-Graduação em Medicina e Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Cristiano V. Bizarro
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
- *Correspondence: Cristiano V. Bizarro,
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Omar AZ, Alshaye NA, Mosa TM, El-Sadany SK, Hamed EA, El-Atawy MA. Synthesis and Antimicrobial Activity Screening of Piperazines Bearing N, N'-Bis(1,3,4-thiadiazole) Moiety as Probable Enoyl-ACP Reductase Inhibitors. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123698. [PMID: 35744824 PMCID: PMC9228617 DOI: 10.3390/molecules27123698] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 05/29/2022] [Accepted: 05/29/2022] [Indexed: 11/16/2022]
Abstract
A new N,N'-disubstituted piperazine conjugated with 1,3,4-thiadiazole and 1,2,4-triazole was prepared and the chemical structures were identified by IR, NMR and elemental analysis. All the prepared compounds were tested for their antimicrobial activity. The antimicrobial results indicated that the tested compounds showed significant antibacterial activity against gram-negative strains, especially E. coli, relative to gram-positive bacteria. Docking analysis was performed to support the biological results; binding modes with the active site of enoyl reductase amino acids from E. coli showed very good scores, ranging from -6.1090 to -9.6184 kcal/mol. Correlation analysis was performed for the inhibition zone (nm) and the docking score.
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Affiliation(s)
- Alaa Z. Omar
- Chemistry Department, Faculty of Science, Alexandria University, P.O. 426 Ibrahemia, Alexandria 21321, Egypt; (T.M.M.); (S.K.E.-S.); (E.A.H.)
- Correspondence: (A.Z.O.); (M.A.E.-A.)
| | - Najla A. Alshaye
- Department of Chemistry, College of Science, Princess Nourah Bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia;
| | - Tawfik M. Mosa
- Chemistry Department, Faculty of Science, Alexandria University, P.O. 426 Ibrahemia, Alexandria 21321, Egypt; (T.M.M.); (S.K.E.-S.); (E.A.H.)
| | - Samir K. El-Sadany
- Chemistry Department, Faculty of Science, Alexandria University, P.O. 426 Ibrahemia, Alexandria 21321, Egypt; (T.M.M.); (S.K.E.-S.); (E.A.H.)
| | - Ezzat A. Hamed
- Chemistry Department, Faculty of Science, Alexandria University, P.O. 426 Ibrahemia, Alexandria 21321, Egypt; (T.M.M.); (S.K.E.-S.); (E.A.H.)
| | - Mohamed A. El-Atawy
- Chemistry Department, Faculty of Science, Alexandria University, P.O. 426 Ibrahemia, Alexandria 21321, Egypt; (T.M.M.); (S.K.E.-S.); (E.A.H.)
- Chemistry Department, Faculty of Science, Taibah University, Yanbu 46423, Saudi Arabia
- Correspondence: (A.Z.O.); (M.A.E.-A.)
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28
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Kandsi F, Elbouzidi A, Lafdil FZ, Meskali N, Azghar A, Addi M, Hano C, Maleb A, Gseyra N. Antibacterial and Antioxidant Activity of Dysphania ambrosioides (L.) Mosyakin and Clemants Essential Oils: Experimental and Computational Approaches. Antibiotics (Basel) 2022; 11:482. [PMID: 35453233 PMCID: PMC9031865 DOI: 10.3390/antibiotics11040482] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/01/2022] [Accepted: 04/03/2022] [Indexed: 02/06/2023] Open
Abstract
Dysphania ambrosioides (L.) Mosyakin and Clemants, also known as Mexican tea, and locally known as Mkhinza, is a polymorphic annual and perennial herb, and it is widely used in folk medicine to treat a broad range of illnesses in Morocco. The aim of this study was to determine the phytochemical content and the antioxidant and the antibacterial properties of essential oils isolated from D. ambrosioides aerial components, growing in Eastern Morocco (Figuig). Hydrodistillation was used to separate D. ambrosioides essential oils, and the abundance of each phytocompound was determined by using Gas Chromatography coupled with Mass Spectrometry (GC-MS). In vitro 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging assay and inhibition of β-carotene/linoleic acid bleaching assays were used to determine D. ambrosioides essential oils' antioxidant activity. The findings revealed relative antioxidative power and modest radical scavenging. The antibacterial activity of the essential oils was broad-spectrum, with Escherichia coli, Staphylococcus aureus, and Enterococcus faecalis as the most susceptible strains tested. To elucidate the physicochemical nature, drug-likeness, and the antioxidant and antibacterial action of the identified phytocomponents, computational techniques, such as ADMET analysis, and molecular docking were used.
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Affiliation(s)
- Fahd Kandsi
- Laboratory of Bioresources, Biotechnology, Ethnopharmacology and Health, Faculty of Sciences, Mohammed First University, B.P. 717, Oujda 60000, Morocco; (F.K.); (F.Z.L.); (N.G.)
| | - Amine Elbouzidi
- Laboratoire d’Amélioration des Productions Agricoles, Biotechnologie et Environnement (LAPABE), Faculté des Sciences, Université Mohammed Premier, Oujda 60000, Morocco; (A.E.); (N.M.)
| | - Fatima Zahra Lafdil
- Laboratory of Bioresources, Biotechnology, Ethnopharmacology and Health, Faculty of Sciences, Mohammed First University, B.P. 717, Oujda 60000, Morocco; (F.K.); (F.Z.L.); (N.G.)
| | - Nada Meskali
- Laboratoire d’Amélioration des Productions Agricoles, Biotechnologie et Environnement (LAPABE), Faculté des Sciences, Université Mohammed Premier, Oujda 60000, Morocco; (A.E.); (N.M.)
| | - Ali Azghar
- Laboratoire de Microbiologie, Centre Hospitalier Universitaire (CHU), Oujda 60000, Morocco; (A.A.); (A.M.)
| | - Mohamed Addi
- Laboratoire d’Amélioration des Productions Agricoles, Biotechnologie et Environnement (LAPABE), Faculté des Sciences, Université Mohammed Premier, Oujda 60000, Morocco; (A.E.); (N.M.)
| | - Christophe Hano
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRAE USC1328, University of Orleans, CEDEX 2, 45067 Orléans, France
- Le StudiumInstitue for Advanced Studies, 1 Rue Dupanloup, 45000 Orléans, France
| | - Adil Maleb
- Laboratoire de Microbiologie, Centre Hospitalier Universitaire (CHU), Oujda 60000, Morocco; (A.A.); (A.M.)
| | - Nadia Gseyra
- Laboratory of Bioresources, Biotechnology, Ethnopharmacology and Health, Faculty of Sciences, Mohammed First University, B.P. 717, Oujda 60000, Morocco; (F.K.); (F.Z.L.); (N.G.)
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29
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Katiki M, Neetu N, Pratap S, Kumar P. Biochemical and structural basis for Moraxella catarrhalis enoyl-acyl carrier protein reductase (FabI) inhibition by triclosan and estradiol. Biochimie 2022; 198:8-22. [PMID: 35276316 DOI: 10.1016/j.biochi.2022.02.008] [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: 09/04/2021] [Revised: 02/06/2022] [Accepted: 02/22/2022] [Indexed: 11/02/2022]
Abstract
The enoyl-acyl carrier protein reductase (ENR) is an established drug target and catalyzes the last reduction step of the fatty acid elongation cycle. Here, we report the crystal structures of FabI from Moraxella catarrhalis (McFabI) in the apo form, binary complex with NAD+ and ternary complex with NAD + -triclosan (TCL) determined at 2.36, 2.12 and 2.22 Å resolutions, respectively. The comparative study of these three structures revealed three different conformational states for the substrate-binding loop (SBL), including an unstructured intermediate, a structured intermediate and a closed conformation in the apo, binary and ternary complex forms, respectively; indicating the flexibility of SBL during the ligand binding. Virtual screening has suggested that estradiol cypionate may be a potential inhibitor of McFabI. Subsequently, estradiol (EST), the natural form of estradiol cypionate, was assessed for its FabI-binding and -inhibition properties. In vitro studies demonstrated that TCL and EST bind to McFabI with high affinity (KD = 0.038 ± 0.004 and 5 ± 0.06 μM respectively) and inhibit its activity (Ki = 62.93 ± 3.95 nM and 25.97 ± 1.93 μM respectively) and suppress the growth of M. catarrhalis. These findings reveal that TCL and EST inhibit the McFabI activity and thereby affect cell growth. This study suggests that estradiol may be exploited as a novel scaffold for the designing and development of more potential FabI inhibitors.
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Affiliation(s)
- Madhusudhanarao Katiki
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Neetu Neetu
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Shivendra Pratap
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Pravindra Kumar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India.
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30
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Abstract
Ceragenins are a family of synthetic amphipathic molecules designed to mimic the properties of naturally occurring cationic antimicrobial peptides (CAMPs). Although ceragenins have potent antimicrobial activity, whether their mode of action is similar to that of CAMPs has remained elusive. Here, we reported the results of a comparative study of the bacterial responses to two well-studied CAMPs, LL37 and colistin, and two ceragenins with related structures, CSA13 and CSA131. Using transcriptomic and proteomic analyses, we found that Escherichia coli responded similarly to both CAMPs and ceragenins by inducing a Cpx envelope stress response. However, whereas E. coli exposed to CAMPs increased expression of genes involved in colanic acid biosynthesis, bacteria exposed to ceragenins specifically modulated functions related to phosphate transport, indicating distinct mechanisms of action between these two classes of molecules. Although traditional genetic approaches failed to identify genes that confer high-level resistance to ceragenins, using a Clustered Regularly Interspaced Short Palindromic Repeats interference (CRISPRi) approach we identified E. coli essential genes that when knocked down modify sensitivity to these molecules. Comparison of the essential gene-antibiotic interactions for each of the CAMPs and ceragenins identified both overlapping and distinct dependencies for their antimicrobial activities. Overall, this study indicated that, while some bacterial responses to ceragenins overlap those induced by naturally occurring CAMPs, these synthetic molecules target the bacterial envelope using a distinctive mode of action. IMPORTANCE The development of novel antibiotics is essential because the current arsenal of antimicrobials will soon be ineffective due to the widespread occurrence of antibiotic resistance. The development of naturally occurring cationic antimicrobial peptides (CAMPs) for therapeutics to combat antibiotic resistance has been hampered by high production costs and protease sensitivity, among other factors. The ceragenins are a family of synthetic CAMP mimics that kill a broad spectrum of bacterial species but are less expensive to produce, resistant to proteolytic degradation, and seemingly resistant to the development of high-level resistance. Determining how ceragenins function may identify new essential biological pathways of bacteria that are less prone to the development of resistance and will further our understanding of the design principles for maximizing the effects of synthetic CAMPs.
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31
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Hussein M, Wong LJ, Zhao J, Rees VE, Allobawi R, Sharma R, Rao GG, Baker M, Li J, Velkov T. Unique mechanistic insights into pathways associated with the synergistic activity of polymyxin B and caspofungin against multidrug-resistant Klebsiella pneumoniae. Comput Struct Biotechnol J 2022; 20:1077-1087. [PMID: 35284046 PMCID: PMC8897686 DOI: 10.1016/j.csbj.2022.02.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 11/03/2022] Open
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32
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Singh P, Verma RK, Chatterjee S. The diffusible signal factor synthase, RpfF, in Xanthomonas oryzae pv. oryzae is required for the maintenance of membrane integrity and virulence. MOLECULAR PLANT PATHOLOGY 2022; 23:118-132. [PMID: 34704368 PMCID: PMC8659556 DOI: 10.1111/mpp.13148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/03/2021] [Accepted: 09/24/2021] [Indexed: 05/12/2023]
Abstract
The Xanthomonas group of phytopathogens communicate with a fatty acid-like cell-cell signalling molecule, cis-11-2-methyl-dodecenoic acid, also known as diffusible signal factor (DSF). In the pathogen of rice, Xanthomonas oryzae pv. oryzae, DSF is involved in the regulation of several virulence-associated functions, including production and secretion of several cell wall hydrolysing type II secretion effectors. To understand the role of DSF in the secretion of type II effectors, we characterized DSF synthase-deficient (rpfF) and DSF-deficient, type II secretion (xpsE) double mutants. Mutant analysis by expression analysis, secretion assay, fatty acid analysis, and physiological studies indicated that rpfF mutants exhibit hypersecretion of several type II effectors due to a perturbed membrane and DSF is required for maintaining membrane integrity. The rpfF mutants exhibited significantly higher uptake of 1-N-phenylnapthylamine and ethidium bromide, and up-regulation of rpoE (σE ). Increasing the osmolarity of the medium could rescue the hypersecretion phenotype of the rpfF mutant. The rpfF mutant exhibited highly reduced virulence. We report for the first time that in X. oryzae pv. oryzae RpfF is involved in the maintenance of membrane integrity by playing a regulatory role in the fatty acid synthesis pathway.
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Affiliation(s)
- Prashantee Singh
- Laboratory of Plant Microbe InteractionsCentre for DNA Fingerprinting and DiagnosticsUppalIndia
- Graduate StudiesManipal Academy of Higher EducationMangaluruIndia
| | - Raj Kumar Verma
- Laboratory of Plant Microbe InteractionsCentre for DNA Fingerprinting and DiagnosticsUppalIndia
| | - Subhadeep Chatterjee
- Laboratory of Plant Microbe InteractionsCentre for DNA Fingerprinting and DiagnosticsUppalIndia
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33
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Whaley SG, Radka CD, Subramanian C, Frank MW, Rock CO. Malonyl-acyl carrier protein decarboxylase activity promotes fatty acid and cell envelope biosynthesis in Proteobacteria. J Biol Chem 2021; 297:101434. [PMID: 34801557 PMCID: PMC8666670 DOI: 10.1016/j.jbc.2021.101434] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/02/2021] [Accepted: 11/09/2021] [Indexed: 11/20/2022] Open
Abstract
Bacterial fatty acid synthesis in Escherichia coli is initiated by the condensation of an acetyl-CoA with a malonyl-acyl carrier protein (ACP) by the β-ketoacyl-ACP synthase III enzyme, FabH. E. coli ΔfabH knockout strains are viable because of the yiiD gene that allows FabH-independent fatty acid synthesis initiation. However, the molecular function of the yiiD gene product is not known. Here, we show the yiiD gene product is a malonyl-ACP decarboxylase (MadA). MadA has two independently folded domains: an amino-terminal N-acetyl transferase (GNAT) domain (MadAN) and a carboxy-terminal hot dog dimerization domain (MadAC) that encodes the malonyl-ACP decarboxylase function. Members of the proteobacterial Mad protein family are either two domain MadA (GNAT-hot dog) or standalone MadB (hot dog) decarboxylases. Using structure-guided, site-directed mutagenesis of MadB from Shewanella oneidensis, we identified Asn45 on a conserved catalytic loop as critical for decarboxylase activity. We also found that MadA, MadAC, or MadB expression all restored normal cell size and growth rates to an E. coli ΔfabH strain, whereas the expression of MadAN did not. Finally, we verified that GlmU, a bifunctional glucosamine-1-phosphate N-acetyl transferase/N-acetyl-glucosamine-1-phosphate uridylyltransferase that synthesizes the key intermediate UDP-GlcNAc, is an ACP binding protein. Acetyl-ACP is the preferred glucosamine-1-phosphate N-acetyl transferase/N-acetyl-glucosamine-1-phosphate uridylyltransferase substrate, in addition to being the substrate for the elongation-condensing enzymes FabB and FabF. Thus, we conclude that the Mad family of malonyl-ACP decarboxylases supplies acetyl-ACP to support the initiation of fatty acid, lipopolysaccharide, peptidoglycan, and enterobacterial common antigen biosynthesis in Proteobacteria.
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Affiliation(s)
- Sarah G Whaley
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Christopher D Radka
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Chitra Subramanian
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Matthew W Frank
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Charles O Rock
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee, USA.
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34
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Pang D, Huang Z, Li Q, Wang E, Liao S, Li E, Zou Y, Wang W. Antibacterial Mechanism of Cinnamaldehyde: Modulation of Biosynthesis of Phosphatidylethanolamine and Phosphatidylglycerol in Staphylococcus aureus and Escherichia coli. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:13628-13636. [PMID: 34739242 DOI: 10.1021/acs.jafc.1c04977] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Cinnamaldehyde is a natural antimicrobial food preservative. Previous studies have suggested that cinnamaldehyde interacts with the cell membrane, but the molecular targets of cinnamaldehyde action on foodborne pathogens are still unclear. In this study, the structural changes of Staphylococcus aureus and Escherichia coli cells were observed after cinnamaldehyde treatment. Then, quantitative real-time polymerase chain reaction (PCR) and parallel reaction monitoring were used for determining the effects of cinnamaldehyde treatment of these bacteria on the expression of genes and proteins associated with glycerophospholipid biosynthesis. Changes in fatty acids (raw materials for the biosynthesis of glycerophospholipids) and glycerophospholipids in S. aureus and E. coli after cinnamaldehyde treatment were analyzed to confirm the results of gene and protein expression experiments. Cinnamaldehyde regulated the glycerophospholipid biosynthesis pathways of these foodborne pathogens, mainly targeting phosphatidylglycerol and phosphatidylethanolamine, which resulted in the disruption of cell membrane integrity.
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Affiliation(s)
- Daorui Pang
- Sericultural & Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences; Guangdong Key Laboratory of Agricultural Products Processing; Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs, Guangzhou 510610, Guangdong, China
| | - Zhaoxiang Huang
- Sericultural & Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences; Guangdong Key Laboratory of Agricultural Products Processing; Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs, Guangzhou 510610, Guangdong, China
| | - Qian Li
- Sericultural & Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences; Guangdong Key Laboratory of Agricultural Products Processing; Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs, Guangzhou 510610, Guangdong, China
| | - Erpei Wang
- Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla 92037, California, United States
| | - Sentai Liao
- Sericultural & Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences; Guangdong Key Laboratory of Agricultural Products Processing; Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs, Guangzhou 510610, Guangdong, China
| | - Erna Li
- Sericultural & Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences; Guangdong Key Laboratory of Agricultural Products Processing; Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs, Guangzhou 510610, Guangdong, China
| | - Yuxiao Zou
- Sericultural & Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences; Guangdong Key Laboratory of Agricultural Products Processing; Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs, Guangzhou 510610, Guangdong, China
| | - Weifei Wang
- Sericultural & Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences; Guangdong Key Laboratory of Agricultural Products Processing; Key Laboratory of Functional Foods, Ministry of Agriculture and Rural Affairs, Guangzhou 510610, Guangdong, China
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35
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Ali S, Alam M, Hasan GM, Hassan MI. Potential therapeutic targets of Klebsiella pneumoniae: a multi-omics review perspective. Brief Funct Genomics 2021; 21:63-77. [PMID: 34448478 DOI: 10.1093/bfgp/elab038] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/03/2021] [Accepted: 08/04/2021] [Indexed: 11/15/2022] Open
Abstract
The multidrug resistance developed in many organisms due to the prolonged use of antibiotics has been an increasing global health crisis. Klebsiella pneumoniae is a causal organism for various infections, including respiratory, urinary tract and biliary diseases. Initially, immunocompromised individuals are primarily affected by K. pneumoniae. Due to the emergence of hypervirulent strains recently, both healthy and immunocompetent individuals are equally susceptible to K. pneumoniae infections. The infections caused by multidrug-resistant and hypervirulent K. pneumoniae strains are complicated to treat, illustrating an urgent need to develop novel and more practical approaches to combat the pathogen. We focused on the previously performed high-throughput analyses by other groups to discover several novel enzymes that may be considered attractive drug targets of K. pneumoniae. These targets qualify most of the selection criteria for drug targeting, including an absence of its homolog's gene in the host. The capsule, lipopolysaccharide, fimbriae, siderophores and essential virulence factors facilitate the pathogen entry, infection and survival inside the host. This review discusses K. pneumoniae pathophysiology, including its virulence determinants and further the potential drug targets that might facilitate the discovery of novel drugs and effective treatment regimens shortly.
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Affiliation(s)
- Sabeeha Ali
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar New Delhi 110025, India
| | - Manzar Alam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar New Delhi 110025, India
| | - Gulam Mustafa Hasan
- Department of Biochemistry, College of Medicine, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar New Delhi 110025, India
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Paiva P, Medina FE, Viegas M, Ferreira P, Neves RPP, Sousa JPM, Ramos MJ, Fernandes PA. Animal Fatty Acid Synthase: A Chemical Nanofactory. Chem Rev 2021; 121:9502-9553. [PMID: 34156235 DOI: 10.1021/acs.chemrev.1c00147] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Fatty acids are crucial molecules for most living beings, very well spread and conserved across species. These molecules play a role in energy storage, cell membrane architecture, and cell signaling, the latter through their derivative metabolites. De novo synthesis of fatty acids is a complex chemical process that can be achieved either by a metabolic pathway built by a sequence of individual enzymes, such as in most bacteria, or by a single, large multi-enzyme, which incorporates all the chemical capabilities of the metabolic pathway, such as in animals and fungi, and in some bacteria. Here we focus on the multi-enzymes, specifically in the animal fatty acid synthase (FAS). We start by providing a historical overview of this vast field of research. We follow by describing the extraordinary architecture of animal FAS, a homodimeric multi-enzyme with seven different active sites per dimer, including a carrier protein that carries the intermediates from one active site to the next. We then delve into this multi-enzyme's detailed chemistry and critically discuss the current knowledge on the chemical mechanism of each of the steps necessary to synthesize a single fatty acid molecule with atomic detail. In line with this, we discuss the potential and achieved FAS applications in biotechnology, as biosynthetic machines, and compare them with their homologous polyketide synthases, which are also finding wide applications in the same field. Finally, we discuss some open questions on the architecture of FAS, such as their peculiar substrate-shuttling arm, and describe possible reasons for the emergence of large megasynthases during evolution, questions that have fascinated biochemists from long ago but are still far from answered and understood.
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Affiliation(s)
- Pedro Paiva
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Fabiola E Medina
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Autopista Concepción-Talcahuano, 7100 Talcahuano, Chile
| | - Matilde Viegas
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro Ferreira
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Rui P P Neves
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - João P M Sousa
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Maria J Ramos
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro A Fernandes
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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37
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Calvelo VY, Crisante D, Elliot M, Nodwell JR. The ARC2 response in Streptomcyes coelicolor requires the global regulatory genes afsR and afsS. MICROBIOLOGY-SGM 2021; 167. [PMID: 33945461 DOI: 10.1099/mic.0.001047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
ARC2 is a synthetic compound, related in structure and mechanism to the antibiotic triclosan, that activates the production of many specialized metabolites in the Streptomyces genus of bacteria. In this work, we demonstrate that the addition of ARC2 to Streptomyces coelicolor cultures results in considerable alterations in overall gene expression including most notably the specialized metabolic genes. Using actinorhodin production as a model system, we show that the effect of ARC2 depends on the pleiotropic regulators afsR and afsS but not afsK. We find that the constitutive expression of afsS can bypass the need for afsR but not the reverse, while the constitutive expression of afsK had no effect on actinorhodin production. These data are consistent with a model in which ARC2 activates a cell stress response that depends on AfsR activating the expression of the afsS gene such that AfsS then triggers the production of actinorhodin.
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Affiliation(s)
- Vanessa Yoon Calvelo
- Department of Biochemistry University of Toronto MaRS Discovery District 661 University Avenue Toronto, Ontario CANADA M5G 1M1, Canada
| | - David Crisante
- Department of Biology McMaster University 1280 Main Street West Hamilton, Ontario CANADA L8S 4K1, Canada
| | - Marie Elliot
- Department of Biology McMaster University 1280 Main Street West Hamilton, Ontario CANADA L8S 4K1, Canada
| | - Justin Rea Nodwell
- Department of Biochemistry University of Toronto MaRS Discovery District 661 University Avenue Toronto, Ontario CANADA M5G 1M1, Canada
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38
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Eltschkner S, Kehrein J, Le TA, Davoodi S, Merget B, Basak S, Weinrich JD, Schiebel J, Tonge PJ, Engels B, Sotriffer C, Kisker C. A Long Residence Time Enoyl-Reductase Inhibitor Explores an Extended Binding Region with Isoenzyme-Dependent Tautomer Adaptation and Differential Substrate-Binding Loop Closure. ACS Infect Dis 2021; 7:746-758. [PMID: 33710875 DOI: 10.1021/acsinfecdis.0c00437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The enoyl-acyl carrier protein (ACP) reductase (ENR) is a key enzyme within the bacterial fatty-acid synthesis pathway. It has been demonstrated that small-molecule inhibitors carrying the diphenylether (DPE) scaffold bear a great potential for the development of highly specific and effective drugs against this enzyme class. Interestingly, different substitution patterns of the DPE scaffold have been shown to lead to varying effects on the kinetic and thermodynamic behavior toward ENRs from different organisms. Here, we investigated the effect of a 4'-pyridone substituent in the context of the slow tight-binding inhibitor SKTS1 on the inhibition of the Staphylococcus aureus enoyl-ACP-reductase saFabI and the closely related isoenzyme from Mycobacterium tuberculosis, InhA, and explored a new interaction site of DPE inhibitors within the substrate-binding pocket. Using high-resolution crystal structures of both complexes in combination with molecular dynamics (MD) simulations, kinetic measurements, and quantum mechanical (QM) calculations, we provide evidence that the 4'-pyridone substituent adopts different tautomeric forms when bound to the two ENRs. We furthermore elucidate the structural determinants leading to significant differences in the residence time of SKTS1 on both enzymes.
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Affiliation(s)
- Sandra Eltschkner
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, University of Würzburg, 97080 Würzburg, Germany
- Molecular Ecology and Evolution Lab, Department of Biology, Lund University, 223 62 Lund, Sweden
| | - Josef Kehrein
- Institute of Pharmacy and Food Chemistry, University of Würzburg, 97074 Würzburg, Germany
| | - Thien Anh Le
- Institute of Physical and Theoretical Chemistry, University of Würzburg, 97074 Würzburg, Germany
- Department of Experimental Physics 5 (Biophysics), University of Würzburg, 97074 Würzburg, Germany
| | - Shabnam Davoodi
- Institute for Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Benjamin Merget
- Institute of Pharmacy and Food Chemistry, University of Würzburg, 97074 Würzburg, Germany
| | - Sneha Basak
- Institute for Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Jonas D. Weinrich
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, University of Würzburg, 97080 Würzburg, Germany
- Department of Microbiology, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Johannes Schiebel
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Peter J. Tonge
- Institute for Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Bernd Engels
- Institute of Physical and Theoretical Chemistry, University of Würzburg, 97074 Würzburg, Germany
| | - Christoph Sotriffer
- Institute of Pharmacy and Food Chemistry, University of Würzburg, 97074 Würzburg, Germany
| | - Caroline Kisker
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, University of Würzburg, 97080 Würzburg, Germany
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Qumar U, Hassan J, Naz S, Haider A, Raza A, Ul-Hamid A, Haider J, Shahzadi I, Ahmad I, Ikram M. Silver decorated 2D nanosheets of GO and MoS 2serve as nanocatalyst for water treatment and antimicrobial applications as ascertained with molecular docking evaluation. NANOTECHNOLOGY 2021; 32:255704. [PMID: 33556921 DOI: 10.1088/1361-6528/abe43c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 02/08/2021] [Indexed: 06/12/2023]
Abstract
In this work, synthesis of graphene oxide (GO) and reduced graphene oxide (rGO) was realized through a modified Hummers route. Different concentrations (5 and 10 wt%) of Ag were doped in MoS2and rGO using a hydrothermal technique. Synthesized Ag-MoS2and Ag-rGO were evaluated through XRD that confirmed the hexagonal structure of MoS2along with the transformation of GO to Ag-rGO as indicated by a shift in XRD peaks while Mo-O bonding and S=O functional groups were confirmed with FTIR. Morphological information of GO and formation of MoS2nanopetals as well as interlayer spacing were verified through FESEM and HRTEM respectively. Raman analysis was employed to probe any evidence regarding defect densities of GO. Optical properties of GO, MoS2, Ag-rGO, and Ag-MoS2were visualized through UV-vis and PL spectroscopy. Prepared products were employed as nanocatalysts to purify industrial wastewater. Experimental results revealed that Ag-rGO and Ag-MoS2showed 99% and 80% response in photocatalytic activity. Besides, the nanocatalyst (Ag-MoS2and Ag-rGO) exhibited 6.05 mm inhibition zones againstS. aureusgram positive (G+) and 3.05 mm forE. coligram negative (G-) in antibacterial activity. To rationalize biocidal mechanism of Ag-doped MoS2NPs and Ag-rGO,in silicomolecular docking study was employed for two enzymes i.e.β-lactamase and D-alanine-D-alanine ligase B (ddlB) from cell wall biosynthetic pathway and enoyl-[acylcarrier-protein] reductase (FabI) from fatty acid biosynthetic pathway belonging toS. aureus. The present study provides evidence for the development of cost-effective, environment friendly and viable candidate for photocatalytic and antimicrobial applications.
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Affiliation(s)
- U Qumar
- Department of Physics, Riphah Institute of Computing and Applied Sciences (RICAS), Riphah International University, 14 Ali Road, Lahore, Pakistan
| | - J Hassan
- Department of Physics, Riphah Institute of Computing and Applied Sciences (RICAS), Riphah International University, 14 Ali Road, Lahore, Pakistan
| | - S Naz
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, People's Republic of China
| | - A Haider
- Department of Clinical Medicine and Surgery, University of Veterinary and Animal Sciences, Lahore 54000, Punjab, Pakistan
| | - A Raza
- Department of Physics, Riphah Institute of Computing and Applied Sciences (RICAS), Riphah International University, 14 Ali Road, Lahore, Pakistan
| | - A Ul-Hamid
- Center for Engineering Research, Research Institute, King Fahd University of Petroleum & Minerals, Dhahran, 31261, Saudi Arabia
| | - J Haider
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, People's Republic of China
| | - I Shahzadi
- College of Pharmacy, University of the Punjab, Lahore, 54000, Pakistan
| | - I Ahmad
- Department of Chemistry, Allama Iqbal Open University, Islamabad 44000, Pakistan
| | - M Ikram
- Solar Cell Applications Research Lab, Department of Physics, Government College University Lahore, 54000, Punjab, Pakistan
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40
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Bartholow TG, Sztain T, Patel A, Lee DJ, Young MA, Abagyan R, Burkart MD. Elucidation of transient protein-protein interactions within carrier protein-dependent biosynthesis. Commun Biol 2021; 4:340. [PMID: 33727677 PMCID: PMC7966745 DOI: 10.1038/s42003-021-01838-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 02/11/2021] [Indexed: 01/31/2023] Open
Abstract
Fatty acid biosynthesis (FAB) is an essential and highly conserved metabolic pathway. In bacteria, this process is mediated by an elaborate network of protein•protein interactions (PPIs) involving a small, dynamic acyl carrier protein that interacts with dozens of other partner proteins (PPs). These PPIs have remained poorly characterized due to their dynamic and transient nature. Using a combination of solution-phase NMR spectroscopy and protein-protein docking simulations, we report a comprehensive residue-by-residue comparison of the PPIs formed during FAB in Escherichia coli. This technique describes and compares the molecular basis of six discrete binding events responsible for E. coli FAB and offers insights into a method to characterize these events and those in related carrier protein-dependent pathways.
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Affiliation(s)
- Thomas G Bartholow
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Terra Sztain
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Ashay Patel
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - D John Lee
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
- Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Megan A Young
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Ruben Abagyan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, USA
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA.
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41
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Costa Júnior DB, Araújo JSC, Oliveira LDM, Neri FSM, Moreira POL, Taranto AG, Fonseca AL, Varotti FDP, Leite FHA. A novel antiplasmodial compound: integration of in silico and in vitro assays. J Biomol Struct Dyn 2021; 40:6295-6307. [PMID: 33554762 DOI: 10.1080/07391102.2021.1882339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Malaria is a disease caused by Plasmodium genus. which P. falciparum is responsible for the most severe form of the disease, cerebral malaria. In 2018, 405,000 people died of malaria. Antimalarial drugs have serious adverse effects and limited efficacy due to multidrug-resistant strains. One way to overcome these limitations is the use of computational approaches for prioritizing candidates to phenotypic assays and/or in vitro assays against validated targets. Plasmodium falciparum Enoyl-ACP reductase (PfENR) is noteworthy because it catalyzes the rate-limiting step of the biosynthetic pathway of fatty acid. Thus, the study aimed to identify potential PfENR inhibitors by ligand (2D molecular similarity and pharmacophore models) and structure-based virtual screening (molecular docking). 2D similarity-based virtual screening using Tanimoto Index (> 0.45) selected 29,236 molecules from natural products subset available in ZINC database (n = 181,603). Next, 10 pharmacophore models for PfENR inhibitors were generated and evaluated based on the internal statistical parameters from GALAHAD™ and ROC/AUC curve. These parameters selected a suitable pharmacophore model with one hydrophobic center and two hydrogen bond acceptors. The alignment of the filtered molecules on best pharmacophore model resulted in the selection of 10,977 molecules. These molecules were directed to the docking-based virtual screening by AutoDock Vina 1.1.2 program. These strategies selected one compound to phenotypic assays against parasite. ZINC630259 showed EC50 = 0.12 ± 0.018 µM in antiplasmodial assays and selective index similar to other antimalarial drugs. Finally, MM/PBSA method showed stability of molecule within PfENR binding site (ΔGbinding=-57.337 kJ/mol).Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- David Bacelar Costa Júnior
- Programa de pós-graduação em Biotecnologia, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
| | | | - Larissa de Mattos Oliveira
- Programa de pós-graduação em Biotecnologia, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
| | - Flávio Simas Moreira Neri
- Programa de pós-graduação em Ciências Farmacêuticas, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
| | | | - Alex Gutterres Taranto
- Laboratório de Bioinformática e Desenho de Fármacos, Universidade Federal de São João Del-Rei, Feira de Santana, Brazil
| | - Amanda Luisa Fonseca
- Laboratório de Bioquímica Medicinal, Universidade Federal de São João Del-Rei, Feira de Santana, Brazil
| | - Fernando de Pilla Varotti
- Laboratório de Bioquímica Medicinal, Universidade Federal de São João Del-Rei, Feira de Santana, Brazil
| | - Franco Henrique Andrade Leite
- Programa de pós-graduação em Biotecnologia, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil.,Programa de pós-graduação em Ciências Farmacêuticas, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil.,Laboratório de Qumioinformática e Avaliação Biológica, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
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42
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Ye Z, Moreb EA, Li S, Lebeau J, Menacho-Melgar R, Munson M, Lynch MD. Escherichia coli Cas1/2 Endonuclease Complex Modifies Self-Targeting CRISPR/Cascade Spacers Reducing Silencing Guide Stability. ACS Synth Biol 2021; 10:29-37. [PMID: 33331764 DOI: 10.1021/acssynbio.0c00398] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
CRISPR-based interference has become common in various applications from genetic circuits to dynamic metabolic control. In E. coli, the native CRISPR Cascade system can be utilized for silencing by deletion of the cas3 nuclease along with expression of guide RNA arrays, where multiple genes can be silenced from a single transcript. We notice the loss of spacer sequences from guide arrays utilized for dynamic silencing. We report that unstable guide arrays are due to expression of the Cas1/2 endonuclease complex. We propose a model wherein basal Cas1/2 endonuclease activity results in the loss of spacers from guide arrays. Subsequently, mutant guide arrays can be amplified through selection. Replacing a constitutive promoter driving Cascade complex expression with a tightly controlled inducible promoter improves guide array stability, while minimizing leaky gene silencing. Additionally, these results demonstrate the potential of Cas1/2 mediated guide deletion as a mechanism to avoid CRISPR based autoimmunity.
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Affiliation(s)
- Zhixia Ye
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
- DMC Biotechnologies, Inc., Durham, North Carolina 27701, United States
| | - Eirik A Moreb
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Shuai Li
- DMC Biotechnologies, Inc., Durham, North Carolina 27701, United States
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Juliana Lebeau
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Romel Menacho-Melgar
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Matthew Munson
- DMC Biotechnologies, Inc., Durham, North Carolina 27701, United States
| | - Michael D Lynch
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
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43
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Cools F, Delputte P, Cos P. The search for novel treatment strategies for Streptococcus pneumoniae infections. FEMS Microbiol Rev 2021; 45:6064299. [PMID: 33399826 PMCID: PMC8371276 DOI: 10.1093/femsre/fuaa072] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 01/01/2021] [Indexed: 12/13/2022] Open
Abstract
This review provides an overview of the most important novel treatment strategies against Streptococcus pneumoniae infections published over the past 10 years. The pneumococcus causes the majority of community-acquired bacterial pneumonia cases, and it is one of the prime pathogens in bacterial meningitis. Over the last 10 years, extensive research has been conducted to prevent severe pneumococcal infections, with a major focus on (i) boosting the host immune system and (ii) discovering novel antibacterials. Boosting the immune system can be done in two ways, either by actively modulating host immunity, mostly through administration of selective antibodies, or by interfering with pneumococcal virulence factors, thereby supporting the host immune system to effectively overcome an infection. While several of such experimental therapies are promising, few have evolved to clinical trials. The discovery of novel antibacterials is hampered by the high research and development costs versus the relatively low revenues for the pharmaceutical industry. Nevertheless, novel enzymatic assays and target-based drug design, allow the identification of targets and the development of novel molecules to effectively treat this life-threatening pathogen.
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Affiliation(s)
- F Cools
- Laboratory for Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - P Delputte
- Laboratory for Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - P Cos
- Laboratory for Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
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44
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Yogiara, Mordukhova EA, Kim D, Kim WG, Hwang JK, Pan JG. The food-grade antimicrobial xanthorrhizol targets the enoyl-ACP reductase (FabI) in Escherichia coli. Bioorg Med Chem Lett 2020; 30:127651. [PMID: 33130290 DOI: 10.1016/j.bmcl.2020.127651] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 10/14/2020] [Accepted: 10/24/2020] [Indexed: 11/28/2022]
Abstract
Xanthorrhizol, isolated from the Indonesian Java turmeric Curcuma xanthorrhiza, displays broad-spectrum antibacterial activity. We report herein the evidence that mechanism of action of xanthorrhizol may involve FabI, an enoyl-(ACP) reductase, inhibition. The predicted Y156V substitution in the FabI enzyme promoted xanthorrhizol resistance, while the G93V mutation originally known for triclosan resistance was not effective against xanthorrhizol. Two other mutations, F203L and F203V, conferred FabI enzyme resistance to both xanthorrhizol and triclosan. These results showed that xanthorrhizol is a food-grade antimicrobial compound targeting FabI but with a different mode of binding from triclosan.
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Affiliation(s)
- Yogiara
- Department of Biotechnology, Yonsei University, 50-Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea; Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, Jalan Jenderal Sudirman 51, Jakarta 12930, Indonesia.
| | - Elena A Mordukhova
- GenoFocus Inc., 65 Techno 1-ro, Gwanpyeong-dong, Yuseong-gu, Daejeon 34014, Republic of Korea.
| | - Dooil Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 111 Gwahangno, Yuseong, Daejeon 34141, Republic of Korea.
| | - Won-Gon Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 111 Gwahangno, Yuseong, Daejeon 34141, Republic of Korea.
| | - Jae-Kwan Hwang
- Department of Biotechnology, Yonsei University, 50-Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea.
| | - Jae-Gu Pan
- GenoFocus Inc., 65 Techno 1-ro, Gwanpyeong-dong, Yuseong-gu, Daejeon 34014, Republic of Korea; Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 111 Gwahangno, Yuseong, Daejeon 34141, Republic of Korea.
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45
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Shahriar S, Ahsan T, Khan A, Akhteruzzaman S, Shehreen S, Sajib AA. Aspartame, acesulfame K and sucralose- influence on the metabolism of Escherichia coli. Metabol Open 2020; 8:100072. [PMID: 33336183 PMCID: PMC7732866 DOI: 10.1016/j.metop.2020.100072] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 11/18/2020] [Accepted: 12/02/2020] [Indexed: 12/13/2022] Open
Abstract
Gut microbes play a crucial role in the maintenance of human health. Components in the diet of the host affect their metabolism and diversity. Here, we investigated the influences of three commonly used non-caloric artificial sweeteners-aspartame, acesulfame K and sucralose-on the growth and metabolism of an omnipresent gut microbe Escherichia coli K-12. Methods: Growth of E. coli in the presence of aspartame, acesulfame K and sucralose in media was assessed and the influences of these artificial sweeteners on metabolism were investigated by relative expression analysis of genes encoding the rate limiting steps of important metabolic pathways as well as their global metabolomic profiles. Results: As a whole, E. coli growth was inhibited by aspartame and induced by acesulfame potassium, while the effect of sucralose on growth was less prominent. Although the expressions of multiple key enzymes that regulate important metabolic pathways were significantly altered by all three sweeteners, acesulfame K caused the most notable changes in this regard. In multivariate analysis with the metabolite profiles, the sucralose-treated cells clustered the closest to the untreated cells, while the acesulfame potassium treated cells were the most distant. These sweeteners affect multiple metabolic pathways in E. coli, which include propanoate, phosphonate, phosphinate and fatty acid metabolism, pentose phosphate pathway, and biosynthesis of several amino acids including lysine and the aromatic amino acids. Similar to the gene expression pattern, acesulfame potassium treated E. coli showed the largest deviation in their metabolite profiles compared to the untreated cells.
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Affiliation(s)
- Shayan Shahriar
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Tamim Ahsan
- Department of Genetic Engineering & Biotechnology, Bangabandhu Sheikh Mujibur Rahman Maritime University, Dhaka, Bangladesh
| | - Abira Khan
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Sharif Akhteruzzaman
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Saadlee Shehreen
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Abu Ashfaqur Sajib
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh
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46
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Ibrahim ZY, Uzairu A, Shallangwa G, Abechi S. Theoretical design of novel antimalarial agents against P. falciparum strain, Dd 2 through the QSAR modeling of synthesized 2'-substituted triclosan derivatives. Heliyon 2020; 6:e05032. [PMID: 33015389 PMCID: PMC7522386 DOI: 10.1016/j.heliyon.2020.e05032] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 08/21/2020] [Accepted: 09/18/2020] [Indexed: 01/21/2023] Open
Abstract
In an attempt to design compounds with higher antimalarial activities, quantitative structure-activity relationship (QSAR) technique was utilized in the development of a molecular model for some synthesized 2′-substituted triclosan derivatives through a hybrid of the GA-MLR method. The model was found to have excellent statistical parameters (R2 = 0.8919, R2Adj = 0.8728, LOF = 0.2563). The descriptors mean effect (MF) revealed BCUTw-1l, which increases with an increase in molecular weight, to be the most contributive to the antimalarial activity. Consequently, compound 3, with the highest activities (pEC50 = 6.9586) was deployed as the design template. The molecular weight of the template was increasing through substitutions of its atoms at several positions with heavier atoms/groups to increases the descriptor (BCUTw-1l) value. Twelves (12) theoretical derivatives of the template were designed where six of the designed derivatives have better activity than the design template. The most active designed compound, 3L was found to have the highest antimalarial activity (pEC50 = 7.930) than that of the design template.
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Affiliation(s)
- Zakari Ya'u Ibrahim
- Department of Chemistry, Faculty of Physical Sciences, Ahmadu Bello University, P.M.B 1045, Zaria, Nigeria
| | - Adamu Uzairu
- Department of Chemistry, Faculty of Physical Sciences, Ahmadu Bello University, P.M.B 1045, Zaria, Nigeria
| | - Gideon Shallangwa
- Department of Chemistry, Faculty of Physical Sciences, Ahmadu Bello University, P.M.B 1045, Zaria, Nigeria
| | - Stephen Abechi
- Department of Chemistry, Faculty of Physical Sciences, Ahmadu Bello University, P.M.B 1045, Zaria, Nigeria
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Akolkar HN, Dengale SG, Deshmukh KK, Karale BK, Darekar NR, Khedkar VM, Shaikh MH. Design, Synthesis and Biological Evaluation of Novel Furan & Thiophene Containing Pyrazolyl Pyrazolines as Antimalarial Agents. Polycycl Aromat Compd 2020. [DOI: 10.1080/10406638.2020.1821231] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Hemantkumar N. Akolkar
- P.G. and Research, Department of Chemistry, Radhabai Kale Mahila Mahavidyalaya, Ahmednagar, India
| | - Sujata G. Dengale
- P.G. and Research, Department of Chemistry, Sangamner Nagarpalika Arts, D. J. Malpani Commerce, B.N. Sarada Science College, Sangamner, India
| | - Keshav K. Deshmukh
- P.G. and Research, Department of Chemistry, Sangamner Nagarpalika Arts, D. J. Malpani Commerce, B.N. Sarada Science College, Sangamner, India
| | - Bhausaheb K. Karale
- P.G. and Research, Department of Chemistry, Radhabai Kale Mahila Mahavidyalaya, Ahmednagar, India
| | - Nirmala R. Darekar
- P.G. and Research, Department of Chemistry, Radhabai Kale Mahila Mahavidyalaya, Ahmednagar, India
| | - Vijay M. Khedkar
- Department of Pharmaceutical Chemistry, School of Pharmacy, Vishwakarma University, Pune, India
| | - Mubarak H. Shaikh
- P.G. and Research, Department of Chemistry, Radhabai Kale Mahila Mahavidyalaya, Ahmednagar, India
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Posttranslational Control of PlsB Is Sufficient To Coordinate Membrane Synthesis with Growth in Escherichia coli. mBio 2020; 11:mBio.02703-19. [PMID: 32817111 PMCID: PMC7439487 DOI: 10.1128/mbio.02703-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
How do bacterial cells grow without breaking their membranes? Although the biochemistry of fatty acid and membrane synthesis is well known, how membrane synthesis is balanced with growth and metabolism has remained unclear. This is partly due to the many control points that have been discovered within the membrane synthesis pathways. By precisely establishing the contributions of individual pathway enzymes, our results simplify the model of membrane biogenesis in the model bacterial species Escherichia coli. Specifically, we found that allosteric control of a single enzyme, PlsB, is sufficient to balance growth with membrane synthesis and to ensure that growing E. coli cells produce sufficient membrane. Identifying the signals that activate and deactivate PlsB will resolve the issue of how membrane synthesis is synchronized with growth. Every cell must produce enough membrane to contain itself. However, the mechanisms by which the rate of membrane synthesis is coupled with the rate of cell growth remain unresolved. By comparing substrate and enzyme concentrations of the fatty acid and phospholipid synthesis pathways of Escherichia coli across a 3-fold range of carbon-limited growth rates, we show that the rate of membrane phospholipid synthesis during steady-state growth is determined principally through allosteric control of a single enzyme, PlsB. Due to feedback regulation of the fatty acid pathway, PlsB activity also indirectly controls synthesis of lipopolysaccharide, a major component of the outer membrane synthesized from a fatty acid synthesis intermediate. Surprisingly, concentrations of the enzyme that catalyzes the committed step of lipopolysaccharide synthesis (LpxC) do not differ across steady-state growth conditions, suggesting that steady-state lipopolysaccharide synthesis is modulated primarily via indirect control by PlsB. In contrast to steady-state regulation, we found that responses to environmental perturbations are triggered directly via changes in acetyl coenzyme A (acetyl-CoA) concentrations, which enable rapid adaptation. Adaptations are further modulated by ppGpp, which regulates PlsB activity during slow growth and growth arrest. The strong reliance of the membrane synthesis pathway upon posttranslational regulation ensures both the reliability and the responsiveness of membrane synthesis.
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Machinandiarena F, Nakamatsu L, Schujman GE, de Mendoza D, Albanesi D. Revisiting the coupling of fatty acid to phospholipid synthesis in bacteria with FapR regulation. Mol Microbiol 2020; 114:653-663. [PMID: 32671874 DOI: 10.1111/mmi.14574] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/07/2020] [Accepted: 07/11/2020] [Indexed: 12/31/2022]
Abstract
A key aspect in membrane biogenesis is the coordination of fatty acid to phospholipid synthesis rates. In most bacteria, PlsX is the first enzyme of the phosphatidic acid synthesis pathway, the common precursor of all phospholipids. Previously, we proposed that PlsX is a key regulatory point that synchronizes the fatty acid synthase II with phospholipid synthesis in Bacillus subtilis. However, understanding the basis of such coordination mechanism remained a challenge in Gram-positive bacteria. Here, we show that the inhibition of fatty acid and phospholipid synthesis caused by PlsX depletion leads to the accumulation of long-chain acyl-ACPs, the end products of the fatty acid synthase II. Hydrolysis of the acyl-ACP pool by heterologous expression of a cytosolic thioesterase relieves the inhibition of fatty acid synthesis, indicating that acyl-ACPs are feedback inhibitors of this metabolic route. Unexpectedly, inactivation of PlsX triggers a large increase of malonyl-CoA leading to induction of the fap regulon. This finding discards the hypothesis, proposed for B. subtilis and extended to other Gram-positive bacteria, that acyl-ACPs are feedback inhibitors of the acetyl-CoA carboxylase. Finally, we propose that the continuous production of malonyl-CoA during phospholipid synthesis inhibition provides an additional mechanism for fine-tuning the coupling between phospholipid and fatty acid production in bacteria with FapR regulation.
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Affiliation(s)
- Federico Machinandiarena
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Leandro Nakamatsu
- División de Biología Sintética, Ingeniería Metabólica SA (INMET), Rosario, Argentina
| | - Gustavo E Schujman
- División de Biología Sintética, Ingeniería Metabólica SA (INMET), Rosario, Argentina.,CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Diego de Mendoza
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Daniela Albanesi
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
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Ikram M, Umar E, Raza A, Haider A, Naz S, Ul-Hamid A, Haider J, Shahzadi I, Hassan J, Ali S. Dye degradation performance, bactericidal behavior and molecular docking analysis of Cu-doped TiO 2 nanoparticles. RSC Adv 2020; 10:24215-24233. [PMID: 35516171 PMCID: PMC9055104 DOI: 10.1039/d0ra04851h] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 06/18/2020] [Indexed: 11/21/2022] Open
Abstract
Copper-doped TiO2 was prepared with a sol-gel chemical method. Various concentrations (3, 6, and 9 wt%) of Cu dopant were employed. Several techniques were implemented to assess the structural, optical, morphological and chemical properties of the synthesized samples. Evaluation of elemental composition using SEM-EDS and XRF techniques showed the presence of dopant element in the prepared samples. XRD analysis confirmed the presence of anatase (TiO2) phase with interstitial doping. Incorporation of dopant was observed to enhance the crystallinity and increase the crystallite size of the synthesized products. SAED profiles revealed a high degree of crystallinity in the prepared specimens, which was also evident in the XRD spectra. Optical properties studied using UV-vis spectroscopy depicted a shift of the maximum absorption to the visible region (redshift) that signified a reduction in the band gap energy of Cu-doped TiO2 samples. Examination of morphological features with scanning and high-resolution transmission electron microscopes revealed the formation of spherical nanoparticles with a tendency to agglomerate with increasing dopant concentration. Molecular vibrations and the formation of Ti-O-Ti bonds were revealed through FTIR spectra. PL spectroscopy recorded the trapping efficiency and migration of charge carriers, which exhibited electron-hole recombination behavior. Doped nanostructures showed enhanced bactericidal performance and synergism against S. aureus and E. coli. In summary, Cu-doped TiO2 nanostructures were observed to impede bacteria effectively, which is deemed beneficial in overcoming ailments caused by pathogens such as microbial etiologies. Furthermore, molecular docking analysis was conducted to study the interaction of Cu-doped TiO2 nanoparticles with multiple proteins namely β-lactamase (binding score: -4.91 kcal mol-1), ddlB (binding score: -5.67 kcal mol-1) and FabI (binding score: -6.13 kcal mol-1) as possible targets with active site residues. Dye degradation/reduction of control and Cu-doped samples were studied through absorption spectroscopy. The obtained outcomes of the performed experiment indicated that the photocatalytic activity of Cu-TiO2 enhanced with increasing dopant concentration, which is thought to be due to a decreased rate of electron-hole pair recombination. Consequently, it is suggested that Cu-TiO2 can be exploited as an effective candidate for antibacterial and dye degradation applications.
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Affiliation(s)
- M Ikram
- Solar Cell Applications Research Lab, Department of Physics, Government College University Lahore Punjab 54000 Pakistan +923005406667
| | - E Umar
- Department of Physics, Riphah Institute of Computing and Applied Sciences (RICAS), Riphah International University 14 Ali Road Lahore Pakistan
| | - A Raza
- Department of Physics, Riphah Institute of Computing and Applied Sciences (RICAS), Riphah International University 14 Ali Road Lahore Pakistan
| | - A Haider
- Department of Clinical Medicine and Surgery, University of Veterinary and Animal Sciences Lahore 54000 Punjab Pakistan
| | - S Naz
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences Tianjin 300308 China
| | - A Ul-Hamid
- Center for Engineering Research, Research Institute, King Fahd University of Petroleum & Minerals Dhahran 31261 Saudi Arabia
| | - J Haider
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences Tianjin 300308 China
| | - I Shahzadi
- College of Pharmacy, University of the Punjab Lahore 54000 Pakistan
| | - J Hassan
- Department of Physics, Riphah Institute of Computing and Applied Sciences (RICAS), Riphah International University 14 Ali Road Lahore Pakistan
| | - S Ali
- Department of Physics, Riphah Institute of Computing and Applied Sciences (RICAS), Riphah International University 14 Ali Road Lahore Pakistan
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