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Geißler A, Junca H, Kany AM, Daumann LJ, Hirsch AKH, Pieper DH, Sieber SA. Isocyanides inhibit bacterial pathogens by covalent targeting of essential metabolic enzymes. Chem Sci 2024; 15:11946-11955. [PMID: 39092115 PMCID: PMC11290450 DOI: 10.1039/d4sc01940g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 06/23/2024] [Indexed: 08/04/2024] Open
Abstract
Isonitrile natural products, also known as isocyanides, demonstrate potent antimicrobial activities, yet our understanding of their molecular targets remains limited. Here, we focus on the so far neglected group of monoisonitriles to gain further insights into their antimicrobial mode of action (MoA). Screening a focused monoisonitrile library revealed a potent S. aureus growth inhibitor with a different MoA compared to previously described isonitrile antibiotics. Chemical proteomics via competitive cysteine reactivity profiling, uncovered covalent modifications of two essential metabolic enzymes involved in the fatty acid biosynthetic process (FabF) and the hexosamine pathway (GlmS) at their active site cysteines. In-depth studies with the recombinant enzymes demonstrated concentration-dependent labeling, covalent binding to the catalytic site and corresponding functional inhibition by the isocyanide. Thermal proteome profiling and full proteome studies of compound-treated S. aureus further highlighted the destabilization and dysregulation of proteins related to the targeted pathways. Cytotoxicity and the inhibition of cytochrome P450 enzymes require optimization of the hit molecule prior to therapeutic application. The here described novel, covalent isocyanide MoA highlights the versatility of the functional group, making it a useful tool and out-of-the-box starting point for the development of innovative antibiotics.
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Affiliation(s)
- Alexandra Geißler
- Center for Functional Protein Assemblies, Department of Bioscience, TUM School of Natural Sciences, Technical University of Munich Ernst-Otto-Fischer-Straße 8 85748 Garching Germany
| | - Howard Junca
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research Inhoffenstraße 7 38124 Braunschweig Germany
| | - Andreas M Kany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) Campus E8.1 66123 Saarbrücken Germany
- Deutsches Zentrum für Infektionsforschung (DZIF) e.V. 38124 Braunschweig Germany
| | - Lena J Daumann
- Chair of Bioinorganic Chemistry, Heinrich-Heine-Universität Düsseldorf Universitätsstraße 1 40225 Düsseldorf Germany
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) Campus E8.1 66123 Saarbrücken Germany
- Saarland University, Department of Pharmacy 66123 Saarbrücken Germany
- Deutsches Zentrum für Infektionsforschung (DZIF) e.V. 38124 Braunschweig Germany
| | - Dietmar H Pieper
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research Inhoffenstraße 7 38124 Braunschweig Germany
| | - Stephan A Sieber
- Center for Functional Protein Assemblies, Department of Bioscience, TUM School of Natural Sciences, Technical University of Munich Ernst-Otto-Fischer-Straße 8 85748 Garching Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) Campus E8.1 66123 Saarbrücken Germany
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2
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Guan ZB, Deng XT, Zhang ZH, Xu GC, Cheng WL, Liao XR, Cai YJ. Engineering Glucosamine-6-Phosphate Synthase to Achieve Efficient One-Step Biosynthesis of Glucosamine. ACS Chem Biol 2024; 19:1237-1242. [PMID: 38723147 DOI: 10.1021/acschembio.4c00144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
As an important functional monosaccharide, glucosamine (GlcN) is widely used in fields such as medicine, food nutrition, and health care. Here, we report a distinct GlcN biosynthesis method that utilizes engineered Bacillus subtilis glucosamine-6-phosphate synthase (BsGlmS) to convert D-fructose to directly generate GlcN. The best variant obtained by using a combinatorial active-site saturation test/iterative saturation mutagenesis (CAST/ISM) strategy was a quadruple mutant S596D/V597G/S347H/G299Q (BsGlmS-BK19), which has a catalytic activity 1736-fold that of the wild type toward D-fructose. Upon using mutant BK19 as a whole-cell catalyst, D-fructose was converted into GlcN with 65.32% conversion in 6 h, whereas the wild type only attained a conversion rate of 0.31% under the same conditions. Molecular docking and molecular dynamics simulations were implemented to provide insights into the mechanism underlying the enhanced activity of BK19. Importantly, the BsGlmS-BK19 variant specifically catalyzes D-fructose without the need for phosphorylated substrates, representing a significant advancement in GlcN biosynthesis.
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Affiliation(s)
- Zheng-Bing Guan
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Xue-Ting Deng
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Zi-Hao Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Guo-Chao Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Wan-Li Cheng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, People's Republic of China
| | - Xiang-Ru Liao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Yu-Jie Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
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3
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Mahdi IS, Abdula AM, Jassim AMN, Baqi Y. Design, Synthesis, Antimicrobial Properties, and Molecular Docking of Novel Furan-Derived Chalcones and Their 3,5-Diaryl-∆ 2-pyrazoline Derivatives. Antibiotics (Basel) 2023; 13:21. [PMID: 38247580 PMCID: PMC10812776 DOI: 10.3390/antibiotics13010021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/23/2024] Open
Abstract
The present work focuses on the synthesis and preliminary structure activity relationships (SARs) of furan-derived chalcones and their corresponding ∆2-pyrazoline derivatives as antimicrobial agents. Eight novel chalcone derivatives and eight ∆2-pyrazoline compounds were synthesized in moderate to good isolated yields. The target compounds were evaluated as antimicrobial agents against two Gram-positive (Staphylococcus aureus and Staphylococcus epidermidis), two Gram-negative (Escherichia coli and Klebsiella pneumoniae), and fungi (Candida albicans) species. Based on the SARs, chalcones 2a and 2h showed inhibition activity on all tested microbial species, while ∆2-pyrazoline 3d was found to be selective for some microbial species. The most potent compounds (2a, 2h, and 3d) were docked into glucosamine-6-phosphate synthase (GlcN-6-P), the molecular target enzyme for antimicrobial agents, utilizing the Autodock 4.2 program, in order to study their virtual affinity and binding mode with the target enzyme. The selected potent compounds were found to bind to the active site of the enzyme probably in a similar way to that of the substrate as suggested by the docking study. In summary, the newly developed furan-derived chalcones and their ∆2-pyrazoline derivatives could serve as potent leads toward the development of novel antimicrobial agents.
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Affiliation(s)
- Inas S. Mahdi
- Department of Chemistry, College of Science, Mustansiriyah University, Baghdad P.O. Box 14022, Iraq; (I.S.M.); (A.M.N.J.)
| | - Ahmed Mutanabbi Abdula
- Department of Chemistry, College of Science, Mustansiriyah University, Baghdad P.O. Box 14022, Iraq; (I.S.M.); (A.M.N.J.)
| | - Abdulkadir M. Noori Jassim
- Department of Chemistry, College of Science, Mustansiriyah University, Baghdad P.O. Box 14022, Iraq; (I.S.M.); (A.M.N.J.)
| | - Younis Baqi
- Department of Chemistry, College of Science, Sultan Qaboos University, Muscat P.O. Box 36, Oman
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4
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Ballut L, Violot S, Kumar S, Aghajari N, Balaram H. GMP Synthetase: Allostery, Structure, and Function. Biomolecules 2023; 13:1379. [PMID: 37759779 PMCID: PMC10526850 DOI: 10.3390/biom13091379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/05/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Glutamine amidotransferases (GATs) catalyze the hydrolysis of glutamine and transfer the generated ammonia to diverse metabolites. The two catalytic activities, glutaminolysis and the subsequent amination of the acceptor substrate, happen in two distinct catalytic pockets connected by a channel that facilitates the movement of ammonia. The de novo pathway for the synthesis of guanosine monophosphate (GMP) from xanthosine monophosphate (XMP) is enabled by the GAT GMP synthetase (GMPS). In most available crystal structures of GATs, the ammonia channel is evident in their native state or upon ligand binding, providing molecular details of the conduit. In addition, conformational changes that enable the coordination of the two catalytic chemistries are also informed by the available structures. In contrast, despite the first structure of a GMPS being published in 1996, the understanding of catalysis in the acceptor domain and inter-domain crosstalk became possible only after the structure of a glutamine-bound mutant of Plasmodium falciparum GMPS was determined. In this review, we present the current status of our understanding of the molecular basis of catalysis in GMPS, becoming the first comprehensive assessment of the biochemical function of this intriguing enzyme.
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Affiliation(s)
- Lionel Ballut
- Molecular Microbiology and Structural Biochemistry, CNRS, University of Lyon1, UMR5086, 7 Passage du Vercors, CEDEX 07, F-69367 Lyon, France; (L.B.); (S.V.)
| | - Sébastien Violot
- Molecular Microbiology and Structural Biochemistry, CNRS, University of Lyon1, UMR5086, 7 Passage du Vercors, CEDEX 07, F-69367 Lyon, France; (L.B.); (S.V.)
| | - Sanjeev Kumar
- Trivedi School of Biosciences, Ashoka University, Rajiv Gandhi Education City, Sonipat 131029, Haryana, India;
| | - Nushin Aghajari
- Molecular Microbiology and Structural Biochemistry, CNRS, University of Lyon1, UMR5086, 7 Passage du Vercors, CEDEX 07, F-69367 Lyon, France; (L.B.); (S.V.)
| | - Hemalatha Balaram
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur 560064, Bangalore, India
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5
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Remines M, Schoonover M, Knox Z, Kenwright K, Hoffert KM, Coric A, Mead J, Ampfer J, Seye S, Strome ED. Profiling The Compendium Of Changes In Saccharomyces cerevisiae Due To Mutations That Alter Availability Of The Main Methyl Donor S-Adenosylmethionine. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.09.544294. [PMID: 37333147 PMCID: PMC10274911 DOI: 10.1101/2023.06.09.544294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The SAM1 and SAM2 genes encode for S-AdenosylMethionine (AdoMet) synthetase enzymes, with AdoMet serving as the main methyl donor. We have previously shown that independent deletion of these genes alters chromosome stability and AdoMet concentrations in opposite ways in S. cerevisiae. To characterize other changes occurring in these mutants, we grew wildtype, sam1∆/sam1∆, and sam2∆/sam2∆ strains in 15 different Phenotypic Microarray plates with different components, equal to 1440 wells, and measured for growth variations. RNA-Sequencing was also carried out on these strains and differential gene expression determined for each mutant. In this study, we explore how the phenotypic growth differences are linked to the altered gene expression, and thereby predict the mechanisms by which loss of the SAM genes and subsequent AdoMet level changes, impact S. cerevisiae pathways and processes. We present six stories, discussing changes in sensitivity or resistance to azoles, cisplatin, oxidative stress, arginine biosynthesis perturbations, DNA synthesis inhibitors, and tamoxifen, to demonstrate the power of this novel methodology to broadly profile changes due to gene mutations. The large number of conditions that result in altered growth, as well as the large number of differentially expressed genes with wide-ranging functionality, speaks to the broad array of impacts that altering methyl donor abundance can impart, even when the conditions tested were not specifically selected as targeting known methyl involving pathways. Our findings demonstrate that some cellular changes are directly related to AdoMet-dependent methyltransferases and AdoMet availability, some are directly linked to the methyl cycle and its role is production of several important cellular components, and others reveal impacts of SAM gene mutations on previously unconnected pathways.
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Affiliation(s)
- McKayla Remines
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
| | - Makailyn Schoonover
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
| | - Zoey Knox
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
| | - Kailee Kenwright
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
| | - Kellyn M. Hoffert
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
| | - Amila Coric
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
| | - James Mead
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
| | - Joseph Ampfer
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
| | - Serigne Seye
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
| | - Erin D. Strome
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
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6
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Stefaniak J, Nowak MG, Wojciechowski M, Milewski S, Skwarecki AS. Inhibitors of glucosamine-6-phosphate synthase as potential antimicrobials or antidiabetics - synthesis and properties. J Enzyme Inhib Med Chem 2022; 37:1928-1956. [PMID: 35801410 PMCID: PMC9272926 DOI: 10.1080/14756366.2022.2096018] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Glucosamine-6-phosphate synthase (GlcN-6-P synthase) is known as a promising target for antimicrobial agents and antidiabetics. Several compounds of natural or synthetic origin have been identified as inhibitors of this enzyme. This set comprises highly selective l-glutamine, amino sugar phosphate or transition state intermediate cis-enolamine analogues. Relatively low antimicrobial activity of these inhibitors, poorly penetrating microbial cell membranes, has been improved using the pro-drug approach. On the other hand, a number of heterocyclic and polycyclic compounds demonstrating antimicrobial activity have been presented as putative inhibitors of the enzyme, based on the results of molecular docking to GlcN-6-P synthase matrix. The most active compounds of this group could be considered promising leads for development of novel antimicrobial drugs or antidiabetics, provided their selective toxicity is confirmed.
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Affiliation(s)
- Joanna Stefaniak
- Department of Organic Chemistry and BioTechMed Center, Gdańsk University of Technology, Gdańsk, Poland
| | - Michał G Nowak
- Department of Organic Chemistry and BioTechMed Center, Gdańsk University of Technology, Gdańsk, Poland
| | - Marek Wojciechowski
- Department of Pharmaceutical Technology and Biochemistry and BioTechMed Center, Gdańsk University of Technology, Gdańsk, Poland
| | - Sławomir Milewski
- Department of Pharmaceutical Technology and Biochemistry and BioTechMed Center, Gdańsk University of Technology, Gdańsk, Poland
| | - Andrzej S Skwarecki
- Department of Pharmaceutical Technology and Biochemistry and BioTechMed Center, Gdańsk University of Technology, Gdańsk, Poland
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7
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Shivakumaraswamy S, Kumar S, Bellur A, Polisetty SD, Balaram H. Mechanistic Insights into the Functioning of a Two-Subunit GMP Synthetase, an Allosterically Regulated, Ammonia Channeling Enzyme. Biochemistry 2022; 61:1988-2006. [PMID: 36040251 DOI: 10.1021/acs.biochem.2c00151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Guanosine 5'-monophosphate (GMP) synthetases, enzymes that catalyze the conversion of xanthosine 5'-monophosphate (XMP) to GMP, are composed of two different catalytic units, which are either two domains of a polypeptide chain or two subunits that associate to form a complex. The glutamine amidotransferase (GATase) unit hydrolyzes glutamine generating ammonia, and the ATP pyrophosphatase (ATPPase) unit catalyzes the formation of an AMP-XMP intermediate. The substrate-bound ATPPase allosterically activates GATase, and the ammonia thus generated is tunneled to the ATPPase active site where it reacts with AMP-XMP generating GMP. In ammonia channeling enzymes reported thus far, a tight complex of the two subunits is observed, while the interaction of the two subunits of Methanocaldococcus jannaschii GMP synthetase (MjGMPS) is transient with the underlying mechanism of allostery and substrate channeling largely unclear. Here, we present a mechanistic model encompassing the various steps in the catalytic cycle of MjGMPS based on biochemical experiments, crystal structure, and cross-linking mass spectrometry guided integrative modeling. pH dependence of enzyme kinetics establishes that ammonia is tunneled across the subunits with the lifetime of the complex being ≤0.5 s. The crystal structure of the XMP-bound ATPPase subunit reported herein highlights the role of conformationally dynamic loops in enabling catalysis. The structure of MjGMPS derived using restraints obtained from cross-linking mass spectrometry has enabled the visualization of subunit interactions that enable allostery under catalytic conditions. We integrate the results and propose a functional mechanism for MjGMPS detailing the various steps involved in catalysis.
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Affiliation(s)
- Santosh Shivakumaraswamy
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru 560064, India
| | - Sanjeev Kumar
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru 560064, India
| | - Asutosh Bellur
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru 560064, India
| | - Satya Dev Polisetty
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru 560064, India
| | - Hemalatha Balaram
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru 560064, India
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8
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Wyllie JA, McKay MV, Barrow AS, Soares da Costa TP. Biosynthesis of uridine diphosphate N-Acetylglucosamine: An underexploited pathway in the search for novel antibiotics? IUBMB Life 2022; 74:1232-1252. [PMID: 35880704 PMCID: PMC10087520 DOI: 10.1002/iub.2664] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/04/2022] [Indexed: 11/06/2022]
Abstract
Although the prevalence of antibiotic resistance is increasing at an alarming rate, there are a dwindling number of effective antibiotics available. Thus, the development of novel antibacterial agents should be of utmost importance. Peptidoglycan biosynthesis has been and is still an attractive source for antibiotic targets; however, there are several components that remain underexploited. In this review, we examine the enzymes involved in the biosynthesis of one such component, UDP-N-acetylglucosamine, an essential building block and precursor of bacterial peptidoglycan. Furthermore, given the presence of a similar biosynthesis pathway in eukaryotes, we discuss the current knowledge on the differences and similarities between the bacterial and eukaryotic enzymes. Finally, this review also summarises the recent advances made in the development of inhibitors targeting the bacterial enzymes.
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Affiliation(s)
- Jessica A Wyllie
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Mirrin V McKay
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Andrew S Barrow
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Tatiana P Soares da Costa
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, South Australia, Australia
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9
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Bowlin MQ, Long AR, Huffines JT, Gray MJ. The role of nitrogen-responsive regulators in controlling inorganic polyphosphate synthesis in Escherichia coli. MICROBIOLOGY (READING, ENGLAND) 2022; 168:001185. [PMID: 35482529 PMCID: PMC10233264 DOI: 10.1099/mic.0.001185] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 04/10/2022] [Indexed: 12/22/2022]
Abstract
Inorganic polyphosphate (polyP) is synthesized by bacteria under stressful environmental conditions and acts by a variety of mechanisms to promote cell survival. While the kinase that synthesizes polyP (PPK, encoded by the ppk gene) is well known, ppk transcription is not activated by environmental stress and little is understood about how environmental stress signals lead to polyP accumulation. Previous work has shown that the transcriptional regulators DksA, RpoN (σ54) and RpoE (σ24) positively regulate polyP production, but not ppk transcription, in Escherichia coli. In this work, we examine the role of the alternative sigma factor RpoN and nitrogen starvation stress response pathways in controlling polyP synthesis. We show that the RpoN enhancer binding proteins GlnG and GlrR impact polyP production, and uncover a new role for the nitrogen phosphotransferase regulator PtsN (EIIANtr) as a positive regulator of polyP production, acting upstream of DksA, downstream of RpoN and apparently independently of RpoE. However, neither these regulatory proteins nor common nitrogen metabolites appear to act directly on PPK, and the precise mechanism(s) by which polyP production is modulated after stress remain(s) unclear. Unexpectedly, we also found that the genes that impact polyP production vary depending on the composition of the rich media in which the cells were grown before exposure to polyP-inducing stress. These results constitute progress towards deciphering the regulatory networks driving polyP production under stress, and highlight the remarkable complexity of this regulation and its connections to a broad range of stress-sensing pathways.
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Affiliation(s)
- Marvin Q. Bowlin
- Department of Microbiology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Abagail Renee Long
- Department of Microbiology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Joshua T. Huffines
- Department of Microbiology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Michael Jeffrey Gray
- Department of Microbiology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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10
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Nie XK, Chen Y, Zhang SQ, Cui X, Tang Z, Li GX. Chiral Primary Amine Catalyzed Enantioselective Tandem Reactions Based on Heyns Rearrangement: Synthesis of α-Tertiary Amino Ketones. Org Lett 2022; 24:2069-2074. [PMID: 35261250 DOI: 10.1021/acs.orglett.2c00724] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Herein, we disclose a new catalytic asymmetric tandem reaction based on the Heyns rearrangement for the synthesis of chiral α-amino ketones with readily available substrates. The rearrangement is different from the Heyns rearrangement in that the α-amino ketones were obtained without the shift of the carbonyl group. The key to success is using chiral primary amine as a catalyst by mimicking glucosamine-6-phosphate synthase in catalyzing the efficient Heyns rearrangement in organisms.
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Affiliation(s)
- Xiao-Kang Nie
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu, Sichuan 610041, China.,University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, Shijingshan District, Beijing 100049, P. R. China
| | - Yue Chen
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu, Sichuan 610041, China
| | - Shi-Qi Zhang
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu, Sichuan 610041, China
| | - Xin Cui
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu, Sichuan 610041, China
| | - Zhuo Tang
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu, Sichuan 610041, China
| | - Guang-Xun Li
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu, Sichuan 610041, China
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11
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Arshad M, Khan MS, Nami SAA. Norfloxacin Analogues: Drug Likeness, Synthesis, Biological, and Molecular Docking Assessment. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021020047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Sj AR, Ck R, S R, M P. Dehydroabietylamine, A Diterpene from Carthamus tinctorious L. Showing Antibacterial and Anthelmintic Effects with Computational Evidence. Curr Comput Aided Drug Des 2021; 16:231-237. [PMID: 30827256 DOI: 10.2174/1573409915666190301142811] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 02/10/2019] [Accepted: 02/21/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Plant-based drugs provide an outstanding contribution to modern therapeutics, and it is well known that the presence of different phytochemicals is responsible for such pharmacological effects. Carthamus tinctorius L. is one such medicinally important plant whose different solvent extracts have been reported with several pharmacological effects like antibacterial, hepatoprotective, and wound healing. The exploration of phytoconstituents from such a medicinally important plant for different pharmacological effects could produce new and effective drugs to treat human diseases. OBJECTIVE The present study attempts to explore the antibacterial and anthelmintic properties of dehydroabietylamine, a diterpene isolated from Carthamus tinctorius L. followed by the in silico elucidation of its probable mode of action. METHODS The minimum inhibition concentration (MIC) and minimum bactericidal concentration (MBC) of dehydroabietylamine were assessed against Staphylococcus aureus and Pseudomonas aeruginosa, using micro- broth dilution method. The anthelmintic activity of was determined to assess the time taken for paralysis and death of Pheretima Posthuma at different concentrations. Additionally, molecular docking study was conducted to understand the interaction between dehydroabietylamine with target proteins identified for both antibacterial and anthelmintic activity viz., glucosamine-6-phosphate synthase and β-Tubulin, respectively. RESULTS The dehydroabietylamine showed the significant MIC for S. aureus (12.5 μg/ml) and P. aeruginosa (6.25μg/ml), respectively. The result of anthelmintics effect of dehydroabietylamine was found to be dosedependent and compared to the standard drug, albendazole. CONCLUSION The interactions of dehydroabietylamine with the two target proteins with high binding affinity indicated the probable inhibition of target proteins, which could be the cause for prominent antibacterial and antihelminthic effects.
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Affiliation(s)
- Aditya R Sj
- Department of Biotechnology, SBRR Mahajana First Grade College, Mysore, Karnataka, India.,Molecular Biomedicine Laboratory and Department of P.G. Studies and Research in Biotechnology, Sahyadri Science College, Kuvempu University, Shivamogga, Karnataka, India
| | - Ramesh Ck
- Molecular Biomedicine Laboratory and Department of P.G. Studies and Research in Biotechnology, Sahyadri Science College, Kuvempu University, Shivamogga, Karnataka, India
| | - Raghavendra S
- Molecular Biomedicine Laboratory and Department of P.G. Studies and Research in Biotechnology, Sahyadri Science College, Kuvempu University, Shivamogga, Karnataka, India.,Department of Biochemistry, College of Horticulture, University of Horticultural Sciences, Bagalkot, Karnataka, India
| | - Paramesha M
- Molecular Biomedicine Laboratory and Department of P.G. Studies and Research in Biotechnology, Sahyadri Science College, Kuvempu University, Shivamogga, Karnataka, India.,Plant Cell Biotechnology Department, CSIR-Central Food Technological Research Institute, Mysore, Karnataka, India
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13
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Oliveira IA, Allonso D, Fernandes TVA, Lucena DMS, Ventura GT, Dias WB, Mohana-Borges RS, Pascutti PG, Todeschini AR. Enzymatic and structural properties of human glutamine:fructose-6-phosphate amidotransferase 2 (hGFAT2). J Biol Chem 2020; 296:100180. [PMID: 33303629 PMCID: PMC7948480 DOI: 10.1074/jbc.ra120.015189] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 11/24/2022] Open
Abstract
Glycoconjugates play a central role in several cellular processes, and alteration in their composition is associated with numerous human pathologies. Substrates for cellular glycosylation are synthesized in the hexosamine biosynthetic pathway, which is controlled by the glutamine:fructose-6-phosphate amidotransfera-se (GFAT). Human isoform 2 GFAT (hGFAT2) has been implicated in diabetes and cancer; however, there is no information about structural and enzymatic properties of this enzyme. Here, we report a successful expression and purification of a catalytically active recombinant hGFAT2 (rhGFAT2) in Escherichia coli cells fused or not to a HisTag at the C-terminal end. Our enzyme kinetics data suggest that hGFAT2 does not follow the expected ordered bi–bi mechanism, and performs the glucosamine-6-phosphate synthesis much more slowly than previously reported for other GFATs. In addition, hGFAT2 is able to isomerize fructose-6-phosphate into glucose-6-phosphate even in the presence of equimolar amounts of glutamine, which results in unproductive glutamine hydrolysis. Structural analysis of a three-dimensional model of rhGFAT2, corroborated by circular dichroism data, indicated the presence of a partially structured loop in the glutaminase domain, whose sequence is present in eukaryotic enzymes but absent in the E. coli homolog. Molecular dynamics simulations suggest that this loop is the most flexible portion of the protein and plays a key role on conformational states of hGFAT2. Thus, our study provides the first comprehensive set of data on the structure, kinetics, and mechanics of hGFAT2, which will certainly contribute to further studies on the (patho)physiology of hGFAT2.
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Affiliation(s)
- Isadora A Oliveira
- Laboratório de Glicobiologia Estrutural e Funcional, Instituto de Biofísica Carlos Chagas Filho (IBCCF), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil.
| | - Diego Allonso
- Laboratório de Glicobiologia Estrutural e Funcional, Instituto de Biofísica Carlos Chagas Filho (IBCCF), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil; Departamento de Biotecnologia Farmacêutica, Faculdade de Farmácia, UFRJ, Rio de Janeiro, RJ, Brazil
| | - Tácio V A Fernandes
- Laboratório de Modelagem e Dinâmica Molecular, IBCCF, UFRJ, Rio de Janeiro, RJ, Brazil; Laboratório de Macromoléculas, Diretoria de Metrologia Aplicada às Ciências da Vida, Instituto Nacional de Metrologia, Qualidade e Tecnologia (INMETRO), Duque de Caxias, RJ, Brazil
| | - Daniela M S Lucena
- Laboratório de Glicobiologia Estrutural e Funcional, Instituto de Biofísica Carlos Chagas Filho (IBCCF), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Gustavo T Ventura
- Laboratório de Glicobiologia Estrutural e Funcional, Instituto de Biofísica Carlos Chagas Filho (IBCCF), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Wagner Barbosa Dias
- Laboratório de Glicobiologia Estrutural e Funcional, Instituto de Biofísica Carlos Chagas Filho (IBCCF), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | | | - Pedro G Pascutti
- Laboratório de Modelagem e Dinâmica Molecular, IBCCF, UFRJ, Rio de Janeiro, RJ, Brazil
| | - Adriane R Todeschini
- Laboratório de Glicobiologia Estrutural e Funcional, Instituto de Biofísica Carlos Chagas Filho (IBCCF), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil.
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14
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Li P, Li K, Li X, Zhao F, Wang R, Wang J. Improving enzyme activity of glucosamine-6-phosphate synthase by semi-rational design strategy and computer analysis. Biotechnol Lett 2020; 42:2319-2332. [PMID: 32601959 DOI: 10.1007/s10529-020-02949-3] [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] [Received: 11/10/2019] [Accepted: 06/24/2020] [Indexed: 11/30/2022]
Abstract
OBJECTIVE To improve enzyme activity of Glucosamine-6-phosphate synthase (Glms) of Bacillus subtilis by site saturation mutagenesis at Leu593, Ala594, Lys595, Ser596 and Val597 based on computer-aided semi-rational design. RESULTS The results indicated that L593S had the greatest effect on the activity of BsGlms and the enzyme activity increased from 5 to 48 U/mL. The mutation of L593S increased the yield of glucosamine by 1.6 times that of the original strain. The binding energy of the mutant with substrate was reduced from - 743.864 to - 768.246 kcal/mol. Molecular dynamics simulation results showed that Ser593 enhanced the flexibility of the protein, which ultimately led to increased enzyme activity. CONCLUSION We successfully improved BsGlms activity through computer simulation and site saturation mutagenesis. This combination of methodologies may fit into an efficient workflow for improving Glms and other proteins activity.
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Affiliation(s)
- Piwu Li
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP) (Qilu University of Technology), Jinan, 250353, Shandong, People's Republic of China.,Key Laboratory of Shandong Microbial Engineering, QILU University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
| | - Kang Li
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
| | - Xu Li
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
| | - Fei Zhao
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
| | - Ruiming Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP) (Qilu University of Technology), Jinan, 250353, Shandong, People's Republic of China.,Key Laboratory of Shandong Microbial Engineering, QILU University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
| | - Junqing Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP) (Qilu University of Technology), Jinan, 250353, Shandong, People's Republic of China. .,Key Laboratory of Shandong Microbial Engineering, QILU University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China.
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15
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Sharma N, Ahalawat N, Sandhu P, Strauss E, Mondal J, Anand R. Role of allosteric switches and adaptor domains in long-distance cross-talk and transient tunnel formation. SCIENCE ADVANCES 2020; 6:eaay7919. [PMID: 32284973 PMCID: PMC7124931 DOI: 10.1126/sciadv.aay7919] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 01/08/2020] [Indexed: 06/11/2023]
Abstract
Transient tunnels that assemble and disassemble to facilitate passage of unstable intermediates in enzymes containing multiple reaction centers are controlled by allosteric cues. Using the 140-kDa purine biosynthetic enzyme PurL as a model system and a combination of biochemical and x-ray crystallographic studies, we show that long-distance communication between ~25-Å distal active sites is initiated by an allosteric switch, residing in a conserved catalytic loop, adjacent to the synthetase active site. Further, combinatory experiments seeded from molecular dynamics simulations help to delineate transient states that bring out the central role of nonfunctional adaptor domains. We show that carefully orchestrated conformational changes, facilitated by interplay of dynamic interactions at the allosteric switch and adaptor-domain interface, control reactivity and concomitant formation of the ammonia tunnel. This study asserts that substrate channeling is modulated by allosteric hotspots that alter protein energy landscape, thereby allowing the protein to adopt transient conformations paramount to function.
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Affiliation(s)
- Nandini Sharma
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Navjeet Ahalawat
- Center for Interdisciplinary Science, Tata Institute of Fundamental Research, Hyderabad 500107, India
| | - Padmani Sandhu
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Erick Strauss
- Department of Biochemistry, Stellenbosch University, Stellenbosch 7602, South Africa
| | - Jagannath Mondal
- Center for Interdisciplinary Science, Tata Institute of Fundamental Research, Hyderabad 500107, India
| | - Ruchi Anand
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
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16
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Ruegenberg S, Horn M, Pichlo C, Allmeroth K, Baumann U, Denzel MS. Loss of GFAT-1 feedback regulation activates the hexosamine pathway that modulates protein homeostasis. Nat Commun 2020; 11:687. [PMID: 32019926 PMCID: PMC7000685 DOI: 10.1038/s41467-020-14524-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 01/14/2020] [Indexed: 01/03/2023] Open
Abstract
Glutamine fructose-6-phosphate amidotransferase (GFAT) is the key enzyme in the hexosamine pathway (HP) that produces uridine 5′-diphospho-N-acetyl-d-glucosamine (UDP-GlcNAc), linking energy metabolism with posttranslational protein glycosylation. In Caenorhabditis elegans, we previously identified gfat-1 gain-of-function mutations that elevate UDP-GlcNAc levels, improve protein homeostasis, and extend lifespan. GFAT is highly conserved, but the gain-of-function mechanism and its relevance in mammalian cells remained unclear. Here, we present the full-length crystal structure of human GFAT-1 in complex with various ligands and with important mutations. UDP-GlcNAc directly interacts with GFAT-1, inhibiting catalytic activity. The longevity-associated G451E variant shows drastically reduced sensitivity to UDP-GlcNAc inhibition in enzyme activity assays. Our structural and functional data point to a critical role of the interdomain linker in UDP-GlcNAc inhibition. In mammalian cells, the G451E variant potently activates the HP. Therefore, GFAT-1 gain-of-function through loss of feedback inhibition constitutes a potential target for the treatment of age-related proteinopathies. Mutations in the hexosamine pathway key enzyme glutamine fructose-6-phosphate amidotransferase (GFAT-1) improve protein quality control and extend C. elegans lifespan. Here the authors present the crystal structures of full-length human GFAT-1 alone and with bound ligands and perform activity assays, which show that gain-of-function in the longevity-associated G451E variant is caused by a loss of feedback regulation.
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Affiliation(s)
- Sabine Ruegenberg
- Max Planck Institute for Biology of Ageing, 50931, Cologne, Germany.,University of Cologne, Institute of Biochemistry, 50674, Cologne, Germany
| | - Moritz Horn
- Max Planck Institute for Biology of Ageing, 50931, Cologne, Germany
| | - Christian Pichlo
- University of Cologne, Institute of Biochemistry, 50674, Cologne, Germany
| | - Kira Allmeroth
- Max Planck Institute for Biology of Ageing, 50931, Cologne, Germany
| | - Ulrich Baumann
- University of Cologne, Institute of Biochemistry, 50674, Cologne, Germany.
| | - Martin S Denzel
- Max Planck Institute for Biology of Ageing, 50931, Cologne, Germany. .,CECAD-Cluster of Excellence, University of Cologne, 50931, Cologne, Germany. .,Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931, Cologne, Germany.
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17
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Mapping the Allosteric Communication Network of Aminodeoxychorismate Synthase. J Mol Biol 2019; 431:2718-2728. [DOI: 10.1016/j.jmb.2019.05.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 05/10/2019] [Accepted: 05/13/2019] [Indexed: 01/31/2023]
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18
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Semmelmann F, Hupfeld E, Heizinger L, Merkl R, Sterner R. A Fold-Independent Interface Residue Is Crucial for Complex Formation and Allosteric Signaling in Class I Glutamine Amidotransferases. Biochemistry 2019; 58:2584-2588. [DOI: 10.1021/acs.biochem.9b00286] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Florian Semmelmann
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Enrico Hupfeld
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Leonhard Heizinger
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Rainer Merkl
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Reinhard Sterner
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
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19
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Periyasami G, Kamalraj S, Padmanaban R, Yeswanth Kumar S, Stalin A, Arumugam N, Suresh Kumar R, Rahaman M, Durairaju P, Alrehaili A, Aldalbahi A. Glucosamine-6-phosphate synthase inhibiting C3-β-cholesterol tethered spiro heterocyclic conjugates: Synthesis and their insight of DFT and docking study. Bioorg Chem 2019; 88:102920. [PMID: 30991194 DOI: 10.1016/j.bioorg.2019.102920] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 03/27/2019] [Accepted: 04/09/2019] [Indexed: 11/16/2022]
Abstract
A series of novel covalent cholesterol-spiro pyrrolidine/pyrrolizidine heterocyclic hybrids possessing biologically active oxindole, indanedione, and acenaphthylene-1-one have been synthesized by the reaction of C3-β-cholesteroalacrylate with heterocyclic di- and tri-ketones. All the sixteen compounds were obtained as a single isomer in good yield through a stereo- and regio- selective 1,3-dipolar cycloaddition methodology. Stereochemistry of the spiranic cycloadducts has been established by spectroscopic analysis and the regioselectivity outcome of the spiro adducts has been accomplished by DFT calculations at B3LYP/6-31G (d,p) level study. In vitro antibacterial activity of the newly synthesized cycloadducts were evaluated against highly pathogenic Gram-positive and Gram-negative bacteria and the most active compounds 5a, 13, and 14 underwent automated in silico molecular docking analysis in order to validate their effective orientation as a inhibitors bound in the active site of glucosamine-6-phosphate synthase (1XFF) enzyme by employing AutoDock Tools.
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Affiliation(s)
- Govindasami Periyasami
- Department of Chemistry, College of Science, King Saud University, Riyadh, Saudi Arabia; Department of Organic Chemistry, University of Madras, Guindy Campus, Chennai, India.
| | - Subban Kamalraj
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, India; Centre for Advanced Studies in Botany & Centre for Herbal Sciences, University of Madras, Guindy Campus, Chennai 600 025, Tamil Nadu, India
| | - Ramanathan Padmanaban
- Department of Chemistry, School of Physical, Chemical & Applied Sciences, Pondicherry University, Puducherry, India
| | - Santhakumar Yeswanth Kumar
- Department of Chemistry, School of Physical, Chemical & Applied Sciences, Pondicherry University, Puducherry, India
| | - Antony Stalin
- Division of Bioinformatics, Entomology Research Institute, Loyola College, Chennai 600 034, Tamil Nadu, India; Centre for Advanced Studies in Botany & Centre for Herbal Sciences, University of Madras, Guindy Campus, Chennai 600 025, Tamil Nadu, India
| | - Natarajan Arumugam
- Department of Chemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Raju Suresh Kumar
- Department of Chemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mostafizur Rahaman
- Department of Chemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Periyan Durairaju
- Department of Chemistry, Thiruvalluar Government Arts College, Periyar University, Raispuram, India
| | - Abdulaziz Alrehaili
- Department of Chemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Ali Aldalbahi
- Department of Chemistry, College of Science, King Saud University, Riyadh, Saudi Arabia.
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20
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Ansari A, Ali A, Asif M, Rauf MA, Owais M. Facile one-pot multicomponent synthesis and molecular docking studies of steroidal oxazole/thiazole derivatives with effective antimicrobial, antibiofilm and hemolytic properties. Steroids 2018; 134:22-36. [PMID: 29653115 DOI: 10.1016/j.steroids.2018.04.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 03/17/2018] [Accepted: 04/06/2018] [Indexed: 10/17/2022]
Abstract
A series of steroidal oxazole and thiazole derivatives have been synthesized employing thiosemicarbazide/semicarbazide hydrochloride and ethyl 2-chloroacetoacetate with a simple and facile one-pot multicomponent reaction pathway. The antimicrobial activity of newly synthesized compounds were evaluated against four bacterial strains namely Gram-negative (Escherichia coliand Pseudomonas aeruginosa) and Gram-positive bacteria (Staphylococcus aureus and Listeria monocytogenes) in addition to pathogenic fungi (Candida albicans and Cryptococcus neoformans). Bioactivity assay manifested that most of the compounds exhibited good antimicrobial activity. To provide additional insight into antimicrobial activity, the compounds were also tested for their antibiofilm activity against S. aureus biofilm. Moreover, molecular docking study shows binding of compounds with amino acid residues of DNA gyrase and glucosamine-6-phosphate synthase (promising antimicrobial target) through hydrogen bonding interactions. Hemolytic activity have been also investigated to ascertain the effect of compounds over RBC lysis and results indicate good prospects for biocompatibility. The expedient synthesis of steroidal heterocycles, effective antibacterial and antifungal behavior against various clinically relevant human pathogens, promising biocompatibility offer opportunities for further modification and potential applications as therapeutic agents.
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Affiliation(s)
- Anam Ansari
- Steroid Research Laboratory, Department of Chemistry, Aligarh Muslim University, Aligarh 202 002, India
| | - Abad Ali
- Steroid Research Laboratory, Department of Chemistry, Aligarh Muslim University, Aligarh 202 002, India; Organometallic Synthesis and Catalysis Group, Chemical Engineering Division, CSIR-National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune 411 008, Maharashtra, India
| | - Mohd Asif
- Steroid Research Laboratory, Department of Chemistry, Aligarh Muslim University, Aligarh 202 002, India
| | - Mohd Ahmar Rauf
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Mohammad Owais
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
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21
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Molecular insights into the antifungal mechanism of bacilysin. J Mol Model 2018; 24:118. [DOI: 10.1007/s00894-018-3645-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 03/28/2018] [Indexed: 01/14/2023]
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22
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Identification of a Direct Biosynthetic Pathway for UDP- N-Acetylgalactosamine from Glucosamine-6-Phosphate in Thermophilic Crenarchaeon Sulfolobus tokodaii. J Bacteriol 2018; 200:JB.00048-18. [PMID: 29507091 DOI: 10.1128/jb.00048-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 02/23/2018] [Indexed: 11/20/2022] Open
Abstract
Most organisms, from Bacteria to Eukarya, synthesize UDP-N-acetylglucosamine (UDP-GlcNAc) from fructose-6-phosphate via a four-step reaction, and UDP-N-acetylgalactosamine (UDP-GalNAc) can only be synthesized from UDP-GlcNAc by UDP-GlcNAc 4-epimerase. In Archaea, the bacterial-type UDP-GlcNAc biosynthetic pathway was reported for Methanococcales. However, the complete biosynthetic pathways for UDP-GlcNAc and UDP-GalNAc present in one archaeal species are unidentified. Previous experimental analyses on enzymatic activities of the ST0452 protein, identified from the thermophilic crenarchaeon Sulfolobus tokodaii, predicted the presence of both a bacterial-type UDP-GlcNAc and an independent UDP-GalNAc biosynthetic pathway in this archaeon. In the present work, functional analyses revealed that the recombinant ST2186 protein possessed an glutamine:fructose-6-phosphate amidotransferase activity and that the recombinant ST0242 protein possessed a phosphoglucosamine-mutase activity. Along with the acetyltransferase and uridyltransferase activities of the ST0452 protein, the activities of the ST2186 and ST0242 proteins confirmed the presence of a bacterial-type UDP-GlcNAc biosynthetic pathway in S. tokodaii In contrast, the UDP-GlcNAc 4-epimerase homologue gene was not detected within the genomic data. Thus, it was expected that galactosamine-1-phosphate or galactosamine-6-phosphate (GalN-6-P) was provided by conversion of glucosamine-1-phosphate or glucosamine-6-phosphate (GlcN-6-P). A novel epimerase converting GlcN-6-P to GalN-6-P was detected in a cell extract of S. tokodaii, and the N-terminal sequence of the purified protein indicated that the novel epimerase was encoded by the ST2245 gene. Along with the ST0242 phosphogalactosamine-mutase activity, this observation confirmed the presence of a novel UDP-GalNAc biosynthetic pathway from GlcN-6-P in S. tokodaii Discovery of the novel pathway provides a new insight into the evolution of nucleotide sugar metabolic pathways.IMPORTANCE In this work, a novel protein capable of directly converting glucosamine-6-phosphate to galactosamine-6-phosphate was successfully purified from a cell extract of the thermophilic crenarchaeon Sulfolobus tokodaii Confirmation of this novel activity using the recombinant protein indicates that S. tokodaii possesses a novel UDP-GalNAc biosynthetic pathway derived from glucosamine-6-phosphate. The distributions of this and related genes indicate the presence of three different types of UDP-GalNAc biosynthetic pathways: a direct pathway using a novel enzyme and two conversion pathways from UDP-GlcNAc using known enzymes. Additionally, Crenarchaeota species lacking all three pathways were found, predicting the presence of one more unknown pathway. Identification of these novel proteins and pathways provides important insights into the evolution of nucleotide sugar biosynthesis, as well as being potentially important industrially.
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23
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Efficient Synthesis and Bioactivity of Novel Triazole Derivatives. MOLECULES (BASEL, SWITZERLAND) 2018; 23:molecules23040709. [PMID: 29561766 PMCID: PMC6017136 DOI: 10.3390/molecules23040709] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Revised: 03/12/2018] [Accepted: 03/15/2018] [Indexed: 11/16/2022]
Abstract
Triazole pesticides are organic nitrogen-containing heterocyclic compounds, which contain 1,2,3-triazole ring. In order to develop potential glucosamine-6-phosphate synthase (GlmS) inhibitor fungicides, forty compounds of triazole derivatives were synthesized in an efficient way, thirty nine of them were new compounds. The structures of all the compounds were confirmed by high resolution mass spectrometer (HRMS), ¹H-NMR and 13C-NMR. The fungicidal activities results based on means of mycelium growth rate method indicated that some of the compounds exhibited good fungicidal activities against P. CapasiciLeonian, Sclerotinia sclerotiorum (Lib.) de Bary, Pyricularia oryzae Cav. and Fusarium oxysporum Schl. F.sp. vasinfectum (Atk.) Snyd. & Hans. at the concentration of 50 µg/mL, especially the inhibitory rates of compounds 1-d and 1-f were over 80%. At the same time, the preliminary studies based on the Elson-Morgan method indicated that the compounds exhibited some inhibitory activity toward glucosamine-6-phosphate synthase (GlmS). These compounds will be further studied as potential antifungal lead compounds. The structure-activity relationships (SAR) were discussed in terms of the effects of the substituents on both the benzene and the sugar ring.
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24
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Krause M, Foks H, Gobis K. Pharmacological Potential and Synthetic Approaches of Imidazo[4,5-b]pyridine and Imidazo[4,5-c]pyridine Derivatives. Molecules 2017; 22:molecules22030399. [PMID: 28273868 PMCID: PMC6155225 DOI: 10.3390/molecules22030399] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 03/02/2017] [Indexed: 12/23/2022] Open
Abstract
The structural resemblance between the fused imidazopyridine heterocyclic ring system and purines has prompted biological investigations to assess their potential therapeutic significance. They are known to play a crucial role in numerous disease conditions. The discovery of their first bioactivity as GABAA receptor positive allosteric modulators divulged their medicinal potential. Proton pump inhibitors, aromatase inhibitors, and NSAIDs were also found in this chemical group. Imidazopyridines have the ability to influence many cellular pathways necessary for the proper functioning of cancerous cells, pathogens, components of the immune system, enzymes involved in carbohydrate metabolism, etc. The collective results of biochemical and biophysical properties foregrounded their medicinal significance in central nervous system, digestive system, cancer, inflammation, etc. In recent years, new preparative methods for the synthesis of imidazopyridines using various catalysts have been described. The present manuscript to the best of our knowledge is the complete compilation on the synthesis and medicinal aspects of imidazo[4,5-b]pyridines and imidazo[4,5-c]pyridines reported from the year 2000 to date, including structure–activity relationships.
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Affiliation(s)
- Malwina Krause
- Department of Organic Chemistry, Medical University of Gdańsk, 107 Gen. Hallera Ave., 80-416 Gdańsk, Poland.
| | - Henryk Foks
- Department of Organic Chemistry, Medical University of Gdańsk, 107 Gen. Hallera Ave., 80-416 Gdańsk, Poland.
| | - Katarzyna Gobis
- Department of Organic Chemistry, Medical University of Gdańsk, 107 Gen. Hallera Ave., 80-416 Gdańsk, Poland.
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25
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Wei W, Monard G, Gauld J. Computational insights into substrate binding and catalytic mechanism of the glutaminase domain of glucosamine-6-phosphate synthase (GlmS). RSC Adv 2017. [DOI: 10.1039/c7ra04906d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The mechanistic cysteinyl of GlmS can activate its thiol using its own α-amine without the need for a bridging water.
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Affiliation(s)
- Wanlei Wei
- Department of Chemistry and Biochemistry
- University of Windsor
- Windsor
- Canada
| | - Gerald Monard
- Université de Lorraine
- UMR 7565 SRSMC
- F-54506 Vandoeuvre-les-Nancy
- France
| | - James W. Gauld
- Department of Chemistry and Biochemistry
- University of Windsor
- Windsor
- Canada
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26
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Abstract
Bacillus subtilis is one of the best-studied organisms. Due to the broad knowledge and annotation and the well-developed genetic system, this bacterium is an excellent starting point for genome minimization with the aim of constructing a minimal cell. We have analyzed the genome of B. subtilis and selected all genes that are required to allow life in complex medium at 37°C. This selection is based on the known information on essential genes and functions as well as on gene and protein expression data and gene conservation. The list presented here includes 523 and 119 genes coding for proteins and RNAs, respectively. These proteins and RNAs are required for the basic functions of life in information processing (replication and chromosome maintenance, transcription, translation, protein folding, and secretion), metabolism, cell division, and the integrity of the minimal cell. The completeness of the selected metabolic pathways, reactions, and enzymes was verified by the development of a model of metabolism of the minimal cell. A comparison of the MiniBacillus genome to the recently reported designed minimal genome of Mycoplasma mycoides JCVI-syn3.0 indicates excellent agreement in the information-processing pathways, whereas each species has a metabolism that reflects specific evolution and adaptation. The blueprint of MiniBacillus presented here serves as the starting point for a successive reduction of the B. subtilis genome.
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27
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Chennu MMPR, Abdul RS, Yejella RP. Molecular docking based screening of G6PS with 1, 5 Benzothiazepine derivates for a potential inhibitor. Bioinformation 2015; 11:525-8. [PMID: 26770025 PMCID: PMC4702029 DOI: 10.6026/97320630011525] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 12/17/2015] [Accepted: 12/17/2015] [Indexed: 11/23/2022] Open
Abstract
Glucosamine-6-phosphate synthase (G6PS) (EC 2.6.1.16) is a known target for anti-bacterial and anti-fungal infections. Therefore, it is of interest to design potential inhibitors using 1, 5 benzo-thiazepine skeleton with appropriate modifications. We report the binding data for 20 derivatives of the skeleton molecule to G6PS having binding energy from -7.35 to -9.99 Kcal/mol with predicted IC50 value range of 4.11 to 47.68 nano-molar. It should be noted that this data should be further evaluated using in vitro and in vivo studies for safety, activity, efficacy and toxicity.
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Affiliation(s)
| | - Rahaman Shaik Abdul
- Department of pharmaceutical chemistry, Nirmala college of Pharmacy ,Mangalagiri
| | - Rajendra Prasad Yejella
- Department of Pharmaceutical Chemistry, University college of Pharmaceutical Sciences, Andhra University, Visakhapatanam
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28
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Active site coupling in Plasmodium falciparum GMP synthetase is triggered by domain rotation. Nat Commun 2015; 6:8930. [PMID: 26592566 PMCID: PMC4673825 DOI: 10.1038/ncomms9930] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 10/19/2015] [Indexed: 11/24/2022] Open
Abstract
GMP synthetase (GMPS), a key enzyme in the purine biosynthetic pathway performs catalysis through a coordinated process across two catalytic pockets for which the mechanism remains unclear. Crystal structures of Plasmodium falciparum GMPS in conjunction with mutational and enzyme kinetic studies reported here provide evidence that an 85° rotation of the GATase domain is required for ammonia channelling and thus for the catalytic activity of this two-domain enzyme. We suggest that conformational changes in helix 371–375 holding catalytic residues and in loop 376–401 along the rotation trajectory trigger the different steps of catalysis, and establish the central role of Glu374 in allostery and inter-domain crosstalk. These studies reveal the mechanism of domain rotation and inter-domain communication, providing a molecular framework for the function of all single polypeptide GMPSs and form a solid basis for rational drug design targeting this therapeutically important enzyme. GMP synthetase, a key enzyme in purine biosynthesis, is of interest for understanding purine metabolism processes and for developing therapeutic applications. Here, the authors propose a molecular mechanism and the structural basis for the catalytic activity of this enzyme.
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29
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Moraes GL, Gomes GC, Monteiro de Sousa PR, Alves CN, Govender T, Kruger HG, Maguire GEM, Lamichhane G, Lameira J. Structural and functional features of enzymes of Mycobacterium tuberculosis peptidoglycan biosynthesis as targets for drug development. Tuberculosis (Edinb) 2015; 95:95-111. [PMID: 25701501 DOI: 10.1016/j.tube.2015.01.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 01/13/2015] [Accepted: 01/19/2015] [Indexed: 10/24/2022]
Abstract
Tuberculosis (TB) is the second leading cause of human mortality from infectious diseases worldwide. The WHO reported 1.3 million deaths and 8.6 million new cases of TB in 2012. Mycobacterium tuberculosis (M. tuberculosis), the infectious bacteria that causes TB, is encapsulated by a thick and robust cell wall. The innermost segment of the cell wall is comprised of peptidoglycan, a layer that is required for survival and growth of the pathogen. Enzymes that catalyse biosynthesis of the peptidoglycan are essential and are therefore attractive targets for discovery of novel antibiotics as humans lack similar enzymes making it possible to selectively target bacteria only. In this paper, we have reviewed the structures and functions of enzymes GlmS, GlmM, GlmU, MurA, MurB, MurC, MurD, MurE and MurF from M. tuberculosis that are involved in peptidoglycan biosynthesis. In addition, we report homology modelled 3D structures of those key enzymes from M. tuberculosis of which the structures are still unknown. We demonstrated that natural substrates can be successfully docked into the active sites of the GlmS and GlmU respectively. It is therefore expected that the models and the data provided herein will facilitate translational research to develop new drugs to treat TB.
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Affiliation(s)
- Gleiciane Leal Moraes
- Laboratório de Planejamento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, CEP 66075-110 Belém, PA, Brazil
| | - Guelber Cardoso Gomes
- Laboratório de Planejamento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, CEP 66075-110 Belém, PA, Brazil; Instituto de Ciências Biológicas, Universidade Federal do Pará, CEP 66075-110 Belém, PA, Brazil
| | - Paulo Robson Monteiro de Sousa
- Laboratório de Planejamento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, CEP 66075-110 Belém, PA, Brazil
| | - Cláudio Nahum Alves
- Laboratório de Planejamento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, CEP 66075-110 Belém, PA, Brazil
| | - Thavendran Govender
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, South Africa
| | - Hendrik G Kruger
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, South Africa
| | - Glenn E M Maguire
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, South Africa
| | - Gyanu Lamichhane
- Johns Hopkins University School of Medicine, Taskforce to Study Resistance Emergence & Antimicrobial Development Technology, 1503 E. Jefferson St, Baltimore, MD 21231, USA
| | - Jerônimo Lameira
- Laboratório de Planejamento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, CEP 66075-110 Belém, PA, Brazil; Instituto de Ciências Biológicas, Universidade Federal do Pará, CEP 66075-110 Belém, PA, Brazil.
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30
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Identification and Characterization of Bioactive Compounds Targeting Uropathogenic Escherichia colifrom Sanjin Tablets. J CHEM-NY 2015. [DOI: 10.1155/2015/789809] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Sanjin Tablets are completely natural preparation with significant efficacy in treating urinary tract infection. To identify the bioactive compounds from Sanjin Tablets, we separated components capable of binding to the soluble proteins of uropathogenicEscherichia coli(UPEC) by affinity binding and characterized their identities using liquid chromatography-mass spectrometry (LC-MS) analysis. Our study discovered eight compounds withE. coliprotein-binding capabilities, and all these compounds were tracked back to the original natural ingredients of Sanjin Tablets. These compounds presented essentially no antibacteria activity, indicating that they affect UPEC by means other than directly killing the cells. Further molecular modeling analysis predicted molecular targets for these compounds and mapped the residues potentially involved in compound-target interactions. All the predicted targets turned out to be critical proteins regulating the metabolisms ofE. coli, suggesting that these compounds may affect metabolic pathways in UPEC and inhibit pathogenesis. These data will benefit future design of drugs with higher efficacy and specificity on targeting pathogenic bacteria.
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31
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Dance I. A molecular pathway for the egress of ammonia produced by nitrogenase. Sci Rep 2013; 3:3237. [PMID: 24241241 PMCID: PMC3831235 DOI: 10.1038/srep03237] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 11/01/2013] [Indexed: 01/19/2023] Open
Abstract
Nitrogenase converts N2 to NH3, at one face of an Fe-Mo-S cluster (FeMo-co) buried in the protein. Through exploration of cavities in the structures of nitrogenase proteins, a pathway for the egress of ammonia from its generation site to the external medium is proposed. This pathway is conserved in the three species Azotobacter vinelandii, Klebsiella pneumoniae and Clostridium pasteurianum. A molecular mechanism for the translocation of NH3 by skipping through a sequence of hydrogen bonds involving eleven water molecules and surrounding aminoacids has been developed. The putative mechanism requires movement aside of some water molecules by up to ~ 1Å. Consistent with this, the surrounding protein is comprised of different chains and has little secondary structure: protein fluctuations are part of the mechanism. This NH3 pathway is well separated from the water chain and embedded proton wire that have been proposed for serial supply of protons to FeMo-co. Verification procedures are suggested.
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Affiliation(s)
- Ian Dance
- School of Chemistry, University of New South Wales, Sydney 2052, Australia
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32
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Affiliation(s)
- Artur Gora
- Loschmidt Laboratories,
Department
of Experimental Biology and Research Centre for Toxic Compounds in
the Environment, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Jan Brezovsky
- Loschmidt Laboratories,
Department
of Experimental Biology and Research Centre for Toxic Compounds in
the Environment, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories,
Department
of Experimental Biology and Research Centre for Toxic Compounds in
the Environment, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
- International Centre for Clinical
Research, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
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33
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Efficient synthesis and anti-fungal activity of oleanolic acid oxime esters. Molecules 2013; 18:3615-29. [PMID: 23519202 PMCID: PMC6270060 DOI: 10.3390/molecules18033615] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 03/14/2013] [Accepted: 03/15/2013] [Indexed: 11/28/2022] Open
Abstract
In order to develop potential glucosamine-6-phosphate synthase inhibitors and anti-fungal agents, twenty five oleanolic acid oxime esters were synthesized in an efficient way. The structures of the new compounds were confirmed by MS, HRMS, 1H-NMR and 13C-NMR. Preliminary studies based on means of the Elson-Morgan method indicated that many compounds exhibited some inhibitory activity of glucosamine-6-phosphate synthase (GlmS), and the original fungicidal activities results showed that some of the compounds exhibited good fungicidal activities towards Sclerotinia sclerotiorum (Lib.) de Bary, Rhizoctonia solani Kuhn and Botrytis cinerea Pers at the concentration of 50 µg/mL. These compounds would thus merit further study and development as antifungal agents.
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34
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List F, Vega M, Razeto A, Häger M, Sterner R, Wilmanns M. Catalysis Uncoupling in a Glutamine Amidotransferase Bienzyme by Unblocking the Glutaminase Active Site. ACTA ACUST UNITED AC 2012; 19:1589-99. [DOI: 10.1016/j.chembiol.2012.10.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2012] [Revised: 10/02/2012] [Accepted: 10/11/2012] [Indexed: 11/30/2022]
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35
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Czarnecka J, Kwiatkowska K, Gabriel I, Wojciechowski M, Milewski S. EngineeringCandida albicansglucosamine-6-phosphate synthase for efficient enzyme purification. J Mol Recognit 2012; 25:564-70. [DOI: 10.1002/jmr.2175] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Justyna Czarnecka
- Department of Pharmaceutical Technology and Biochemistry; Gdańsk University of Technology; 11/12 Narutowicza St; 80-233; Gdańsk; Poland
| | - Karolina Kwiatkowska
- Department of Pharmaceutical Technology and Biochemistry; Gdańsk University of Technology; 11/12 Narutowicza St; 80-233; Gdańsk; Poland
| | - Iwona Gabriel
- Department of Pharmaceutical Technology and Biochemistry; Gdańsk University of Technology; 11/12 Narutowicza St; 80-233; Gdańsk; Poland
| | - Marek Wojciechowski
- Department of Pharmaceutical Technology and Biochemistry; Gdańsk University of Technology; 11/12 Narutowicza St; 80-233; Gdańsk; Poland
| | - Sławomir Milewski
- Department of Pharmaceutical Technology and Biochemistry; Gdańsk University of Technology; 11/12 Narutowicza St; 80-233; Gdańsk; Poland
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36
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Mouilleron S, Badet-Denisot MA, Pecqueur L, Madiona K, Assrir N, Badet B, Golinelli-Pimpaneau B. Structural basis for morpheein-type allosteric regulation of Escherichia coli glucosamine-6-phosphate synthase: equilibrium between inactive hexamer and active dimer. J Biol Chem 2012; 287:34533-46. [PMID: 22851174 DOI: 10.1074/jbc.m112.380378] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The amino-terminal cysteine of glucosamine-6-phosphate synthase (GlmS) acts as a nucleophile to release and transfer ammonia from glutamine to fructose 6-phosphate through a channel. The crystal structure of the C1A mutant of Escherichia coli GlmS, solved at 2.5 Å resolution, is organized as a hexamer, where the glutaminase domains adopt an inactive conformation. Although the wild-type enzyme is active as a dimer, size exclusion chromatography, dynamic and quasi-elastic light scattering, native polyacrylamide gel electrophoresis, and ultracentrifugation data show that the dimer is in equilibrium with a hexameric state, in vitro and in cellulo. The previously determined structures of the wild-type enzyme, alone or in complex with glucosamine 6-phosphate, are also consistent with a hexameric assembly that is catalytically inactive because the ammonia channel is not formed. The shift of the equilibrium toward the hexameric form in the presence of cyclic glucosamine 6-phosphate, together with the decrease of the specific activity with increasing enzyme concentration, strongly supports product inhibition through hexamer stabilization. Altogether, our data allow us to propose a morpheein model, in which the active dimer can rearrange into a transiently stable form, which has the propensity to form an inactive hexamer. This would account for a physiologically relevant allosteric regulation of E. coli GlmS. Finally, in addition to cyclic glucose 6-phosphate bound at the active site, the hexameric organization of E. coli GlmS enables the binding of another linear sugar molecule. Targeting this sugar-binding site to stabilize the inactive hexameric state is therefore suggested for the development of specific antibacterial inhibitors.
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Affiliation(s)
- Stéphane Mouilleron
- Laboratoire d'Enzymologie et Biochimie Structurales, Centre de Recherche de Gif, CNRS, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
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37
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Singh S, Phillips GN, Thorson JS. The structural biology of enzymes involved in natural product glycosylation. Nat Prod Rep 2012; 29:1201-37. [PMID: 22688446 DOI: 10.1039/c2np20039b] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The glycosylation of microbial natural products often dramatically influences the biological and/or pharmacological activities of the parental metabolite. Over the past decade, crystal structures of several enzymes involved in the biosynthesis and attachment of novel sugars found appended to natural products have emerged. In many cases, these studies have paved the way to a better understanding of the corresponding enzyme mechanism of action and have served as a starting point for engineering variant enzymes to facilitate to production of differentially-glycosylated natural products. This review specifically summarizes the structural studies of bacterial enzymes involved in biosynthesis of novel sugar nucleotides.
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Affiliation(s)
- Shanteri Singh
- Laboratory for Biosynthetic Chemistry, Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
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38
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Jędrzejczak R, Wojciechowski M, Andruszkiewicz R, Sowiński P, Kot-Wasik A, Milewski S. Inactivation of glucosamine-6-phosphate synthase by N3-oxoacyl derivatives of L-2,3-diaminopropanoic acid. Chembiochem 2012; 13:85-96. [PMID: 22125025 DOI: 10.1002/cbic.201100587] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Indexed: 11/09/2022]
Abstract
N(3)-Oxoacyl derivatives of L-2,3-diaminopropanoic acid 1-4, containing either an epoxide group or a conjugated double bond system, inactivate Saccharomyces cerevisiae glucosamine-6-phosphate (GlcN-6-P) synthase in a time- and concentration dependent manner. The results of kinetics studies on inactivation suggested a biphasic course, with formation of the enzyme-ligand complex preceding irreversible modification of the enzyme. The examined compounds differed markedly in their affinity to the enzyme active site. Inhibitors containing a phenyl ketone moiety bound much more strongly than their methyl ketone counterparts. The molecular mechanism of enzyme inactivation by phenyl ketone compounds 1 and 3 was elucidated by using a stepwise approach with 2D NMR, MS and UV-visible spectroscopy. A substituted thiazine derivative was identified as the final product of a model reaction between an epoxide compound, 1, and L-cysteine ethyl ester (CEE); and the respective cyclic product, found as a result of reaction between 1 and CGIF tetrapeptide, was identical to the N-terminal fragment of GlcN-6-P synthase. On the other hand, the reaction of a double-bond-containing compound, 3, with CEE, CGIF and GlcN-6-P synthase led to the formation of a C-S bond, without any further conversion or rearrangement. Molecular mechanisms of the reactions studied are proposed.
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Affiliation(s)
- Robert Jędrzejczak
- Department of Pharmaceutical Technology and Biochemistry, Gdańsk University of Technology, Gdańsk, Poland
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39
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Hollenhorst MA, Ntai I, Badet B, Kelleher NL, Walsh CT. A head-to-head comparison of eneamide and epoxyamide inhibitors of glucosamine-6-phosphate synthase from the dapdiamide biosynthetic pathway. Biochemistry 2011; 50:3859-61. [PMID: 21520904 DOI: 10.1021/bi2004735] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The dapdiamides make up a family of antibiotics that have been presumed to be cleaved in the target cell to enzyme-inhibitory N-acyl-2,3-diaminopropionate (DAP) warheads containing two alternative electrophilic moieties. Our prior biosynthetic studies revealed that an eneamide warhead is made first and converted to an epoxyamide via a three-enzyme branch pathway. Here we provide a rationale for this logic. We report that the R,R-epoxyamide warhead is a more efficient covalent inactivator of glucosamine-6-phosphate synthase by 1 order of magnitude versus the eneamide, and this difference correlates with a >10-fold difference in antibiotic activity for the corresponding acyl-DAP dipeptides.
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Affiliation(s)
- Marie A Hollenhorst
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
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