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Shams K, Khan I, Ahmad S, Ullah A, Azam S, Liaqat Z, Jalil H, Ahmad F, Albekairi NA, Alshammari AM, Wei DQ. Highly Drug-Resistant Escherichia coli from Hospital Wastewater with Several Evolutionary Mutations: An Integrated Insights from Molecular, Computational, and Biophysics. Mol Biotechnol 2025:10.1007/s12033-025-01410-y. [PMID: 40091143 DOI: 10.1007/s12033-025-01410-y] [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: 11/18/2024] [Accepted: 02/10/2025] [Indexed: 03/19/2025]
Abstract
Many people around the world are still unable to get access to clean drinking water. Escherichia coli is a common waterborne pathogen that frequently results from insufficient hygiene measures and needs attention to address health problems. The present study aimed to evaluate antibiotic resistance of Escherichia coli isolated from wastewater and drinking water samples of hospital and non-hospital settings at Peshawar. Out of 462 samples collected, 111 tested positive for E. coli. The majority of isolates were resistant to many antibiotics including Ampicillin, Gentamicin, Tobramycin, Imipenem, Meropenem, Tetracycline, Cefepime, Amikacin, Piperacillin, Levofloxacin, Ciprofloxacin, Ceftriaxone, and Cefazolin. However, they showed susceptibility to Chloramphenicol, Fosfomycin 200 mg, Colistin, and Tigecycline. Genetic analysis revealed various antibiotic resistance genes within the isolates, i.e., marA(20%), marB(40%) marR(30%), rob(30%), and soxS(35%). Following PCR, the resulting products underwent next-generation sequencing. marA exhibited T10P and D101H mutations, while MarR showed substitutions at M1G, V142S, L143P, and P144C positions. In Rob, D2I, A4P, L10F, I12N, and L253P mutations were observed. The SoxS displayed alterations at H105P, R106A, and L107V positions. Asinex antibacterial library was used to study molecular docking based on virtual screening. SWISS ADME was used to in silico evaluate the pharmacokinetics of these substances. 100 ns molecular dynamics simulation was conducted to estimate free binding energies, confirmation, and stability of the binding mode of the identified compounds. Screening results revealed that LAS-52505571, LAS52171241, LAS52202332, and LAS22461675 compounds showed high affinity to MarA, MarR, SoxS, and Rob proteins, respectively, with the lowest binding energies across the library. In brief, the current study aimed at establishing potential chemical entities that could facilitate the evolution of silicon drugs against antibiotic-resistant E. coli strains.
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Affiliation(s)
- Khadija Shams
- Centre of Biotechnology and Microbiology, University of Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Ibrar Khan
- Centre of Biotechnology and Microbiology, University of Peshawar, Khyber Pakhtunkhwa, Pakistan.
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, 25000, Pakistan.
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Nayang, People's Republic of China.
| | - Asad Ullah
- Centre of Biotechnology and Microbiology, University of Peshawar, Khyber Pakhtunkhwa, Pakistan
- Department of Health and Biological Sciences, Abasyn University, Peshawar, 25000, Pakistan
| | - Sadiq Azam
- Centre of Biotechnology and Microbiology, University of Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Zainab Liaqat
- Centre of Biotechnology and Microbiology, University of Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Huma Jalil
- Centre of Biotechnology and Microbiology, University of Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Faisal Ahmad
- World Health Organization, Park Road, Chak Shahzad, Islamabad, 44000, Pakistan
- National Institute of Health, Park Road, Chak Shahzad, Islamabad, 44000, Pakistan
| | - Norah Abdullah Albekairi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Post Box 2455, Riyadh, 11451, Saudi Arabia
| | - Abdulrahman Mohammed Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Post Box 2455, Riyadh, 11451, Saudi Arabia
| | - Dong-Qing Wei
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Nayang, People's Republic of China
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Shirakawa KT, Sala FA, Miyachiro MM, Job V, Trindade DM, Dessen A. Architecture and genomic arrangement of the MurE-MurF bacterial cell wall biosynthesis complex. Proc Natl Acad Sci U S A 2023; 120:e2219540120. [PMID: 37186837 PMCID: PMC10214165 DOI: 10.1073/pnas.2219540120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 04/05/2023] [Indexed: 05/17/2023] Open
Abstract
Peptidoglycan (PG) is a central component of the bacterial cell wall, and the disruption of its biosynthetic pathway has been a successful antibacterial strategy for decades. PG biosynthesis is initiated in the cytoplasm through sequential reactions catalyzed by Mur enzymes that have been suggested to associate into a multimembered complex. This idea is supported by the observation that in many eubacteria, mur genes are present in a single operon within the well conserved dcw cluster, and in some cases, pairs of mur genes are fused to encode a single, chimeric polypeptide. We performed a vast genomic analysis using >140 bacterial genomes and mapped Mur chimeras in numerous phyla, with Proteobacteria carrying the highest number. MurE-MurF, the most prevalent chimera, exists in forms that are either directly associated or separated by a linker. The crystal structure of the MurE-MurF chimera from Bordetella pertussis reveals a head-to-tail, elongated architecture supported by an interconnecting hydrophobic patch that stabilizes the positions of the two proteins. Fluorescence polarization assays reveal that MurE-MurF interacts with other Mur ligases via its central domains with KDs in the high nanomolar range, backing the existence of a Mur complex in the cytoplasm. These data support the idea of stronger evolutionary constraints on gene order when encoded proteins are intended for association, establish a link between Mur ligase interaction, complex assembly and genome evolution, and shed light on regulatory mechanisms of protein expression and stability in pathways of critical importance for bacterial survival.
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Affiliation(s)
- Karina T. Shirakawa
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo13084-971, Brazil
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, CEP Campinas, São Paulo13083-862, Brazil
| | - Fernanda Angélica Sala
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo13084-971, Brazil
| | - Mayara M. Miyachiro
- Univ. Grenoble Alpes, CNRS, Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Biologie Structurale, Bacterial Pathogenesis Group, GrenobleF-38044, France
| | - Viviana Job
- Univ. Grenoble Alpes, CNRS, Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Biologie Structurale, Bacterial Pathogenesis Group, GrenobleF-38044, France
| | - Daniel Maragno Trindade
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo13084-971, Brazil
| | - Andréa Dessen
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo13084-971, Brazil
- Univ. Grenoble Alpes, CNRS, Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Biologie Structurale, Bacterial Pathogenesis Group, GrenobleF-38044, France
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3
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Subedi BP, Schofield LR, Carbone V, Wolf M, Martin WF, Ronimus RS, Sutherland-Smith AJ. Structural characterisation of methanogen pseudomurein cell wall peptide ligases homologous to bacterial MurE/F murein peptide ligases. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36178458 DOI: 10.1099/mic.0.001235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Archaea have diverse cell wall types, yet none are identical to bacterial peptidoglycan (murein). Methanogens Methanobacteria and Methanopyrus possess cell walls of pseudomurein, a structural analogue of murein. Pseudomurein differs from murein in containing the unique archaeal sugar N-acetyltalosaminuronic acid instead of N-acetylmuramic acid, β-1,3 glycosidic bonds in place of β-1,4 bonds and only l-amino acids in the peptide cross-links. We have determined crystal structures of methanogen pseudomurein peptide ligases (termed pMurE) from Methanothermus fervidus (Mfer762) and Methanothermobacter thermautotrophicus (Mth734) that are structurally most closely related to bacterial MurE peptide ligases. The homology of the archaeal pMurE and bacterial MurE enzymes is clear both in the overall structure and at the level of each of the three domains. In addition, we identified two UDP-binding sites in Mfer762 pMurE, one at the exterior surface of the interface of the N-terminal and middle domains, and a second site at an inner surface continuous with the highly conserved interface of the three domains. Residues involved in ATP binding in MurE are conserved in pMurE, suggesting that a similar ATP-binding pocket is present at the interface of the middle and the C-terminal domains of pMurE. The presence of pMurE ligases in members of the Methanobacteriales and Methanopyrales, that are structurally related to bacterial MurE ligases, supports the idea that the biosynthetic origins of archaeal pseudomurein and bacterial peptidoglycan cell walls are evolutionarily related.
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Affiliation(s)
- Bishwa P Subedi
- AgResearch Ltd, Grasslands, Tennent Drive, Palmerston North, 4442, New Zealand.,School of Natural Sciences, Massey University, Palmerston North 4442, New Zealand.,Present address: Faculty of Medicine, Nursing and Health Sciences, Monash Biomedicine Discovery Institute, Monash University, Victoria 3800, Australia
| | - Linley R Schofield
- AgResearch Ltd, Grasslands, Tennent Drive, Palmerston North, 4442, New Zealand
| | - Vincenzo Carbone
- AgResearch Ltd, Grasslands, Tennent Drive, Palmerston North, 4442, New Zealand
| | - Maximilian Wolf
- AgResearch Ltd, Grasslands, Tennent Drive, Palmerston North, 4442, New Zealand.,Present address: Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, Centre for Water and Environmental Research, University of Duisburg-Essen, 45141 Essen, Germany
| | - William F Martin
- Institute for Molecular Evolution, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Ron S Ronimus
- AgResearch Ltd, Grasslands, Tennent Drive, Palmerston North, 4442, New Zealand
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Lee TH, Kim KS, Kim JH, Jeong JH, Woo HR, Park SR, Sohn MH, Lee HJ, Rhee JH, Cha SS, Hwang JH, Chung KM. Novel short peptide tag from a bacterial toxin for versatile applications. J Immunol Methods 2020; 479:112750. [PMID: 31981564 DOI: 10.1016/j.jim.2020.112750] [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: 06/24/2019] [Revised: 12/25/2019] [Accepted: 01/21/2020] [Indexed: 11/26/2022]
Abstract
The specific recognition between a monoclonal antibody (mAb) and its epitope can be used in a tag system that has proved valuable in a wide range of biological applications. Herein, we describe a novel tag called RA-tag that is composed of a seven amino acid sequence (DIDLSRI) and recognized by a highly specific mAb, 47RA, against the bacterial toxin Vibrio vulnificus RtxA1/MARTXVv. By using recombinant proteins with the RA-tag at the N-terminal, C-terminal, or an internal site, we demonstrated that the tag system could be an excellent biological system for both protein purification and protein detection in enzyme-linked immunosorbent, Western blot, flow cytometry, and immunofluorescence staining analyses in Escherichia coli, mammalian cell lines, yeast, and plant. In addition, our RA-tag/47RA mAb combination showed high sensitivity and reliable affinity (KD = 5.90 × 10-8 M) when compared with conventional tags. Overall, our results suggest that the RA-tag system could facilitate the development of a broadly applicable tag system for biological research.
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Affiliation(s)
- Tae Hee Lee
- Department of Microbiology and Immunology, Jeonbuk National University Medical School, Jeonju, Jeonbuk 54896, Republic of Korea; Institute for Medical Science, Jeonbuk National University Medical School, Jeonju, Jeonbuk 54896, Republic of Korea
| | - Kwang Soo Kim
- Department of Microbiology, Chonnam National University Medical School, Hwasun-gun 58128, Republic of Korea; Combinatorial Tumor Immunotherapy Medical Research Center, Chonnam National University Medical School, Hwasun-gun 58128, Republic of Korea
| | - Jin Hee Kim
- Subtropical Horticulture Research Institute, Jeju National University, Jeju 63243, Republic of Korea; Department of New Biology, DGIST, Daegu 42988, Republic of Korea
| | - Jae-Ho Jeong
- Department of Microbiology, Chonnam National University Medical School, Hwasun-gun 58128, Republic of Korea; Combinatorial Tumor Immunotherapy Medical Research Center, Chonnam National University Medical School, Hwasun-gun 58128, Republic of Korea
| | - Hye Ryun Woo
- Department of New Biology, DGIST, Daegu 42988, Republic of Korea
| | - So Ra Park
- New Drug Development Center, Osong Medical Innovation Foundation, Cheongju, Chungbuk 28160, Republic of Korea
| | - Myung-Ho Sohn
- New Drug Development Center, Osong Medical Innovation Foundation, Cheongju, Chungbuk 28160, Republic of Korea
| | - Hyeon Ju Lee
- Department of Microbiology and Immunology, Jeonbuk National University Medical School, Jeonju, Jeonbuk 54896, Republic of Korea
| | - Joon Haeng Rhee
- Department of Microbiology, Chonnam National University Medical School, Hwasun-gun 58128, Republic of Korea; Combinatorial Tumor Immunotherapy Medical Research Center, Chonnam National University Medical School, Hwasun-gun 58128, Republic of Korea; Clinical Vaccine R&D Center, Chonnam National University Medical School, Hwasun-gun 58128, Republic of Korea; Vaxcell-Bio Therapeutics, Hwasun-gun 58141, Republic of Korea
| | - Sun-Shin Cha
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Joo-Hee Hwang
- Department of Internal Medicine, Jeonbuk National University Medical School, Jeonju, Jeonbuk 54896, Republic of Korea; Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, Jeonbuk 54907, Republic of Korea.
| | - Kyung Min Chung
- Department of Microbiology and Immunology, Jeonbuk National University Medical School, Jeonju, Jeonbuk 54896, Republic of Korea; Institute for Medical Science, Jeonbuk National University Medical School, Jeonju, Jeonbuk 54896, Republic of Korea; Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, Jeonbuk 54907, Republic of Korea.
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5
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Nöldeke ER, Stehle T. Unraveling the mechanism of peptidoglycan amidation by the bifunctional enzyme complex GatD/MurT: A comparative structural approach. Int J Med Microbiol 2019; 309:151334. [PMID: 31383542 DOI: 10.1016/j.ijmm.2019.151334] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 07/11/2019] [Accepted: 07/17/2019] [Indexed: 10/26/2022] Open
Abstract
The bacterial cell wall provides structural integrity to the cell and protects the cell from internal pressure and the external environment. During the course of the twelve-year funding period of the Collaborative Research Center 766, our work has focused on conducting structure-function studies of enzymes that modify (synthesize or cleave) cell wall components of a range of bacteria including Staphylococcus aureus, Staphylococcus epidermidis, and Nostoc punctiforme. Several of our structures represent promising targets for interference. In this review, we highlight a recent structure-function analysis of an enzyme complex that is responsible for the amidation of Lipid II, a peptidoglycan precursor, in S. aureus.
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Affiliation(s)
- Erik R Nöldeke
- Interfaculty Institute of Biochemistry, University of Tübingen, D-72076 Tübingen, Germany
| | - Thilo Stehle
- Interfaculty Institute of Biochemistry, University of Tübingen, D-72076 Tübingen, Germany; Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA.
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6
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Ahmad S, Murtaza UA, Raza S, Azam SS. Blocking the catalytic mechanism of MurC ligase enzyme from Acinetobacter baumannii: An in Silico guided study towards the discovery of natural antibiotics. J Mol Liq 2019; 281:117-133. [DOI: 10.1016/j.molliq.2019.02.051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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7
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Nöldeke ER, Muckenfuss LM, Niemann V, Müller A, Störk E, Zocher G, Schneider T, Stehle T. Structural basis of cell wall peptidoglycan amidation by the GatD/MurT complex of Staphylococcus aureus. Sci Rep 2018; 8:12953. [PMID: 30154570 PMCID: PMC6113224 DOI: 10.1038/s41598-018-31098-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 08/06/2018] [Indexed: 01/09/2023] Open
Abstract
The peptidoglycan of Staphylococcus aureus is highly amidated. Amidation of α-D-isoglutamic acid in position 2 of the stem peptide plays a decisive role in the polymerization of cell wall building blocks. S. aureus mutants with a reduced degree of amidation are less viable and show increased susceptibility to methicillin, indicating that targeting the amidation reaction could be a useful strategy to combat this pathogen. The enzyme complex that catalyzes the formation of α-D-isoglutamine in the Lipid II stem peptide was identified recently and shown to consist of two subunits, the glutamine amidotransferase-like protein GatD and the Mur ligase homolog MurT. We have solved the crystal structure of the GatD/MurT complex at high resolution, revealing an open, boomerang-shaped conformation in which GatD is docked onto one end of MurT. Putative active site residues cluster at the interface between GatD and MurT and are contributed by both proteins, thus explaining the requirement for the assembled complex to carry out the reaction. Site-directed mutagenesis experiments confirm the validity of the observed interactions. Small-angle X-ray scattering data show that the complex has a similar conformation in solution, although some movement at domain interfaces can occur, allowing the two proteins to approach each other during catalysis. Several other Gram-positive pathogens, including Streptococcus pneumoniae, Clostridium perfringens and Mycobacterium tuberculosis have homologous enzyme complexes. Combined with established biochemical assays, the structure of the GatD/MurT complex provides a solid basis for inhibitor screening in S. aureus and other pathogens.
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Affiliation(s)
- Erik R Nöldeke
- Interfaculty Institute of Biochemistry, University of Tübingen, D-72076, Tübingen, Germany
| | - Lena M Muckenfuss
- Interfaculty Institute of Biochemistry, University of Tübingen, D-72076, Tübingen, Germany.,Department of Biochemistry, University of Zurich, CH-8057, Zurich, Switzerland
| | - Volker Niemann
- Interfaculty Institute of Biochemistry, University of Tübingen, D-72076, Tübingen, Germany.,Hain Lifescience GmbH, D-72147, Nehren, Germany
| | - Anna Müller
- Institute for Pharmaceutical Microbiology, University of Bonn, D-53115, Bonn, Germany
| | - Elena Störk
- Interfaculty Institute of Biochemistry, University of Tübingen, D-72076, Tübingen, Germany
| | - Georg Zocher
- Interfaculty Institute of Biochemistry, University of Tübingen, D-72076, Tübingen, Germany
| | - Tanja Schneider
- Institute for Pharmaceutical Microbiology, University of Bonn, D-53115, Bonn, Germany
| | - Thilo Stehle
- Interfaculty Institute of Biochemistry, University of Tübingen, D-72076, Tübingen, Germany. .,Vanderbilt University School of Medicine, Nashville, Tennessee, 37232, USA.
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8
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Morlot C, Straume D, Peters K, Hegnar OA, Simon N, Villard AM, Contreras-Martel C, Leisico F, Breukink E, Gravier-Pelletier C, Le Corre L, Vollmer W, Pietrancosta N, Håvarstein LS, Zapun A. Structure of the essential peptidoglycan amidotransferase MurT/GatD complex from Streptococcus pneumoniae. Nat Commun 2018; 9:3180. [PMID: 30093673 PMCID: PMC6085368 DOI: 10.1038/s41467-018-05602-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 07/17/2018] [Indexed: 11/08/2022] Open
Abstract
The universality of peptidoglycan in bacteria underlies the broad spectrum of many successful antibiotics. However, in our times of widespread resistance, the diversity of peptidoglycan modifications offers a variety of new antibacterials targets. In some Gram-positive species such as Streptococcus pneumoniae, Staphylococcus aureus, or Mycobacterium tuberculosis, the second residue of the peptidoglycan precursor, D-glutamate, is amidated into iso-D-glutamine by the essential amidotransferase MurT/GatD complex. Here, we present the structure of this complex at 3.0 Å resolution. MurT has central and C-terminal domains similar to Mur ligases with a cysteine-rich insertion, which probably binds zinc, contributing to the interface with GatD. The mechanism of amidation by MurT is likely similar to the condensation catalyzed by Mur ligases. GatD is a glutaminase providing ammonia that is likely channeled to the MurT active site through a cavity network. The structure and assay presented here constitute a knowledge base for future drug development studies.
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Affiliation(s)
- Cécile Morlot
- Université Grenoble Alpes, CNRS, CEA, IBS UMR 5075, 38044, Grenoble, France
| | - Daniel Straume
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, 1432, Norway
| | - Katharina Peters
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Bioscience, Newcastle University, Newcastle Upon Tyne, NE2 4AX, United Kingdom
| | - Olav A Hegnar
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, 1432, Norway
| | - Nolwenn Simon
- Université Grenoble Alpes, CNRS, CEA, IBS UMR 5075, 38044, Grenoble, France
| | - Anne-Marie Villard
- Université Grenoble Alpes, CNRS, CEA, IBS UMR 5075, 38044, Grenoble, France
| | | | - Francisco Leisico
- Departamento de Química, Universidade Nova de Lisboa, Caparica, 2829-516, Portugal
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, 3584, The Netherlands
| | - Christine Gravier-Pelletier
- Université Paris Descartes, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques UMR 8601 CNRS, Sorbonne Paris Cité (USPC), Paris, 75006, France
| | - Laurent Le Corre
- Université Paris Descartes, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques UMR 8601 CNRS, Sorbonne Paris Cité (USPC), Paris, 75006, France
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Bioscience, Newcastle University, Newcastle Upon Tyne, NE2 4AX, United Kingdom
| | - Nicolas Pietrancosta
- Université Paris Descartes, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques UMR 8601 CNRS, Sorbonne Paris Cité (USPC), Paris, 75006, France
| | - Leiv Sigve Håvarstein
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, 1432, Norway
| | - André Zapun
- Université Grenoble Alpes, CNRS, CEA, IBS UMR 5075, 38044, Grenoble, France.
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9
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Ahmad S, Raza S, Uddin R, Azam SS. Binding mode analysis, dynamic simulation and binding free energy calculations of the MurF ligase from Acinetobacter baumannii. J Mol Graph Model 2017; 77:72-85. [PMID: 28843462 DOI: 10.1016/j.jmgm.2017.07.024] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 07/20/2017] [Accepted: 07/21/2017] [Indexed: 01/16/2023]
Abstract
MurF ligase catalyzes the final cytoplasmic step of bacterial peptidoglycan biosynthesis and, as such, is a validated target for therapeutic intervention. Herein, we performed molecular docking to identify putative inhibitors of Acinetobacter baumannii MurF (AbMurF). Based on comparative docking analysis, compound 114 (ethyl pyridine substituted 3-cyanothiophene) was predicted to potentially be the most active ligand. Computational pharmacokinetic characterization of drug-likeness of the compound showed it to fulfil all the parameters of Muegge and the MDDR rule. A molecular dynamic simulation of 114 indicated the complex to be stable on the basis of an average root mean square deviation (RMSD) value of 2.09Å for the ligand. The stability of the complex was further supported by root mean square fluctuation (RMSF), beta factor and radius of gyration values. Analyzing the complex using radial distribution function (RDF) and a novel analytical tool termed the axial frequency distribution (AFD) illustrated that after simulation the ligand is positioned in close vicinity of the protein active site where Thr42 and Asp43 participate in hydrogen bonding and stabilization of the complex. Binding free energy calculations based on the Poisson-Boltzmann or Generalized-Born Surface Area Continuum Solvation (MM(PB/GB)SA) method indicated the van der Waals contribution to the overall binding energy of the complex to be dominant along with electrostatic contributions involving the hot spot amino acids from the protein active site. The present results indicate that the screened compound 114 may act as a parent structure for designing potent derivatives against AbMurF in specific and MurF of other bacterial pathogens in general.
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Affiliation(s)
- Sajjad Ahmad
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Saad Raza
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Reaz Uddin
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Syed Sikander Azam
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad 45320, Pakistan.
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