1
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Chauhan M, Barot R, Yadav R, Joshi K, Mirza S, Chikhale R, Srivastava VK, Yadav MR, Murumkar PR. The Mycobacterium tuberculosis Cell Wall: An Alluring Drug Target for Developing Newer Anti-TB Drugs-A Perspective. Chem Biol Drug Des 2024; 104:e14612. [PMID: 39237482 DOI: 10.1111/cbdd.14612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 06/26/2024] [Accepted: 08/05/2024] [Indexed: 09/07/2024]
Abstract
The Mycobacterium cell wall is a capsule-like structure comprising of various layers of biomolecules such as mycolic acid, peptidoglycans, and arabinogalactans, which provide the Mycobacteria a sort of cellular shield. Drugs like isoniazid, ethambutol, cycloserine, delamanid, and pretomanid inhibit cell wall synthesis by inhibiting one or the other enzymes involved in cell wall synthesis. Many enzymes present across these layers serve as potential targets for the design and development of newer anti-TB drugs. Some of these targets are currently being exploited as the most druggable targets like DprE1, InhA, and MmpL3. Many of the anti-TB agents present in clinical trials inhibit cell wall synthesis. The present article covers a systematic perspective of developing cell wall inhibitors targeting various enzymes involved in cell wall biosynthesis as potential drug candidates for treating Mtb infection.
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Affiliation(s)
- Monica Chauhan
- Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
| | - Rahul Barot
- Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
| | - Rasana Yadav
- Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
| | - Karan Joshi
- Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
| | - Sadaf Mirza
- Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
| | - Rupesh Chikhale
- The Cambridge Crystallography Data Center, Cambridge, UK
- School of Pharmacy, University College London, London, UK
| | | | - Mange Ram Yadav
- Centre of Research for Development, Parul University, Vadodara, Gujarat, India
| | - Prashant R Murumkar
- Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
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2
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Hodyna D, Klipkov A, Kachaeva M, Shulha Y, Gerus I, Metelytsia L, Kovalishyn V. In Silico Design and In Vitro Assessment of Bicyclic Trifluoromethylated Pyrroles as New Antibacterial and Antifungal Agents. Chem Biodivers 2024; 21:e202400638. [PMID: 38837284 DOI: 10.1002/cbdv.202400638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/31/2024] [Accepted: 06/04/2024] [Indexed: 06/07/2024]
Abstract
QSAR studies on the number of compounds tested as S. aureus inhibitors were performed using an interactive Online Chemical Database and Modeling Environment (OCHEM) web platform. The predictive ability of the developed consensus QSAR model was q2=0.79±0.02. The consensus prediction for the external evaluation set afforded high predictive power (q2=0.82±0.03). The models were applied to screen a virtual chemical library with anti-S. aureus activity. Six promising new bicyclic trifluoromethylated pyrroles were identified, synthesized and evaluated in vitro against S. aureus, E. coli, and A. baumannii for their antibacterial activity and against C. albicans, C. krusei and C. glabrata for their antifungal activity. The synthesized compounds were characterized by 1H, 19F, and 13C NMR and elemental analysis. The antimicrobial activity assessment indicated that trifluoromethylated pyrroles 9 and 11 demonstrated the greatest antibacterial and antifungal effects against all the tested pathogens, especially against multidrug-resistant strains. The acute toxicity of the compounds to Daphnia magna ranged from 1.21 to 33.39 mg/L (moderately and slightly toxic). Based on the docking results, it can be suggested that the antibacterial and antifungal effects of the compounds can be explained by the inhibition of bacterial wall component synthesis.
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Affiliation(s)
- Diana Hodyna
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry of the National Academy of Sciences of Ukraine, 1 Academician Kukhar Str., Kyiv, 02094, Ukraine
| | - Anton Klipkov
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry of the National Academy of Sciences of Ukraine, 1 Academician Kukhar Str., Kyiv, 02094, Ukraine
- National University of Kyiv -, Mohyla Academy, 2, Skovorody Str., Kyiv, 04070, Ukraine
| | - Maryna Kachaeva
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry of the National Academy of Sciences of Ukraine, 1 Academician Kukhar Str., Kyiv, 02094, Ukraine
| | - Yurii Shulha
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry of the National Academy of Sciences of Ukraine, 1 Academician Kukhar Str., Kyiv, 02094, Ukraine
| | - Igor Gerus
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry of the National Academy of Sciences of Ukraine, 1 Academician Kukhar Str., Kyiv, 02094, Ukraine
| | - Larysa Metelytsia
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry of the National Academy of Sciences of Ukraine, 1 Academician Kukhar Str., Kyiv, 02094, Ukraine
| | - Vasyl Kovalishyn
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry of the National Academy of Sciences of Ukraine, 1 Academician Kukhar Str., Kyiv, 02094, Ukraine
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3
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Aktekin MB, Oksuz Z, Turkmenoglu B, Istifli ES, Kuzucu M, Algul O. Synthesis and evaluation of di-heterocyclic benzazole compounds as potential antibacterial and anti-biofilm agents against Staphylococcus aureus. Chem Biol Drug Des 2024; 104:e14601. [PMID: 39085984 DOI: 10.1111/cbdd.14601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/26/2024] [Accepted: 07/19/2024] [Indexed: 08/02/2024]
Abstract
Cumulative escalation in antibiotic-resistant pathogens necessitates the quest for novel antimicrobial agents, as current options continue to diminish bacterial resistance. Herein, we report the synthesis of di-heterocyclic benzazole structures (12-19) and their in vitro evaluation for some biological activities. Compounds 16 and 17 demonstrated potent antibacterial activity (MIC = 7.81 μg/mL) against Staphylococcus aureus, along with significant anti-biofilm activity. Noteworthy is the capability of Compound 17 to inhibit biofilm formation by at least 50% at sub-MIC (3.90 μg/mL) concentration. Furthermore, both compounds exhibited the potential to inhibit preformed biofilm by at least 50% at the MIC concentration (7.81 μg/mL). Additionally, Compounds 16 and 17 were examined for cytotoxic effects in HFF-1 cells, using the MTT method, and screened for binding interactions within the active site of S. aureus DNA gyrase using in silico molecular docking technique, employing AutoDock 4.2.6 and Schrödinger Glidse programs. Overall, our findings highlight Compounds 16 and 17 as promising scaffolds warranting further optimization for the development of effective antibacterial and anti-biofilm agents.
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Affiliation(s)
- Mine Buga Aktekin
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Mersin University, Mersin, Turkey
- Department of Pharmacy Services, Vocational School of Health Services, Tarsus University, Mersin, Turkey
| | - Zehra Oksuz
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Mersin University, Mersin, Turkey
| | - Burcin Turkmenoglu
- Department of Analytical Chemistry, Faculty of Pharmacy, Erzincan Binali Yildirim University, Erzincan, Turkey
| | - Erman Salih Istifli
- Department of Biology, Faculty of Science and Literature, Çukurova University, Adana, Turkey
| | - Mehmet Kuzucu
- Department of Biology, Faculty of Arts and Sciences, Erzincan Binali Yıldırım University, Erzincan, Turkey
| | - Oztekin Algul
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Mersin University, Mersin, Turkey
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erzincan Binali Yildirim University, Erzincan, Turkey
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Imran M, Haider A, Shahzadi A, Mustajab M, Ul-Hamid A, Ullah H, Khan S, Abd-Rabboh HSM, Ikram M. Silver and carbon nitride-doped nickel selenide for effective dye decolorization and bactericidal activity: in silico docking study. RSC Adv 2024; 14:20004-20019. [PMID: 38911830 PMCID: PMC11191054 DOI: 10.1039/d4ra01437e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 06/07/2024] [Indexed: 06/25/2024] Open
Abstract
In this study, nickel selenide (NiSe), Ag/C3N4-NiSe, and C3N4/Ag-NiSe nanowires (NWs) were synthesized via coprecipitation. The prepared NWs were employed for the degradation of the rhodamine B (RhB) dye in the absence of light using sodium borohydride (NaBH4), bactericidal activity against pathogenic Staphylococcus aureus (S. aureus) and in silico docking study to investigate the d-alanine ligase (DDl) and deoxyribonucleic acid (DNA) gyrase of S. aureus. NWs demonstrate a catalytic degradation efficiency of 69.58% toward RhB in a basic medium. The percentage efficacy of the synthesized materials was evaluated as 19.12-42.62% at low and 36.61-49.72% at high concentrations against pathogenic S. aureus. Molecular docking results suggest that both C3N4/Ag-doped NiSe and Ag/C3N4-doped NiSe possess inhibitory activities toward DDl and DNA gyrase of S. aureus, which coincides with the in vitro bactericidal activity. Based on the research outcomes, the synthesized NWs show potential as an effective agent for water purification and resistance to microbial contaminants.
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Affiliation(s)
- Muhammad Imran
- Department of Chemistry, Government College University Faisalabad Pakpattan Road Sahiwal Punjab 57000 Pakistan
| | - Ali Haider
- Department of Clinical Sciences, Faculty of Veterinary and Animal Sciences, Muhammad Nawaz Shareef University of Agriculture Multan 66000 Punjab Pakistan
| | - Anum Shahzadi
- Department of Pharmacy, COMSATS University Islamabad Lahore Campus 54000 Pakistan
| | - Muhammad Mustajab
- Solar Cell Applications Research Lab, Department of Physics, Government College University Lahore Lahore 54000 Punjab Pakistan
| | - Anwar Ul-Hamid
- Core Research Facilities, King Fahd University of Petroleum & Minerals Dhahran 31261 Saudi Arabia
| | - Hameed Ullah
- Laboratory of Nanomaterials for Renewable Energy and Artificial Photosynthesis (NanoREAP), Institute of Physics, UFRGS 91509-900 Porto Alegre Rio Grande do Sul Brazil
| | - Sherdil Khan
- Laboratory of Nanomaterials for Renewable Energy and Artificial Photosynthesis (NanoREAP), Institute of Physics, UFRGS 91509-900 Porto Alegre Rio Grande do Sul Brazil
| | - Hisham S M Abd-Rabboh
- Chemistry Department, College of Science, King Khalid University P. O. Box 9004 Abha 62223 Saudi Arabia
| | - Muhammad Ikram
- Solar Cell Applications Research Lab, Department of Physics, Government College University Lahore Lahore 54000 Punjab Pakistan
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Panda S, Jayasinghe YP, Shinde DD, Bueno E, Stastny A, Bertrand BP, Chaudhari SS, Kielian T, Cava F, Ronning DR, Thomas VC. Staphylococcus aureus counters organic acid anion-mediated inhibition of peptidoglycan cross-linking through robust alanine racemase activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.15.575639. [PMID: 38293037 PMCID: PMC10827132 DOI: 10.1101/2024.01.15.575639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Weak organic acids are commonly found in host niches colonized by bacteria, and they can inhibit bacterial growth as the environment becomes acidic. This inhibition is often attributed to the toxicity resulting from the accumulation of high concentrations of organic anions in the cytosol, which disrupts cellular homeostasis. However, the precise cellular targets that organic anions poison and the mechanisms used to counter organic anion intoxication in bacteria have not been elucidated. Here, we utilize acetic acid, a weak organic acid abundantly found in the gut to investigate its impact on the growth of Staphylococcus aureus. We demonstrate that acetate anions bind to and inhibit d-alanyl-d-alanine ligase (Ddl) activity in S. aureus. Ddl inhibition reduces intracellular d-alanyl-d-alanine (d-Ala-d-Ala) levels, compromising staphylococcal peptidoglycan cross-linking and cell wall integrity. To overcome the effects of acetate-mediated Ddl inhibition, S. aureus maintains a high intracellular d-Ala pool through alanine racemase (Alr1) activity and additionally limits the flux of d-Ala to d-glutamate by controlling d-alanine aminotransferase (Dat) activity. Surprisingly, the modus operandi of acetate intoxication in S. aureus is common to multiple biologically relevant weak organic acids indicating that Ddl is a conserved target of small organic anions. These findings suggest that S. aureus may have evolved to maintain high intracellular d-Ala concentrations, partly to counter organic anion intoxication.
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Affiliation(s)
- Sasmita Panda
- Center for Staphylococcal Research, Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198-5900, USA
| | - Yahani P Jayasinghe
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Dhananjay D Shinde
- Center for Staphylococcal Research, Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198-5900, USA
| | - Emilio Bueno
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, Umea SE-90187, Sweden
| | - Amanda Stastny
- Center for Staphylococcal Research, Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198-5900, USA
| | - Blake P Bertrand
- Center for Staphylococcal Research, Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198-5900, USA
| | - Sujata S Chaudhari
- Center for Staphylococcal Research, Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198-5900, USA
| | - Tammy Kielian
- Center for Staphylococcal Research, Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198-5900, USA
| | - Felipe Cava
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, Umea SE-90187, Sweden
| | - Donald R Ronning
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Vinai C Thomas
- Center for Staphylococcal Research, Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198-5900, USA
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Becker R, Pederick JL, Dawes EG, Bruning JB, Abell AD. Structure-guided design and synthesis of ATP-competitive N-acyl-substituted sulfamide d-alanine-d-alanine ligase inhibitors. Bioorg Med Chem 2023; 96:117509. [PMID: 37948922 DOI: 10.1016/j.bmc.2023.117509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/10/2023] [Accepted: 10/24/2023] [Indexed: 11/12/2023]
Abstract
d-Alanine-d-alanine ligase (Ddl) catalyses the ATP-dependent formation of d-Ala-d-Ala, a critical component in bacterial cell wall biosynthesis and is a validated target for new antimicrobial agents. Here, we describe the structure-guided design, synthesis, and evaluation of ATP-competitive N-acyl-substituted sulfamides 27-36, 42, 46, 47 as inhibitors of Staphylococcus aureus Ddl (SaDdl). A crystal structure of SaDdl complexed with ATP and d-Ala-d-Ala (PDB: 7U9K) identified ATP-mimetic 8 as an initial scaffold for further inhibitor design. Evaluation of 8 in SaDdl enzyme inhibition assays revealed the ability to reduce enzyme activity to 72 ± 8 % (IC50 = 1.6 mM). The sulfamide linker of 8 was extended with 2-(4-methoxyphenyl)ethanol to give 29, to investigate further interactions with the d-Ala pocket of SaDdl, as predicted by molecular docking. This compound reduced enzyme activity to 89 ± 1 %, with replacement of the 4-methoxyphenyl group in 29 with alternative phenyl substituents (27, 28, 31-33, 35, 36) failing to significantly improve on this (80-89 % remaining enzyme activity). Exchanging these phenyl substituents with selected heterocycles (42, 46, 47) did improve activity, with the most active compound (42) reducing SaDdl activity to 70 ± 1 % (IC50 = 1.7 mM), which compares favourably to the FDA-approved inhibitor d-cycloserine (DCS) (IC50 = 0.1 mM). To the best of our knowledge, this is the first reported study of bisubstrate SaDdl inhibitors.
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Affiliation(s)
- Rouven Becker
- Department of Chemistry, School of Physics, Chemistry and Earth Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia; Institute for Photonics and Advanced Sensing, (IPAS), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia; Centre for Nanoscale BioPhotonics (CNBP), University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Jordan L Pederick
- Institute for Photonics and Advanced Sensing, (IPAS), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Edward G Dawes
- Department of Chemistry, School of Physics, Chemistry and Earth Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia; Centre for Nanoscale BioPhotonics (CNBP), University of Adelaide, Adelaide, South Australia 5005, Australia
| | - John B Bruning
- Institute for Photonics and Advanced Sensing, (IPAS), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Andrew D Abell
- Department of Chemistry, School of Physics, Chemistry and Earth Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia; Institute for Photonics and Advanced Sensing, (IPAS), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia; Centre for Nanoscale BioPhotonics (CNBP), University of Adelaide, Adelaide, South Australia 5005, Australia.
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7
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Pederick JL, Woolman JC, Bruning JB. Comparative functional and structural analysis of Pseudomonas aeruginosa d-alanine-d-alanine ligase isoforms as prospective antibiotic targets. FEBS J 2023; 290:5536-5553. [PMID: 37581574 DOI: 10.1111/febs.16932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/02/2023] [Accepted: 08/14/2023] [Indexed: 08/16/2023]
Abstract
Pseudomonas aeruginosa is a major human pathogen in the healthcare setting. The emergence of multi-drug-resistant and extensive drug-resistant P. aeruginosa is of great concern, and clearly indicates that new alternatives to current first-line antibiotics are required in the future. Inhibition of d-alanine-d-alanine production presents as a promising avenue as it is a key component in the essential process of cell wall biosynthesis. In P. aeruginosa, d-alanine-d-alanine production is facilitated by two isoforms, d-alanine-d-alanine ligase A (PaDdlA) and d-alanine-d-alanine ligase B (PaDdlA), but neither enzyme has been individually characterised to date. Here, we present the functional and structural characterisation of PaDdlA and PaDdlB, and assess their potential as antibiotic targets. This was achieved using a combination of in vitro enzyme-activity assays and X-ray crystallography. The former revealed that both isoforms effectively catalyse d-alanine-d-alanine production with near identical efficiency, and that this is effectively disrupted by the model d-alanine-d-alanine ligase inhibitor, d-cycloserine. Next, each isoform was co-crystallised with ATP and either d-alanine-d-alanine or d-cycloserine, allowing direct comparison of the key structural features. Both isoforms possess the same structural architecture and share a high level of conservation within the active site. Although residues forming the d-alanine pocket are completely conserved, the ATP-binding pocket possesses several amino acid substitutions resulting in a differing chemical environment around the ATP adenine base. Together, these findings support that the discovery of dual PaDdlA/PaDdlB competitive inhibitors is a viable approach for developing new antibiotics against P. aeruginosa.
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Affiliation(s)
- Jordan L Pederick
- Institute for Photonics and Advanced Sensing (IPAS), School of Biological Sciences, The University of Adelaide, SA, Australia
| | - Jessica C Woolman
- School of Biological Sciences, The University of Adelaide, SA, Australia
| | - John B Bruning
- Institute for Photonics and Advanced Sensing (IPAS), School of Biological Sciences, The University of Adelaide, SA, Australia
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Hodyna D, Kovalishyn V, Kachaeva M, Shulha Y, Klipkov A, Shaitanova E, Kobzar O, Shablykin O, Metelytsia L. In Silico, in Vitro and in Vivo Study of Substituted Imidazolidinone Sulfonamides as Antibacterial Agents. Chem Biodivers 2023; 20:e202301267. [PMID: 37943002 DOI: 10.1002/cbdv.202301267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 11/10/2023]
Abstract
New substituted imidazolidinone sulfonamides have been developed using a rational drug design strategy. Predictive QSAR models for the search of new antibacterials were created using the OCHEM platform. Regression models were applied to verify a virtual chemical library of new imidazolidinone derivatives designed to have antibacterial activity. A number of substituted imidazolidinone sulfonamides as effective antibacterial agents were identified by QSAR prediction, synthesized and characterized by spectral and elemental, and tested in vitro. Six studied compounds have shown the highest in vitro antibacterial activity against Gram-negative E. coli and Gram-positive S. aureus multidrug-resistant strains. The in vivo acute toxicity of these imidazolidinone sulfonamides based on the LC50 value ranged from 16.01 to 44.35 mg/L (slightly toxic compounds class). The results of molecular docking suggest that the antibacterial mechanism of the compounds can be associated with the inhibition of post-translational modification processes of bacterial peptides and proteins.
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Affiliation(s)
- Diana Hodyna
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry of the National Academy of Sciences of Ukraine, 02094, Academician Kukhar Str, 1, Kyiv, Ukraine
| | - Vasyl Kovalishyn
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry of the National Academy of Sciences of Ukraine, 02094, Academician Kukhar Str, 1, Kyiv, Ukraine
| | - Maryna Kachaeva
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry of the National Academy of Sciences of Ukraine, 02094, Academician Kukhar Str, 1, Kyiv, Ukraine
| | - Yurii Shulha
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry of the National Academy of Sciences of Ukraine, 02094, Academician Kukhar Str, 1, Kyiv, Ukraine
| | - Anton Klipkov
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry of the National Academy of Sciences of Ukraine, 02094, Academician Kukhar Str, 1, Kyiv, Ukraine
| | - Elena Shaitanova
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry of the National Academy of Sciences of Ukraine, 02094, Academician Kukhar Str, 1, Kyiv, Ukraine
| | - Oleksandr Kobzar
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry of the National Academy of Sciences of Ukraine, 02094, Academician Kukhar Str, 1, Kyiv, Ukraine
| | - Oleh Shablykin
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry of the National Academy of Sciences of Ukraine, 02094, Academician Kukhar Str, 1, Kyiv, Ukraine
| | - Larysa Metelytsia
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry of the National Academy of Sciences of Ukraine, 02094, Academician Kukhar Str, 1, Kyiv, Ukraine
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Ngema SS, Khumalo SH, Ojo MC, Pooe OJ, Malilehe TS, Basson AK, Madoroba E. Evaluation of Antimicrobial Activity by Marine Nocardiopsis dassonvillei against Foodborne Listeria monocytogenes and Shiga Toxin-Producing Escherichia coli. Microorganisms 2023; 11:2539. [PMID: 37894198 PMCID: PMC10609338 DOI: 10.3390/microorganisms11102539] [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: 08/09/2023] [Revised: 09/12/2023] [Accepted: 09/30/2023] [Indexed: 10/29/2023] Open
Abstract
The emergence of multidrug-resistant pathogens creates public health challenges, prompting a continuous search for effective novel antimicrobials. This study aimed to isolate marine actinomycetes from South Africa, evaluate their in vitro antimicrobial activity against Listeria monocytogenes and Shiga toxin-producing Escherichia coli, and characterize their mechanisms of action. Marine actinomycetes were isolated and identified by 16S rRNA sequencing. Gas chromatography-mass spectrometry (GC-MS) was used to identify the chemical constituents of bioactive actinomycetes' secondary metabolites. Antibacterial activity of the secondary metabolites was assessed by the broth microdilution method, and their mode of actions were predicted using computational docking. While five strains showed antibacterial activity during primary screening, only Nocardiopsis dassonvillei strain SOD(B)ST2SA2 exhibited activity during secondary screening for antibacterial activity. GC-MS identified five major bioactive compounds: 1-octadecene, diethyl phthalate, pentadecanoic acid, 6-octadecenoic acid, and trifluoroacetoxy hexadecane. SOD(B)ST2SA2's extract demonstrated minimum inhibitory concentration and minimum bactericidal concentration, ranging from 0.78-25 mg/mL and 3.13 to > 25 mg/mL, respectively. Diethyl phthalate displayed the lowest bacterial protein-binding energies (kcal/mol): -7.2, dihydrofolate reductase; -6.0, DNA gyrase B; and -5.8, D-alanine:D-alanine ligase. Thus, marine N. dassonvillei SOD(B)ST2SA2 is a potentially good source of antibacterial compounds that can be used to control STEC and Listeria monocytogenes.
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Affiliation(s)
- Siyanda S. Ngema
- Department of Biochemistry and Microbiology, University of Zululand, Private Bag X1001, KwaDlangezwa 3886, South Africa; (S.S.N.); (S.H.K.); (M.C.O.); (A.K.B.)
| | - Solomuzi H. Khumalo
- Department of Biochemistry and Microbiology, University of Zululand, Private Bag X1001, KwaDlangezwa 3886, South Africa; (S.S.N.); (S.H.K.); (M.C.O.); (A.K.B.)
| | - Michael C. Ojo
- Department of Biochemistry and Microbiology, University of Zululand, Private Bag X1001, KwaDlangezwa 3886, South Africa; (S.S.N.); (S.H.K.); (M.C.O.); (A.K.B.)
| | - Ofentse J. Pooe
- Discipline of Biochemistry, School of Life Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South Africa;
| | - Tsolanku S. Malilehe
- Department of Water and Sanitation, University of Limpopo, Private Bag X1106, Polokwane 0727, South Africa;
| | - Albertus K. Basson
- Department of Biochemistry and Microbiology, University of Zululand, Private Bag X1001, KwaDlangezwa 3886, South Africa; (S.S.N.); (S.H.K.); (M.C.O.); (A.K.B.)
| | - Evelyn Madoroba
- Department of Biochemistry and Microbiology, University of Zululand, Private Bag X1001, KwaDlangezwa 3886, South Africa; (S.S.N.); (S.H.K.); (M.C.O.); (A.K.B.)
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10
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Neto NAS, Aguiar TKB, Costa RJP, Mesquita FP, Oliveira LLBD, Moraes MEAD, Montenegro RC, Carneiro RF, Nagano CS, Freitas CDT, Souza PFN. United we stand, divided we fall: in-depth proteomic evaluation of the synergistic effect of Mo-CBP 3-PepI and Ciprofloxacin against Staphylococcus aureus biofilms. BIOFOULING 2023; 39:838-852. [PMID: 37955278 DOI: 10.1080/08927014.2023.2279992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 10/25/2023] [Indexed: 11/14/2023]
Abstract
Staphylococcus aureus forms biofilms, a structure that protects bacterial cells, conferring more resistance to difficult treatment. Synthetic peptides surge as an alternative to overcome the biofilm of multidrug-resistant pathogens. Mo-CBP3-PepI, when combined with Ciprofloxacin, reduced preformed S. aureus biofilm by 50% at low concentrations (0.2 and 6.2 μg. mL-1, respectively). The goal of this study was to evaluate the proteomic profile of biofilms after treatment with the Mo-CBP3-PepI combined with ciprofloxacin. Here, proteomic analysis confirmed with more depth previously described mechanisms and revealed changes in the accumulation of proteins related to DNA and protein metabolism, cell wall biosynthesis, redox metabolism, quorum sensing, and biofilm formation. Some proteins related to DNA and protein metabolism were reduced, while other proteins, like redox system proteins, disappeared in Ciprofloxacin+Mo-CBP3-PepI treatment. Our results indicated a synergistic effect of these two molecules with several mechanisms against S. aureus biofilm and opened new doors for combined treatments with other drugs.
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Affiliation(s)
- Nilton A S Neto
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Tawanny K B Aguiar
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Rayara J P Costa
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Felipe P Mesquita
- Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Lais L B de Oliveira
- Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Maria E A de Moraes
- Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Raquel C Montenegro
- Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Rômulo F Carneiro
- Department of Fisheries Engineering, Federal University of Ceará (UFC), Fortaleza, CE, Brazil
| | - Celso S Nagano
- Department of Fisheries Engineering, Federal University of Ceará (UFC), Fortaleza, CE, Brazil
| | - Cleverson D T Freitas
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Pedro F N Souza
- Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceará, Fortaleza, CE, Brazil
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11
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Jianu C, Rusu LC, Muntean I, Cocan I, Lukinich-Gruia AT, Goleț I, Horhat D, Mioc M, Mioc A, Șoica C, Bujancă G, Ilie AC, Muntean D. In Vitro and In Silico Evaluation of the Antimicrobial and Antioxidant Potential of Thymus pulegioides Essential Oil. Antioxidants (Basel) 2022; 11:2472. [PMID: 36552681 PMCID: PMC9774620 DOI: 10.3390/antiox11122472] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/08/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
The study was designed to analyze and evaluate the antioxidant and antibacterial properties of the essential oils of Thymus pulegioides L. grown in Western Romania. Thymus pulegioides L. essential oil (TPEO) was extracted by steam distillation (0.71% v/w) using a Craveiro-type apparatus. GC-MS investigation of the TPEO identified 39 different compounds, representing 98.46% of total oil. Findings revealed that thymol (22.89%) is the main compound of TPEO, followed by para-cymene (14.57%), thymol methyl ether (11.19%), isothymol methyl ether (10.45%), and beta-bisabolene (9.53%). The oil exhibits good antibacterial effects; C. parapsilosis, C. albicans, S. pyogenes, and S. aureus were the most sensitive strains. The antioxidant activity of TPEO was evaluated by peroxide and thiobarbituric acid value, 1,1-diphenyl-2-picrylhydrazyl radical (DPPH), [2,2′-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium] (ABTS) radical scavenging assay, and beta-carotene/linoleic acid bleaching testing. The antioxidative data recorded reveal, for the first time, that TPEO inhibits primary and secondary oxidation products, in some particular conditions, better than butylated hydroxyanisole (BHA) with significant statistical difference (p < 0.05). Moreover, TPEO antioxidant capabilities in DPPH and ABTS assays outperformed alpha-tocopherol (p < 0.001) and delta-tocopherol (p < 0.001). Molecular docking analysis revealed that one potential target correlated with the TPEO antimicrobial activity was d-alanine-d-alanine ligase (DDl). The best scoring ligand, linalyl anthranilate, shared highly similar binding patterns with the DDl native inhibitor. Furthermore, molecular docking analysis also showed that the main constituents of TPEO are good candidates for xanthine oxidase and lipoxygenase inhibition, making the essential oil a valuable source for protein-targeted antioxidant compounds. Consequently, TPEO may represent a new potential source of antioxidant and antibacterial agents with applicability in the food and pharmaceutic industries.
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Affiliation(s)
- Călin Jianu
- Faculty of Food Engineering, University of Life Sciences “King Michael I” from Timisoara, Calea Aradului 119, 300645 Timisoara, Romania
| | - Laura-Cristina Rusu
- Faculty of Dental Medicine, “Victor Babes” University of Medicine and Pharmacy, 2nd Eftimie Murgu Square, 300041 Timisoara, Romania
- Multidisciplinary Center for Research, Evaluation, Diagnosis and Therapies in Oral Medicine, “Victor Babes” University of Medicine and Pharmacy, Spl. Tudor Vladimir escu 14A, 300173 Timisoara, Romania
| | - Iulia Muntean
- Faculty of Dental Medicine, “Victor Babes” University of Medicine and Pharmacy, 2nd Eftimie Murgu Square, 300041 Timisoara, Romania
- Multidisciplinary Center for Research, Evaluation, Diagnosis and Therapies in Oral Medicine, “Victor Babes” University of Medicine and Pharmacy, Spl. Tudor Vladimir escu 14A, 300173 Timisoara, Romania
| | - Ileana Cocan
- Faculty of Food Engineering, University of Life Sciences “King Michael I” from Timisoara, Calea Aradului 119, 300645 Timisoara, Romania
| | | | - Ionuț Goleț
- Faculty of Economics and Business Administration, West University of Timisoara, 300233 Timisoara, Romania
| | - Delia Horhat
- Faculty of Medicine, “Victor Babes” University of Medicine and Pharmacy, 2nd Eftimie Murgu Square, 300041 Timisoara, Romania
| | - Marius Mioc
- Faculty of Pharmacy, “Victor Babeș” University of Medicine and Pharmacy, Eftimie Murgu Square 2, 300041 Timisoara, Romania
| | - Alexandra Mioc
- Faculty of Pharmacy, “Victor Babeș” University of Medicine and Pharmacy, Eftimie Murgu Square 2, 300041 Timisoara, Romania
| | - Codruța Șoica
- Faculty of Pharmacy, “Victor Babeș” University of Medicine and Pharmacy, Eftimie Murgu Square 2, 300041 Timisoara, Romania
| | - Gabriel Bujancă
- Faculty of Food Engineering, University of Life Sciences “King Michael I” from Timisoara, Calea Aradului 119, 300645 Timisoara, Romania
| | - Adrian Cosmin Ilie
- Faculty of Medicine, “Victor Babes” University of Medicine and Pharmacy, 2nd Eftimie Murgu Square, 300041 Timisoara, Romania
- Center for Translational Research and Systems Medicine, “Victor Babes” University of Medicine and Pharmacy, 2nd Eftimie Murgu Square, 300041 Timisoara, Romania
| | - Delia Muntean
- Faculty of Medicine, “Victor Babes” University of Medicine and Pharmacy, 2nd Eftimie Murgu Square, 300041 Timisoara, Romania
- Multidisciplinary Research Center on Antimicrobial Resistance, “Victor Babes” University of Medicine and Pharmacy, 2nd Eftimie Murgu Square, 300041 Timisoara, Romania
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12
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Chemical composition, antibacterial activity and antioxidant activity of Citrus bergamia essential oil: Molecular docking simulations. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2022.102123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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13
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Lever J, Kreuder F, Henry J, Hung A, Allard PM, Brkljača R, Rix C, Taki AC, Gasser RB, Kaslin J, Wlodkowic D, Wolfender JL, Urban S. Targeted Isolation of Antibiotic Brominated Alkaloids from the Marine Sponge Pseudoceratina durissima Using Virtual Screening and Molecular Networking. Mar Drugs 2022; 20:md20090554. [PMID: 36135743 PMCID: PMC9503778 DOI: 10.3390/md20090554] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/22/2022] [Accepted: 08/25/2022] [Indexed: 11/23/2022] Open
Abstract
Many targeted natural product isolation approaches rely on the use of pre-existing bioactivity information to inform the strategy used for the isolation of new bioactive compounds. Bioactivity information can be available either in the form of prior assay data or via Structure Activity Relationship (SAR) information which can indicate a potential chemotype that exhibits a desired bioactivity. The work described herein utilizes a unique method of targeted isolation using structure-based virtual screening to identify potential antibacterial compounds active against MRSA within the marine sponge order Verongiida. This is coupled with molecular networking-guided, targeted isolation to provide a novel drug discovery procedure. A total of 12 previously reported bromotyrosine-derived alkaloids were isolated from the marine sponge species Pseudoceratina durissima, and the compound, (+)-aeroplysinin-1 (1) displayed activity against the MRSA pathogen (MIC: <32 µg/mL). The compounds (1−3, 6 and 9) were assessed for their central nervous system (CNS) interaction and behavioral toxicity to zebrafish (Danio rerio) larvae, whereby several of the compounds were shown to induce significant hyperactivity. Anthelmintic activity against the parasitic nematode Haemonchus contorutus was also evaluated (2−4, 6−8).
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Affiliation(s)
- James Lever
- School of Science (Applied Chemistry and Environmental Sciences), RMIT University, GPO Box 2476 Melbourne, VIC 3001, Australia
| | - Florian Kreuder
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Jason Henry
- Neurotoxicology Lab., School of Science (Biosciences), RMIT University, Bundoora, VIC 3083, Australia
| | - Andrew Hung
- School of Science (Applied Chemistry and Environmental Sciences), RMIT University, GPO Box 2476 Melbourne, VIC 3001, Australia
| | | | - Robert Brkljača
- Monash Biomedical Imaging, Monash University, Clayton, VIC 3168, Australia
| | - Colin Rix
- School of Science (Applied Chemistry and Environmental Sciences), RMIT University, GPO Box 2476 Melbourne, VIC 3001, Australia
| | - Aya C. Taki
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agriculture Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Robin B. Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agriculture Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Jan Kaslin
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Donald Wlodkowic
- Neurotoxicology Lab., School of Science (Biosciences), RMIT University, Bundoora, VIC 3083, Australia
| | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU, Rue Michel-Servet 1, 1211 Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU, 1211 Geneva, Switzerland
| | - Sylvia Urban
- School of Science (Applied Chemistry and Environmental Sciences), RMIT University, GPO Box 2476 Melbourne, VIC 3001, Australia
- Correspondence:
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14
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Synthesis, antimicrobial evaluation and molecular modeling studies of novel thiosemicarbazides/semicarbazides derived from p-aminobenzoic acid. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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15
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Ul-Hamid A, Dafalla H, Hakeem AS, Haider A, Ikram M. In-Vitro Catalytic and Antibacterial Potential of Green Synthesized CuO Nanoparticles against Prevalent Multiple Drug Resistant Bovine Mastitogen Staphylococcus aureus. Int J Mol Sci 2022; 23:2335. [PMID: 35216450 PMCID: PMC8878101 DOI: 10.3390/ijms23042335] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/15/2022] [Accepted: 02/16/2022] [Indexed: 01/07/2023] Open
Abstract
Nanoparticles prepared from bio-reduction agents are of keen interest to researchers around the globe due to their ability to mitigate the harmful effects of chemicals. In this regard, the present study aims to synthesize copper oxide nanoparticles (CuO NPs) by utilizing root extracts of ginger and garlic as reducing agents, followed by the characterization and evaluation of their antimicrobial properties against multiple drug resistant (MDR) S. aureus. In this study, UV-vis spectroscopy revealed a reduced degree of absorption with an increase in the extract amount present in CuO. The maximum absorbance for doped NPs was recorded around 250 nm accompanying redshift. X-ray diffraction analysis revealed the monoclinic crystal phase of the particles. The fabricated NPs exhibited spherical shapes with dense agglomeration when examined with FE-SEM and TEM. The crystallite size measured by using XRD was found to be within a range of 23.38-46.64 nm for ginger-doped CuO and 26-56 nm for garlic-doped CuO. Green synthesized NPs of ginger demonstrated higher bactericidal tendencies against MDR S. aureus. At minimum and maximum concentrations of ginger-doped CuO NPs, substantial inhibition areas for MDR S. aureus were (2.05-3.80 mm) and (3.15-5.65 mm), and they were measured as (1.1-3.55 mm) and (1.25-4.45 mm) for garlic-doped NPs. Conventionally available CuO and crude aqueous extract (CAE) of ginger and garlic roots reduced MB in 12, 21, and 38 min, respectively, in comparison with an efficient (100%) reduction of dye in 1 min and 15 s for ginger and garlic doped CuO NPs.
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Affiliation(s)
- Anwar Ul-Hamid
- Core Research Facilities, King Fahd University of Petroleum & Minerals, Dhahran 31261, Saudi Arabia;
- Interdisciplinary Research Center for Advanced Materials, King Fahd University of Petroleum & Minerals, Dhahran 31261, Saudi Arabia
| | - Hatim Dafalla
- Core Research Facilities, King Fahd University of Petroleum & Minerals, Dhahran 31261, Saudi Arabia;
| | - Abbas Saeed Hakeem
- Interdisciplinary Research Center for Hydrogen and Energy Storage, King Fahd University of Petroleum & Minerals, Dhahran 31261, Saudi Arabia;
| | - Ali Haider
- Faculty of Veterinary and Animal Sciences, Muhammad Nawaz Shareef University of Agriculture (MNSUA), Multan 66000, Pakistan;
| | - Muhammad Ikram
- Solar Cell Applications Research Lab, Department of Physics, Government College University, Lahore 54000, Pakistan;
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16
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Chemical Profile of Ruta graveolens, Evaluation of the Antioxidant and Antibacterial Potential of Its Essential Oil, and Molecular Docking Simulations. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app112411753] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The research aimed to investigate the chemical composition and antioxidant and antibacterial potential of the essential oil (EO) isolated from the aerial parts (flowers, leaves, and stems) of Ruta graveolens L., growing in western Romania. Ruta graveolens L. essential oil (RGEO) was isolated by steam distillation (0.29% v/w), and the content was assessed by gas chromatography-mass spectrometry (GC-MS). Findings revealed that 2-Undecanone (76.19%) and 2-Nonanone (7.83%) followed by 2-Undecanol (1.85%) and 2-Tridecanone (1.42%) are the main detected compounds of the oil. The RGEO exerted broad-spectrum antibacterial and antifungal effects, S. pyogenes, S. aureus, and S. mutans being the most susceptible tested strains. The antioxidant activity of RGEO was assessed by peroxide and thiobarbituric acid value, 1,1-diphenyl-2-picrylhydrazyl radical (DPPH), and β-carotene/linoleic acid bleaching testing. The results indicated moderate radical scavenging and relative antioxidative activity in DPPH and β-carotene bleaching tests. However, between the 8th and 16th days of the incubation period, the inhibition of primary oxidation compounds induced by the RGEO was significantly stronger (p < 0.001) than butylated hydroxyanisole (BHA). Molecular docking analysis highlighted that a potential antimicrobial mechanism of the RGEO could be exerted through the inhibition of D-Alanine-d-alanine ligase (DDl) by several RGEO components. Docking analysis also revealed that a high number RGEO components could exert a potential in vitro protein-targeted antioxidant effect through xanthine oxidase and lipoxygenase inhibition. Consequently, RGEO could be a new natural source of antiseptics and antioxidants, representing an option for the use of synthetic additives in the food and pharmaceutical industry.
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17
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Qin Y, Xu L, Teng Y, Wang Y, Ma P. Discovery of novel antibacterial agents: Recent developments in D-alanyl-D-alanine ligase inhibitors. Chem Biol Drug Des 2021; 98:305-322. [PMID: 34047462 DOI: 10.1111/cbdd.13899] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/09/2021] [Accepted: 05/23/2021] [Indexed: 01/14/2023]
Abstract
Bacterial infections can cause serious problems that threaten public health over a long period of time. Moreover, the continuous emergence of drug-resistant bacteria necessitates the development of novel antibacterial agents. D-alanyl-D-alanine ligase (Ddl) is an indispensable adenosine triphosphate-dependent bacterial enzyme involved in the biosynthesis of peptidoglycan precursor, which catalyzes the ligation of two D-alanine molecules into one D-alanyl-D-alanine dipeptide. This dipeptide is an essential component of the intracellular peptidoglycan precursor, uridine diphospho-N-acetylmuramic acid (UDP-MurNAc)-pentapeptide, that maintains the integrity of the bacterial cell wall by cross-linking the peptidoglycan chain, and is crucial for the survival of pathogens. Consequently, Ddl is expected to be a promising target for the development of antibacterial agents. In this review, we present a brief introduction regarding the structure and function of Ddl, as well as an overview of the various Ddl inhibitors currently being used as antibacterial agents, specifically highlighting their inhibitory activities, structure-activity relationships and mechanisms of action.
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Affiliation(s)
- Yinhui Qin
- Department of Pharmacy, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, China
| | - Linlin Xu
- Department of Pharmacy, Taian City Central Hospital, Taian, China
| | - Yuetai Teng
- Department of Pharmacy, Jinan Vocational College of Nursing, Jinan, China
| | - Yinhu Wang
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, China
| | - Peizhi Ma
- Department of Pharmacy, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, China
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18
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Kosikowska U, Wujec M, Trotsko N, Płonka W, Paneth P, Paneth A. Antibacterial Activity of Fluorobenzoylthiosemicarbazides and Their Cyclic Analogues with 1,2,4-Triazole Scaffold. Molecules 2020; 26:E170. [PMID: 33396536 PMCID: PMC7796209 DOI: 10.3390/molecules26010170] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/18/2020] [Accepted: 12/28/2020] [Indexed: 11/17/2022] Open
Abstract
The development of drug-resistant bacteria is currently one of the major challenges in medicine. Therefore, the discovery of novel lead structures for the design of antibacterial drugs is urgently needed. In this structure-activity relationship study, a library of ortho-, meta-, and para-fluorobenzoylthiosemicarbazides, and their cyclic analogues with 1,2,4-triazole scaffold, was created and tested for antibacterial activity against Gram-positive bacteria strains. While all tested 1,2,4-triazoles were devoid of potent activity, the antibacterial response of the thiosemicarbazides was highly dependent on substitution pattern at the N4 aryl position. The optimum activity for these compounds was found for trifluoromethyl derivatives such as 15a, 15b, and 16b, which were active against both the reference strains panel, and pathogenic methicillin-sensitive and methicillin-resistant Staphylococcus aureus clinical isolates at minimal inhibitory concentrations (MICs) ranging from 7.82 to 31.25 μg/mL. Based on the binding affinities obtained from docking, the conclusion can be reached that fluorobenzoylthiosemicarbazides can be considered as potential allosteric d-alanyl-d-alanine ligase inhibitors.
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Affiliation(s)
- Urszula Kosikowska
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University of Lublin, Chodźki 1, 20-093 Lublin, Poland;
| | - Monika Wujec
- Department of Organic Chemistry, Faculty of Pharmacy, Medical University of Lublin, Chodźki 4a, 20-093 Lublin, Poland; (M.W.); (N.T.)
| | - Nazar Trotsko
- Department of Organic Chemistry, Faculty of Pharmacy, Medical University of Lublin, Chodźki 4a, 20-093 Lublin, Poland; (M.W.); (N.T.)
| | | | - Piotr Paneth
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Lodz, Poland;
| | - Agata Paneth
- Department of Organic Chemistry, Faculty of Pharmacy, Medical University of Lublin, Chodźki 4a, 20-093 Lublin, Poland; (M.W.); (N.T.)
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19
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Integron gene cassettes harboring novel variants of D-alanine-D-alanine ligase confer high-level resistance to D-cycloserine. Sci Rep 2020; 10:20709. [PMID: 33244063 PMCID: PMC7691350 DOI: 10.1038/s41598-020-77377-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 11/10/2020] [Indexed: 11/08/2022] Open
Abstract
Antibiotic resistance poses an increasing threat to global health. To tackle this problem, the identification of principal reservoirs of antibiotic resistance genes (ARGs) plus an understanding of drivers for their evolutionary selection are important. During a PCR-based screen of ARGs associated with integrons in saliva-derived metagenomic DNA of healthy human volunteers, two novel variants of genes encoding a d-alanine-d-alanine ligase (ddl6 and ddl7) located within gene cassettes in the first position of a reverse integron were identified. Treponema denticola was identified as the likely host of the ddl cassettes. Both ddl6 and ddl7 conferred high level resistance to d-cycloserine when expressed in Escherichia coli with ddl7 conferring four-fold higher resistance to D-cycloserine compared to ddl6. A SNP was found to be responsible for this difference in resistance phenotype between the two ddl variants. Molecular dynamics simulations were used to explain the mechanism of this phenotypic change at the atomic scale. A hypothesis for the evolutionary selection of ddl containing integron gene cassettes is proposed, based on molecular docking of plant metabolites within the ATP and d-cycloserine binding pockets of Ddl.
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20
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Zhang Y, Gong S, Wang X, Muhammad M, Li Y, Meng S, Li Q, Liu D, Zhang H. Insights into the Inhibition of Aeromonas hydrophila d-Alanine-d-Alanine Ligase by Integration of Kinetics and Structural Analysis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:7509-7519. [PMID: 32609505 DOI: 10.1021/acs.jafc.0c00682] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Aeromonas hydrophila, a pathogenic bacterium, is harmful to humans, domestic animals, and fishes and, moreover, of public health concern due to the emergence of multiple drug-resistant strains. The cell wall has been discovered as a novel and efficient drug target against bacteria, and d-alanine-d-alanine ligase (Ddl) is considered as an essential enzyme in bacterial cell wall biosynthesis. Herein, we studied the A. hydrophila HBNUAh01 Ddl (AhDdl) enzyme activity and kinetics and determined the crystal structure of AhDdl/d-Ala complex at 2.7 Å resolution. An enzymatic assay showed that AhDdl exhibited higher affinity to ATP (Km: 54.1 ± 9.1 μM) compared to d-alanine (Km: 1.01 ± 0.19 mM). The kinetic studies indicated a competitive inhibition of AhDdl by d-cycloserine (DCS), with an inhibition constant (Ki) of 120 μM and the 50% inhibitory concentrations (IC50) value of 0.5 mM. Meanwhile, structural analysis indicated that the AhDdl/d-Ala complex structure adopted a semi-closed conformation form, and the active site was extremely conserved. Noteworthy is that the substrate d-Ala occupied the second d-Ala position, not the first d-Ala position. These results provided more insights for understanding the details of the catalytic mechanism and resources for the development of novel drugs against the diseases caused by A. hydrophila.
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Affiliation(s)
- Yingli Zhang
- College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, P. R. China
| | - Siyu Gong
- College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, P. R. China
| | - Xuan Wang
- College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, P. R. China
| | - Murtala Muhammad
- Department of Biochemistry, Kano University of Science and Technology, Wudil 713281, Nigeria
| | - Yangyang Li
- College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, P. R. China
| | - Shuaishuai Meng
- Engineering Research Center of Industrial Microbiology, Ministry of Education; Collaborative Innovation Center of Haixi Green Bio-Manufacturing Technology, Ministry of Education; College of Life Sciences, Fujian Normal University, Fuzhou 350117, P. R. China
| | - Qin Li
- Engineering Research Center of Industrial Microbiology, Ministry of Education; Collaborative Innovation Center of Haixi Green Bio-Manufacturing Technology, Ministry of Education; College of Life Sciences, Fujian Normal University, Fuzhou 350117, P. R. China
| | - Dong Liu
- College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, P. R. China
| | - Huaidong Zhang
- Engineering Research Center of Industrial Microbiology, Ministry of Education; Collaborative Innovation Center of Haixi Green Bio-Manufacturing Technology, Ministry of Education; College of Life Sciences, Fujian Normal University, Fuzhou 350117, P. R. China
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21
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Ikram M, Umar E, Raza A, Haider A, Naz S, Ul-Hamid A, Haider J, Shahzadi I, Hassan J, Ali S. Dye degradation performance, bactericidal behavior and molecular docking analysis of Cu-doped TiO 2 nanoparticles. RSC Adv 2020; 10:24215-24233. [PMID: 35516171 PMCID: PMC9055104 DOI: 10.1039/d0ra04851h] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 06/18/2020] [Indexed: 11/21/2022] Open
Abstract
Copper-doped TiO2 was prepared with a sol-gel chemical method. Various concentrations (3, 6, and 9 wt%) of Cu dopant were employed. Several techniques were implemented to assess the structural, optical, morphological and chemical properties of the synthesized samples. Evaluation of elemental composition using SEM-EDS and XRF techniques showed the presence of dopant element in the prepared samples. XRD analysis confirmed the presence of anatase (TiO2) phase with interstitial doping. Incorporation of dopant was observed to enhance the crystallinity and increase the crystallite size of the synthesized products. SAED profiles revealed a high degree of crystallinity in the prepared specimens, which was also evident in the XRD spectra. Optical properties studied using UV-vis spectroscopy depicted a shift of the maximum absorption to the visible region (redshift) that signified a reduction in the band gap energy of Cu-doped TiO2 samples. Examination of morphological features with scanning and high-resolution transmission electron microscopes revealed the formation of spherical nanoparticles with a tendency to agglomerate with increasing dopant concentration. Molecular vibrations and the formation of Ti-O-Ti bonds were revealed through FTIR spectra. PL spectroscopy recorded the trapping efficiency and migration of charge carriers, which exhibited electron-hole recombination behavior. Doped nanostructures showed enhanced bactericidal performance and synergism against S. aureus and E. coli. In summary, Cu-doped TiO2 nanostructures were observed to impede bacteria effectively, which is deemed beneficial in overcoming ailments caused by pathogens such as microbial etiologies. Furthermore, molecular docking analysis was conducted to study the interaction of Cu-doped TiO2 nanoparticles with multiple proteins namely β-lactamase (binding score: -4.91 kcal mol-1), ddlB (binding score: -5.67 kcal mol-1) and FabI (binding score: -6.13 kcal mol-1) as possible targets with active site residues. Dye degradation/reduction of control and Cu-doped samples were studied through absorption spectroscopy. The obtained outcomes of the performed experiment indicated that the photocatalytic activity of Cu-TiO2 enhanced with increasing dopant concentration, which is thought to be due to a decreased rate of electron-hole pair recombination. Consequently, it is suggested that Cu-TiO2 can be exploited as an effective candidate for antibacterial and dye degradation applications.
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Affiliation(s)
- M Ikram
- Solar Cell Applications Research Lab, Department of Physics, Government College University Lahore Punjab 54000 Pakistan +923005406667
| | - E Umar
- Department of Physics, Riphah Institute of Computing and Applied Sciences (RICAS), Riphah International University 14 Ali Road Lahore Pakistan
| | - A Raza
- Department of Physics, Riphah Institute of Computing and Applied Sciences (RICAS), Riphah International University 14 Ali Road Lahore Pakistan
| | - A Haider
- Department of Clinical Medicine and Surgery, University of Veterinary and Animal Sciences Lahore 54000 Punjab Pakistan
| | - S Naz
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences Tianjin 300308 China
| | - A Ul-Hamid
- Center for Engineering Research, Research Institute, King Fahd University of Petroleum & Minerals Dhahran 31261 Saudi Arabia
| | - J Haider
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences Tianjin 300308 China
| | - I Shahzadi
- College of Pharmacy, University of the Punjab Lahore 54000 Pakistan
| | - J Hassan
- Department of Physics, Riphah Institute of Computing and Applied Sciences (RICAS), Riphah International University 14 Ali Road Lahore Pakistan
| | - S Ali
- Department of Physics, Riphah Institute of Computing and Applied Sciences (RICAS), Riphah International University 14 Ali Road Lahore Pakistan
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22
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Pederick JL, Thompson AP, Bell SG, Bruning JB. d-Alanine-d-alanine ligase as a model for the activation of ATP-grasp enzymes by monovalent cations. J Biol Chem 2020; 295:7894-7904. [PMID: 32335509 DOI: 10.1074/jbc.ra120.012936] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 04/23/2020] [Indexed: 12/18/2022] Open
Abstract
The ATP-grasp superfamily of enzymes shares an atypical nucleotide-binding site known as the ATP-grasp fold. These enzymes are involved in many biological pathways in all domains of life. One ATP-grasp enzyme, d-alanine-d-alanine ligase (Ddl), catalyzes ATP-dependent formation of the d-alanyl-d-alanine dipeptide essential for bacterial cell wall biosynthesis and is therefore an important antibiotic drug target. Ddl is activated by the monovalent cation (MVC) K+, but despite its clinical relevance and decades of research, how this activation occurs has not been elucidated. We demonstrate here that activating MVCs bind adjacent to the active site of Ddl from Thermus thermophilus and used a combined biochemical and structural approach to characterize MVC activation. We found that TtDdl is a type II MVC-activated enzyme, retaining activity in the absence of MVCs. However, the efficiency of TtDdl increased ∼20-fold in the presence of activating MVCs, and it was maximally activated by K+ and Rb+ ions. A strict dependence on ionic radius of the MVC was observed, with Li+ and Na+ providing little to no TtDdl activation. To understand the mechanism of MVC activation, we solved crystal structures of TtDdl representing distinct catalytic stages in complex with K+, Rb+, or Cs+ Comparison of these structures with apo TtDdl revealed no evident conformational change on MVC binding. Of note, the identified MVC binding site is structurally conserved within the ATP-grasp superfamily. We propose that MVCs activate Ddl by altering the charge distribution of its active site. These findings provide insight into the catalytic mechanism of ATP-grasp enzymes.
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Affiliation(s)
- Jordan L Pederick
- Institute for Photonics and Advanced Sensing, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia.,Department of Molecular and Cellular Biology, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Andrew P Thompson
- Department of Molecular and Cellular Biology, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Stephen G Bell
- Department of Chemistry, The University of Adelaide, Adelaide, South Australia, Australia
| | - John B Bruning
- Institute for Photonics and Advanced Sensing, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia .,Department of Molecular and Cellular Biology, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
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23
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Matoba Y, Uda N, Kudo M, Sugiyama M. Cyclization mechanism catalyzed by an ATP-grasp enzyme essential for d-cycloserine biosynthesis. FEBS J 2019; 287:2763-2778. [PMID: 31793174 DOI: 10.1111/febs.15163] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/20/2019] [Accepted: 12/02/2019] [Indexed: 11/26/2022]
Abstract
In the biosynthetic pathway of an antitubercular antibiotic d-cycloserine (d-CS), O-ureido-d-serine (d-OUS) is converted to d-CS. We have previously demonstrated that DcsG, classified into the ATP-grasp superfamily enzyme, catalyzes the ring formation to generate d-CS, which is accompanied by the cleavage of a bond in the urea moiety of d-OUS to remove a carbamoyl group. Although the general ATP-grasp enzymes catalyze an ATP-dependent ligation reaction between two substrates, DcsG catalyzes specifically the generation of an intramolecular covalent bond. In the present study, cyanate was found in the reaction mixture, suggesting that carbamoyl group is eliminated as an isocyanic acid during the reaction. By the crystallographic and mutational investigations of DcsG, we anticipate the residues necessary for the binding of d-OUS. An acylphosphate intermediate must be bound at the narrow pocket of DcsG in a folded conformation, inducing the bond cleavage and the new bond formation to generate cyanate and d-CS, respectively. DATABASE: Structural data are available in Protein Data Bank database under the accession number 6JIL.
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Affiliation(s)
- Yasuyuki Matoba
- Faculty of Pharmacy, Yasuda Women's University, Hiroshima, Japan
| | - Narutoshi Uda
- Graduate School of Biomedical & Health Sciences, Hiroshima University, Japan
| | - Mako Kudo
- Graduate School of Biomedical & Health Sciences, Hiroshima University, Japan
| | - Masanori Sugiyama
- Graduate School of Biomedical & Health Sciences, Hiroshima University, Japan
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24
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Díaz‐Sáez L, Torrie LS, McElroy SP, Gray D, Hunter WN. Burkholderia pseudomallei d-alanine-d-alanine ligase; detailed characterisation and assessment of a potential antibiotic drug target. FEBS J 2019; 286:4509-4524. [PMID: 31260169 PMCID: PMC6899670 DOI: 10.1111/febs.14976] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 05/27/2019] [Accepted: 06/27/2019] [Indexed: 02/02/2023]
Abstract
Burkholderia pseudomallei is a serious, difficult to treat Gram-negative pathogen and an increase in the occurrence of drug-resistant strains has been detected. We have directed efforts to identify and to evaluate potential drug targets relevant to treatment of infection by B. pseudomallei. We have selected and characterised the essential enzyme d-alanine-d-alanine ligase (BpDdl), required for the ATP-assisted biosynthesis of a peptidoglycan precursor. A recombinant supply of protein supported high-resolution crystallographic and biophysical studies with ligands (AMP and AMP+d-Ala-d-Ala), and comparisons with orthologues enzymes suggest a ligand-induced conformational change occurring that might be relevant to the catalytic cycle. The detailed biochemical characterisation of the enzyme, development and optimisation of ligand binding assays supported the search for novel inhibitors by screening of selected compound libraries. In a similar manner to that observed previously in other studies, we note a paucity of hits that are worth follow-up and then in combination with a computational analysis of the active site, we conclude that this ligase represents a difficult target for drug discovery. Nevertheless, our reagents, protocols and data can underpin future efforts exploiting more diverse chemical libraries and structure-based approaches.
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Affiliation(s)
- Laura Díaz‐Sáez
- Division of Biological Chemistry and Drug DiscoverySchool of Life SciencesUniversity of DundeeUK
| | - Leah S. Torrie
- Drug Discovery UnitWellcome Centre for Anti‐Infectives ResearchSchool of Life SciencesUniversity of DundeeUK
| | - Stuart P. McElroy
- European Screening Centre Newhouse, Biocity ScotlandUniversity of DundeeNewhouseUK
- Present address:
BioAscent Discovery LtdBo'ness RoadNewhouseLanarkshireML1 5UHUK
| | - David Gray
- Drug Discovery UnitWellcome Centre for Anti‐Infectives ResearchSchool of Life SciencesUniversity of DundeeUK
| | - William N. Hunter
- Division of Biological Chemistry and Drug DiscoverySchool of Life SciencesUniversity of DundeeUK
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25
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Chen AY, Adamek RN, Dick BL, Credille CV, Morrison CN, Cohen SM. Targeting Metalloenzymes for Therapeutic Intervention. Chem Rev 2019; 119:1323-1455. [PMID: 30192523 PMCID: PMC6405328 DOI: 10.1021/acs.chemrev.8b00201] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metalloenzymes are central to a wide range of essential biological activities, including nucleic acid modification, protein degradation, and many others. The role of metalloenzymes in these processes also makes them central for the progression of many diseases and, as such, makes metalloenzymes attractive targets for therapeutic intervention. Increasing awareness of the role metalloenzymes play in disease and their importance as a class of targets has amplified interest in the development of new strategies to develop inhibitors and ultimately useful drugs. In this Review, we provide a broad overview of several drug discovery efforts focused on metalloenzymes and attempt to map out the current landscape of high-value metalloenzyme targets.
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Affiliation(s)
- Allie Y Chen
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Rebecca N Adamek
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Benjamin L Dick
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Cy V Credille
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Christine N Morrison
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Seth M Cohen
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
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26
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Hashimoto Y, Kurushima J, Nomura T, Tanimoto K, Tamai K, Yanagisawa H, Shirabe K, Ike Y, Tomita H. Dissemination and genetic analysis of the stealthy vanB gene clusters of Enterococcus faecium clinical isolates in Japan. BMC Microbiol 2018; 18:213. [PMID: 30545294 PMCID: PMC6293572 DOI: 10.1186/s12866-018-1342-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 11/14/2018] [Indexed: 12/18/2022] Open
Abstract
Background VanB-type vancomycin (VAN) resistance gene clusters confer VAN resistances on Enterococcus spp. over a wide range of MIC levels (MIC = 4–1000 mg/L). However, the epidemiology and the molecular characteristics of the VAN susceptible VanB-type Enterococcus still remain unclear. Results We characterized 19 isolates of VanB-type Enterococcus faecium that might colonize in the gut and were not phenotypically resistant to VAN (MIC = 3 mg/L). They were obtained from two hospitals in Japan between 2009 and 2010. These isolates had the identical vanB gene cluster and showed same multilocus sequence typing (MLST) (ST78) and the highly related profiles in pulsed-field gel electrophoresis (PFGE). The vanB gene cluster was located on a plasmid, and was transferable to E. faecium and E. faecalis. Notably, from these VanB-type VREs, VAN resistant (MIC≥16 mg/L) mutants could appear at a frequency of 10− 6–10− 7/parent cell in vitro. Most of these revertants acquired mutations in the vanSB gene, while the remainder of the revertants might have other mutations outside of the vanB gene cluster. All of the revertants we tested showed increases in the VAN-dependent expression of the vanB gene cluster, suggesting that the mutations affected the transcriptional activity and increased the VAN resistance. Targeted mutagenesis revealed that three unique nucleotide substitutions in the vanB gene cluster of these strains attenuated VAN resistance. Conclusions In summary, this study indicated that stealthy VanB-type E. faecium strains that have the potential ability to become resistance to VAN could exist in clinical settings. Electronic supplementary material The online version of this article (10.1186/s12866-018-1342-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yusuke Hashimoto
- Department of Bacteriology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Jun Kurushima
- Department of Bacteriology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Takahiro Nomura
- Department of Bacteriology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Koichi Tanimoto
- Laboratory of Bacterial Drug Resistance, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Kiyoko Tamai
- MIROKU Medical Laboratory Inc, 659-2 Innai, Saku, Nagano, 384-2201, Japan
| | - Hideji Yanagisawa
- MIROKU Medical Laboratory Inc, 659-2 Innai, Saku, Nagano, 384-2201, Japan
| | - Komei Shirabe
- Yamaguchi Prefectural Institute of Public Health and Environment, 2-5-67 Aoi, Yamaguchi, Yamaguchi, 753-0821, Japan
| | - Yasuyoshi Ike
- Department of Bacteriology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Haruyoshi Tomita
- Department of Bacteriology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan. .,Laboratory of Bacterial Drug Resistance, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan.
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27
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Ameryckx A, Thabault L, Pochet L, Leimanis S, Poupaert JH, Wouters J, Joris B, Van Bambeke F, Frédérick R. 1-(2-Hydroxybenzoyl)-thiosemicarbazides are promising antimicrobial agents targeting d-alanine-d-alanine ligase in bacterio. Eur J Med Chem 2018; 159:324-338. [DOI: 10.1016/j.ejmech.2018.09.067] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 08/09/2018] [Accepted: 09/26/2018] [Indexed: 12/21/2022]
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28
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Zapotoczna M, Boksmati N, Donohue S, Bahtiar B, Boland A, Somali HA, Cox A, Humphreys H, O'Gara JP, Brennan M, O'Neill E. Novel anti-staphylococcal and anti-biofilm properties of two anti-malarial compounds: MMV665953 {1-(3-chloro-4-fluorophenyl)-3-(3,4-dichlorophenyl)urea} and MMV665807 {5-chloro-2-hydroxy-N-[3-(trifluoromethyl)phenyl]benzamide}. J Med Microbiol 2017; 66:377-387. [PMID: 28327271 DOI: 10.1099/jmm.0.000446] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
PURPOSE The treatment of device-related infections is challenging and current anti-microbial compounds have poor anti-biofilm activity. We aimed to identify and characterize novel compounds effective in the eradication of Staphylococcus aureus biofilms. METHODOLOGY Two novel compounds, MMV665953 {1-(3-chloro-4-fluorophenyl)-3-(3,4-dichlorophenyl)urea} and MMV665807{5-chloro-2-hydroxy-N-[3-(trifluoromethyl)phenyl]benzamide}, effective in killing S. aureus biofilms, were identified by screening of the open access 'malaria box' chemical library. The minimum bactericidal concentrations, half-maximal inhibition concentration (IC50) values and minimal biofilm killing concentrations effective in the killing of biofilm were determined against meticillin-resistant S. aureus and meticillin-sensitive S. aureus. Fibrin-embedded biofilms were grown under in vivo-relevant conditions, and viability was measured using a resazurin-conversion assay and confocal microscopy. The potential for the development of resistance and cytotoxicity was also assessed. RESULTS MMV665953 and MMV665807 were bactericidal against S. aureus isolates. The IC50 against S. aureus biofilms was at 0.15-0.58 mg l-1 after 24 h treatment, whereas the concentration required to eradicate all tested biofilms was 4 mg l-1, making the compounds more bactericidal than conventional antibiotics. The cytotoxicity against human keratinocytes and primary endothelial cells was determined as IC50 7.47 and 0.18 mg l-1 for MMV665953, and as 1.895 and 0.076 mg l-1 for MMV665807. Neither compound was haemolytic nor caused platelet activation. MMV665953 and MMV665807 derivatives with reduced cytotoxicity exhibited a concomitant loss in anti-staphylococcal activity. CONCLUSION MMV665953 and MMV665807 are more bactericidal against S. aureus biofilms than currently used anti-staphylococcal antibiotics and represent a valuable structural basis for further investigation in the treatment of staphylococcal biofilm-related infections.
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Affiliation(s)
- Marta Zapotoczna
- Department of Clinical Microbiology, Education and Research Centre, Beaumont Hospital, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Nabila Boksmati
- Molecular and Cellular Therapeutics, Irish Centre for Vascular Biology, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Sinead Donohue
- Department of Clinical Microbiology, Education and Research Centre, Beaumont Hospital, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Baizurina Bahtiar
- Molecular and Cellular Therapeutics, Irish Centre for Vascular Biology, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Ahmad Boland
- Molecular and Cellular Therapeutics, Irish Centre for Vascular Biology, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Hamzah Al Somali
- Molecular and Cellular Therapeutics, Irish Centre for Vascular Biology, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Alysia Cox
- Molecular and Cellular Therapeutics, Irish Centre for Vascular Biology, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Hilary Humphreys
- Department of Clinical Microbiology, Education and Research Centre, Beaumont Hospital, Royal College of Surgeons in Ireland, Dublin, Ireland.,Department of Microbiology, Beaumont Hospital, Dublin, Ireland
| | - James P O'Gara
- Department of Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Marian Brennan
- Molecular and Cellular Therapeutics, Irish Centre for Vascular Biology, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Eoghan O'Neill
- Department of Microbiology, Connolly Hospital, Dublin, Ireland.,Department of Clinical Microbiology, Education and Research Centre, Beaumont Hospital, Royal College of Surgeons in Ireland, Dublin, Ireland
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29
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Structural basis for precursor protein-directed ribosomal peptide macrocyclization. Nat Chem Biol 2016; 12:973-979. [PMID: 27669417 PMCID: PMC5117808 DOI: 10.1038/nchembio.2200] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 08/03/2016] [Indexed: 11/08/2022]
Abstract
Macrocyclization is a common feature of natural product biosynthetic pathways including the diverse family of ribosomal peptides. Microviridins are architecturally complex cyanobacterial ribosomal peptides whose members target proteases with potent reversible inhibition. The product structure is constructed by three macrocyclizations catalyzed sequentially by two members of the ATP-grasp family, a unique strategy for ribosomal peptide macrocyclization. Here, we describe the detailed structural basis for the enzyme-catalyzed macrocyclizations in the microviridin J pathway of Microcystis aeruginosa. The macrocyclases, MdnC and MdnB, interact with a conserved α-helix of the precursor peptide using a novel precursor peptide recognition mechanism. The results provide insight into the unique protein/protein interactions key to the chemistry, suggest an origin of the natural combinatorial synthesis of microviridin peptides and provide a framework for future engineering efforts to generate designed compounds.
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30
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Duclert-Savatier N, Bouvier G, Nilges M, Malliavin TE. Building Graphs To Describe Dynamics, Kinetics, and Energetics in the d-ALa:d-Lac Ligase VanA. J Chem Inf Model 2016; 56:1762-75. [PMID: 27579990 PMCID: PMC5039762 DOI: 10.1021/acs.jcim.6b00211] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
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The d-Ala:d-Lac ligase, VanA, plays a critical
role in the resistance of vancomycin. Indeed, it is involved in the
synthesis of a peptidoglycan precursor, to which vancomycin cannot
bind. The reaction catalyzed by VanA requires the opening of the so-called
“ω-loop”, so that the substrates can enter the
active site. Here, the conformational landscape of VanA is explored
by an enhanced sampling approach: the temperature-accelerated molecular
dynamics (TAMD). Analysis of the molecular dynamics (MD) and TAMD
trajectories recorded on VanA permits a graphical description of the
structural and kinetics aspects of the conformational space of VanA,
where the internal mobility and various opening modes of the ω-loop
play a major role. The other important feature is the correlation
of the ω-loop motion with the movements of the opposite domain,
defined as containing the residues A149–Q208. Conformational
and kinetic clusters have been determined and a path describing the
ω-loop opening was extracted from these clusters. The determination
of this opening path, as well as the relative importance of hydrogen
bonds along the path, permit one to propose some key residue interactions
for the kinetics of the ω-loop opening.
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Affiliation(s)
- Nathalie Duclert-Savatier
- Département de Biologie Structurale et Chimie, Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528 , 25, rue du Dr Roux, 75015 Paris, France
| | - Guillaume Bouvier
- Département de Biologie Structurale et Chimie, Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528 , 25, rue du Dr Roux, 75015 Paris, France
| | - Michael Nilges
- Département de Biologie Structurale et Chimie, Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528 , 25, rue du Dr Roux, 75015 Paris, France
| | - Thérèse E Malliavin
- Département de Biologie Structurale et Chimie, Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528 , 25, rue du Dr Roux, 75015 Paris, France
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31
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Tran HT, Hong MK, Ngo HPT, Huynh KH, Ahn YJ, Wang Z, Kang LW. Structure of D-alanine-D-alanine ligase from Yersinia pestis: nucleotide phosphate recognition by the serine loop. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2016; 72:12-21. [PMID: 26894530 DOI: 10.1107/s2059798315021671] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 11/15/2015] [Indexed: 01/14/2023]
Abstract
D-Alanyl-D-alanine is an essential precursor of bacterial peptidoglycan and is synthesized by D-alanine-D-alanine ligase (DDL) with hydrolysis of ATP; this reaction makes DDL an important drug target for the development of antibacterial agents. Five crystal structures of DDL from Yersinia pestis (YpDDL) were determined at 1.7-2.5 Å resolution: apo, AMP-bound, ADP-bound, adenosine 5'-(β,γ-imido)triphosphate-bound, and D-alanyl-D-alanine- and ADP-bound structures. YpDDL consists of three domains, in which four loops, loop 1, loop 2 (the serine loop), loop 3 (the ω-loop) and loop 4, constitute the binding sites for two D-alanine molecules and one ATP molecule. Some of them, especially the serine loop and the ω-loop, show flexible conformations, and the serine loop is mainly responsible for the conformational change in substrate nucleotide phosphates. Enzyme-kinetics assays were carried out for both the D-alanine and ATP substrates and a substrate-binding mechanism was proposed for YpDDL involving conformational changes of the loops.
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Affiliation(s)
- Huyen Thi Tran
- Department of Biological Sciences, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 143-701, Republic of Korea
| | - Myoung Ki Hong
- Department of Biological Sciences, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 143-701, Republic of Korea
| | - Ho Phuong Thuy Ngo
- Department of Biological Sciences, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 143-701, Republic of Korea
| | - Kim Hung Huynh
- Department of Biological Sciences, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 143-701, Republic of Korea
| | - Yeh Jin Ahn
- Department of Life Science, Sangmyung University, 7 Hongji-dong, Jongno-gu, Seoul 110-743, Republic of Korea
| | - Zhong Wang
- Center for Cellular & Structural Biology, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Lin Woo Kang
- Department of Biological Sciences, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 143-701, Republic of Korea
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32
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Vemula H, Ayon NJ, Gutheil WG. Cytoplasmic peptidoglycan intermediate levels in Staphylococcus aureus. Biochimie 2015; 121:72-8. [PMID: 26612730 DOI: 10.1016/j.biochi.2015.11.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 11/18/2015] [Indexed: 11/27/2022]
Abstract
Intracellular cytoplasmic peptidoglycan (PG) intermediate levels were determined in Staphylococcus aureus during log-phase growth in enriched media. Levels of UDP-linked intermediates were quantitatively determined using ion pairing LC-MS/MS in negative mode, and amine intermediates were quantitatively determined stereospecifically as their Marfey's reagent derivatives in positive mode. Levels of UDP-linked intermediates in S. aureus varied from 1.4 μM for UDP-GlcNAc-Enolpyruvyate to 1200 μM for UDP-MurNAc. Levels of amine intermediates (L-Ala, D-Ala, D-Ala-D-Ala, L-Glu, D-Glu, and L-Lys) varied over a range of from 860 μM for D-Ala-D-Ala to 30-260 mM for the others. Total PG was determined from the D-Glu content of isolated PG, and used to estimate the rate of PG synthesis (in terms of cytoplasmic metabolite flux) as 690 μM/min. The total UDP-linked intermediates pool (2490 μM) is therefore sufficient to sustain growth for 3.6 min. Comparison of UDP-linked metabolite levels with published pathway enzyme characteristics demonstrates that enzymes on the UDP-branch range from >80% saturation for MurA, Z, and C, to <5% saturation for MurB. Metabolite levels were compared with literature values for Escherichia coli, with the major difference in UDP-intermediates being the level of UDP-MurNAc, which was high in S. aureus (1200 μM) and low in E. coli (45 μM).
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Affiliation(s)
- Harika Vemula
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, 2464 Charlotte Street, Kansas City, MO 64108, USA
| | - Navid J Ayon
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, 2464 Charlotte Street, Kansas City, MO 64108, USA
| | - William G Gutheil
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, 2464 Charlotte Street, Kansas City, MO 64108, USA.
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The crystal structure of the D-alanine-D-alanine ligase from Acinetobacter baumannii suggests a flexible conformational change in the central domain before nucleotide binding. J Microbiol 2015; 53:776-82. [PMID: 26502962 DOI: 10.1007/s12275-015-5475-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 10/20/2015] [Accepted: 10/20/2015] [Indexed: 10/22/2022]
Abstract
Acinetobacter baumannii, which is emerging as a multidrug-resistant nosocomial pathogen, causes a number of diseases, including pneumonia, bacteremia, meningitis, and skin infections. With ATP hydrolysis, the D-alanine-D-alanine ligase (DDL) catalyzes the synthesis of D-alanyl-D-alanine, which is an essential component of bacterial peptidoglycan. In this study, we determined the crystal structure of DDL from A. baumannii (AbDDL) at a resolution of 2.2 Å. The asymmetric unit contained six protomers of AbDDL. Five protomers had a closed conformation in the central domain, while one protomer had an open conformation in the central domain. The central domain with an open conformation did not interact with crystallographic symmetry-related protomers and the conformational change of the central domain was not due to crystal packing. The central domain of AbDDL can have an ensemble of the open and closed conformations before the binding of substrate ATP. The conformational change of the central domain is important for the catalytic activity and the detail information will be useful for the development of inhibitors against AbDDL and putative antibacterial agents against A. baumannii. The AbDDL structure was compared with that of other DDLs that were in complex with potent inhibitors and the catalytic activity of AbDDL was confirmed using enzyme kinetics assays.
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Dwivedi UN, Tiwari S, Singh P, Singh S, Awasthi M, Pandey VP. Treponema pallidum putative novel drug target identification and validation: rethinking syphilis therapeutics with plant-derived terpenoids. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2015; 19:104-14. [PMID: 25683888 DOI: 10.1089/omi.2014.0154] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Syphilis, a slow progressive and the third most common sexually transmitted disease found worldwide, is caused by a spirochete gram negative bacteria Treponema pallidum. Emergence of antibiotic resistant T. pallidum has led to a search for novel drugs and their targets. Subtractive genomics analyses of pathogen T. pallidum and host Homo sapiens resulted in identification of 126 proteins essential for survival and viability of the pathogen. Metabolic pathway analyses of these essential proteins led to discovery of nineteen proteins distributed among six metabolic pathways unique to T. pallidum. One hundred plant-derived terpenoids, as potential therapeutic molecules against T. pallidum, were screened for their drug likeness and ADMET (absorption, distribution, metabolism, and toxicity) properties. Subsequently the resulting nine terpenoids were docked with five unique T. pallidum targets through molecular modeling approaches. Out of five targets analyzed, D-alanine:D-alanine ligase was found to be the most promising target, while terpenoid salvicine was the most potent inhibitor. A comparison of the inhibitory potential of the best docked readily available natural compound, namely pomiferin (flavonoid) with that of the best docked terpenoid salvicine, revealed that salvicine was a more potent inhibitor than that of pomiferin. To the best of our knowledge, this is the first report of a terpenoid as a potential therapeutic molecule against T. pallidum with D-alanine:D-alanine ligase as a novel target. Further studies are warranted to evaluate and explore the potential clinical ramifications of these findings in relation to syphilis that has public health importance worldwide.
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Affiliation(s)
- Upendra N Dwivedi
- Department of Biochemistry, Centre of Excellence in Bioinformatics, Bioinformatics Infrastructure Facility, University of Lucknow , Lucknow, U.P., India
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Cdc123, a Cell Cycle Regulator Needed for eIF2 Assembly, Is an ATP-Grasp Protein with Unique Features. Structure 2015. [PMID: 26211610 DOI: 10.1016/j.str.2015.06.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Eukaryotic initiation factor 2 (eIF2), a heterotrimeric guanosine triphosphatase, has a central role in protein biosynthesis by supplying methionylated initiator tRNA to the ribosomal translation initiation complex and by serving as a target for translational control in response to stress. Recent work identified a novel step indispensable for eIF2 function: assembly of eIF2 from its three subunits by the cell proliferation protein Cdc123. We report the first crystal structure of a Cdc123 representative, that from Schizosaccharomyces pombe, both isolated and bound to domain III of Saccharomyces cerevisiae eIF2γ. The structures show that Cdc123 resembles enzymes of the ATP-grasp family. Indeed, Cdc123 binds ATP-Mg(2+), and conserved residues contacting ATP-Mg(2+) are essential for Cdc123 to support eIF2 assembly and cell viability. A docking of eIF2αγ onto Cdc123, combined with genetic and biochemical experiments, allows us to propose a model explaining how Cdc123 participates in the biogenesis of eIF2 through facilitating assembly of eIF2γ to eIF2α.
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Burroughs AM, Zhang D, Aravind L. The eukaryotic translation initiation regulator CDC123 defines a divergent clade of ATP-grasp enzymes with a predicted role in novel protein modifications. Biol Direct 2015; 10:21. [PMID: 25976611 PMCID: PMC4431377 DOI: 10.1186/s13062-015-0053-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 04/07/2015] [Indexed: 12/26/2022] Open
Abstract
Abstract Deciphering the origin of uniquely eukaryotic features of sub-cellular systems, such as the translation apparatus, is critical in reconstructing eukaryogenesis. One such feature is the highly conserved, but poorly understood, eukaryotic protein CDC123, which regulates the abundance of the eukaryotic translation initiation eIF2 complex and binds one of its components eIF2γ. We show that the eukaryotic protein CDC123 defines a novel clade of ATP-grasp enzymes distinguished from all other members of the superfamily by a RAGNYA domain with two conserved lysines (henceforth the R2K clade). Combining the available biochemical and genetic data on CDC123 with the inferred enzymatic function, we propose that the eukaryotic CDC123 proteins are likely to function as ATP-dependent protein-peptide ligases which modify proteins by ribosome-independent addition of an oligopeptide tag. We also show that the CDC123 family emerged first in bacteria where it appears to have diversified along with the two other families of the R2K clade. The bacterial CDC123 family members are of two distinct types, one found as part of type VI secretion systems which deliver polymorphic toxins and the other functioning as potential effectors delivered to amoeboid eukaryotic hosts. Representatives of the latter type have also been independently transferred to phylogenetically unrelated amoeboid eukaryotes and their nucleo-cytoplasmic large DNA viruses. Similarly, the two other prokaryotic R2K clade families are also proposed to participate in biological conflicts between bacteriophages and their hosts. These findings add further evidence to the recently proposed hypothesis that the horizontal transfer of enzymatic effectors from the bacterial endosymbionts of the stem eukaryotes played a fundamental role in the emergence of the characteristically eukaryotic regulatory systems and sub-cellular structures. Reviewers This article was reviewed by Michael Galperin and Sandor Pongor. Electronic supplementary material The online version of this article (doi:10.1186/s13062-015-0053-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- A Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA.
| | - Dapeng Zhang
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA.
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA.
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Principal Component Analysis reveals correlation of cavities evolution and functional motions in proteins. J Mol Graph Model 2014; 55:13-24. [PMID: 25424655 DOI: 10.1016/j.jmgm.2014.10.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 10/16/2014] [Accepted: 10/18/2014] [Indexed: 11/24/2022]
Abstract
Protein conformation has been recognized as the key feature determining biological function, as it determines the position of the essential groups specifically interacting with substrates. Hence, the shape of the cavities or grooves at the protein surface appears to drive those functions. However, only a few studies describe the geometrical evolution of protein cavities during molecular dynamics simulations (MD), usually with a crude representation. To unveil the dynamics of cavity geometry evolution, we developed an approach combining cavity detection and Principal Component Analysis (PCA). This approach was applied to four systems subjected to MD (lysozyme, sperm whale myoglobin, Dengue envelope protein and EF-CaM complex). PCA on cavities allows us to perform efficient analysis and classification of the geometry diversity explored by a cavity. Additionally, it reveals correlations between the evolutions of the cavities and structures, and can even suggest how to modify the protein conformation to induce a given cavity geometry. It also helps to perform fast and consensual clustering of conformations according to cavity geometry. Finally, using this approach, we show that both carbon monoxide (CO) location and transfer among the different xenon sites of myoglobin are correlated with few cavity evolution modes of high amplitude. This correlation illustrates the link between ligand diffusion and the dynamic network of internal cavities.
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Hong W, Chen L, Xie J. Molecular basis underlying Mycobacterium tuberculosis D-cycloserine resistance. Is there a role for ubiquinone and menaquinone metabolic pathways? Expert Opin Ther Targets 2014; 18:691-701. [PMID: 24773568 DOI: 10.1517/14728222.2014.902937] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Tuberculosis remains a formidable threat to global public health. Multidrug-resistant tuberculosis presents increasing burden on the control strategy. D-Cycloserine (DCS) is an effective second-line drug against Mycobacterium tuberculosis (M. tuberculosis), the causative agent of tuberculosis. Though less potent than isoniazid (INH) and streptomycin, DCS is crucial for antibiotic-resistant tuberculosis. One advantage of DCS is that less drug-resistant M. tuberculosis is reported in comparison with first-line antituberculosis drugs such as INH and rifampin. AREAS COVERED In this review, we summarise our current knowledge of DCS, and review the drug target and low-level resistance of DCS in M. tuberculosis. We summarise the metabolism of D-alanine (D-Ala) and peptidoglycan biosynthesis in bacteria. We first compared the amino acid similarity of Mycobacterium alanine racemase and D-Ala:D-alanine ligase and quite unexpectedly found that the two enzymes are highly conserved among Mycobacterium. EXPERT OPINION We summarise the drug targets of DCS and possible mechanisms underlying its low-level resistance for the first time. One significant finding is that ubiquinone and menaquinone metabolism-related genes are novel genes underlying DCS resistance in Escherichia coli and with homologues in M. tuberculosis. Further understanding of DCS targets and basis for its low-level resistance might inspire us to improve the use of DCS or find better drug targets.
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Affiliation(s)
- Weiling Hong
- Southwest University, Institute of Modern Biopharmaceuticals, School of Life Sciences, State Key Laboratory Breeding Base of Eco-Enviroment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education , Beibei, Chongqing 400715 , China +86 23 68367 108 ; +86 23 68367 108 ;
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Doan TTN, Kim JK, Ngo HPT, Tran HT, Cha SS, Min Chung K, Huynh KH, Ahn YJ, Kang LW. Crystal structures of d-alanine-d-alanine ligase from Xanthomonas oryzae pv. oryzae alone and in complex with nucleotides. Arch Biochem Biophys 2014; 545:92-9. [PMID: 24440607 DOI: 10.1016/j.abb.2014.01.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 01/04/2014] [Accepted: 01/09/2014] [Indexed: 10/25/2022]
Abstract
D-Alanine-D-alanine ligase (DDL) catalyzes the biosynthesis of d-alanyl-d-alanine, an essential bacterial peptidoglycan precursor, and is an important drug target for the development of antibacterials. We determined four different crystal structures of DDL from Xanthomonas oryzae pv. oryzae (Xoo) causing Bacteria Blight (BB), which include apo, ADP-bound, ATP-bound, and AMPPNP-bound structures at the resolution between 2.3 and 2.0 Å. Similarly with other DDLs, the active site of XoDDL is formed by three loops from three domains at the center of enzyme. Compared with d-alanyl-d-alanine and ATP-bound TtDDL structure, the γ-phosphate of ATP in XoDDL structure was shifted outside toward solution. We swapped the ω-loop (loop3) of XoDDL with those of Escherichia coli and Helicobacter pylori DDLs, and measured the enzymatic kinetics of wild-type XoDDL and two mutant XoDDLs with the swapped ω-loops. Results showed that the direct interactions between ω-loop and other two loops are essential for the active ATP conformation for D-ala-phosphate formation.
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Affiliation(s)
- Thanh Thi Ngoc Doan
- Department of Advanced Technology Fusion, Konkuk University, Hwayang dong, Gwangjin-gu, Seoul 143-01, Republic of Korea
| | - Jin-Kwang Kim
- Department of Advanced Technology Fusion, Konkuk University, Hwayang dong, Gwangjin-gu, Seoul 143-01, Republic of Korea
| | - Ho-Phuong-Thuy Ngo
- Department of Biological Sciences, Konkuk University, Seoul 143-701, Republic of Korea
| | - Huyen-Thi Tran
- Department of Biological Sciences, Konkuk University, Seoul 143-701, Republic of Korea
| | - Sun-Shin Cha
- Marine Biotechnology Research Division, Korea Institute of Ocean Science and Technology, Ansan 426-744, Republic of Korea
| | - Kyung Min Chung
- Department of Microbiology and Immunology, Chonbuk National University Medical School, Jeonju, Jeonbuk 561-756, Republic of Korea
| | - Kim-Hung Huynh
- Department of Biological Sciences, Konkuk University, Seoul 143-701, Republic of Korea
| | - Yeh-Jin Ahn
- Department of Green Life Science, College of Convergence, Sangmyung University, 7 Hongji-dong, Jongno-gu, Seoul 110-743, Republic of Korea
| | - Lin-Woo Kang
- Department of Biological Sciences, Konkuk University, Seoul 143-701, Republic of Korea; Institute for Cellular and Structural Bioloy, Sun Yat-Sen University, Guangzhou, People's Republic of China.
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Prosser GA, de Carvalho LPS. Reinterpreting the mechanism of inhibition of Mycobacterium tuberculosis D-alanine:D-alanine ligase by D-cycloserine. Biochemistry 2013; 52:7145-9. [PMID: 24033232 PMCID: PMC3944805 DOI: 10.1021/bi400839f] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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d-Cycloserine is a second-line
drug approved for use in
the treatment of patients infected with Mycobacterium tuberculosis, the etiologic agent of tuberculosis. The unique mechanism of action
of d-cycloserine, compared with those of other clinically
employed antimycobacterial agents, represents an untapped and exploitable
resource for future rational drug design programs. Here, we show that d-cycloserine is a slow-onset inhibitor of MtDdl and that this
behavior is specific to the M. tuberculosis enzyme
orthologue. Furthermore, evidence is presented that indicates d-cycloserine binds exclusively to the C-terminal d-alanine binding site, even in the absence of bound d-alanine
at the N-terminal binding site. Together, these results led us to
propose a new model of d-alanine:d-alanine ligase
inhibition by d-cycloserine and suggest new opportunities
for rational drug design against an essential, clinically validated
mycobacterial target.
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Affiliation(s)
- Gareth A Prosser
- Mycobacterial Research Division, MRC National Institute for Medical Research , The Ridgeway, Mill Hill, London NW7 1AA, U.K
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Prosser GA, de Carvalho LPS. Kinetic mechanism and inhibition of Mycobacterium tuberculosis D-alanine:D-alanine ligase by the antibiotic D-cycloserine. FEBS J 2013; 280:1150-66. [PMID: 23286234 DOI: 10.1111/febs.12108] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 12/17/2012] [Accepted: 12/19/2012] [Indexed: 11/30/2022]
Abstract
D-cycloserine (DCS) is an antibiotic that is currently used in second-line treatment of tuberculosis. DCS is a structural analogue of D-alanine, and targets two enzymes involved in the cytosolic stages of peptidoglycan synthesis: alanine racemase (Alr) and D-alanine:D-alanine ligase (Ddl). The mechanisms of inhibition of DCS have been well-assessed using Alr and Ddl enzymes from various bacterial species, but little is known regarding the interactions of DCS with the mycobacterial orthologues of these enzymes. We have over-expressed and purified recombinant Mycobacterium tuberculosis Ddl (MtDdl; Rv2981c), and report a kinetic examination of the enzyme with both its native substrate and DCS. MtDdl is activated by K(+), follows an ordered ter ter mechanism and displays distinct affinities for D-Ala at each D-Ala binding site (K(m,D-Ala1) = 0.075 mm, K(m,D-Ala2) = 3.6 mm). ATP is the first substrate to bind and is necessary for subsequent binding of D-alanine or DCS. The pH dependence of MtDdl kinetic parameters indicate that general base chemistry is involved in the catalytic step. DCS was found to competitively inhibit D-Ala binding at both MtDdl D-Ala sites with equal affinity (K(i,DCS1) = 14 μm, K(i,DCS2) = 25 μm); however, each enzyme active site can only accommodate a single DCS molecule at a given time. The pH dependence of K(i,DCS2) revealed a loss of DCS binding affinity at high pH (pK(a) = 7.5), suggesting that DCS binds optimally in the zwitterionic form. The results of this study may assist in the design and development of novel Ddl-specific inhibitors for use as anti-mycobacterial agents.
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Affiliation(s)
- Gareth A Prosser
- Mycobacterial Research Division, Medical Research Council National Institute for Medical Research, London, UK
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Pedreño S, Pisco JP, Larrouy-Maumus G, Kelly G, de Carvalho LPS. Mechanism of feedback allosteric inhibition of ATP phosphoribosyltransferase. Biochemistry 2012; 51:8027-38. [PMID: 22989207 PMCID: PMC3466779 DOI: 10.1021/bi300808b] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
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MtATP-phosphoribosyltransferase catalyzes the first and
committed
step in l-histidine biosynthesis in Mycobacterium
tuberculosis and is therefore subjected to allosteric feedback
regulation. Because of its essentiality, this enzyme is being studied
as a potential target for novel anti-infectives. To understand the
basis for its regulation, we characterized the allosteric inhibition
using gel filtration, steady-state and pre-steady-state kinetics,
and the pH dependence of inhibition and binding. Gel filtration experiments
indicate that MtATP-phosphoribosyltransferase is a hexamer in solution,
in the presence or absence of l-histidine. Steady-state kinetic
studies demonstrate that l-histidine inhibition is uncompetitive
versus ATP and noncompetitive versus PRPP. At pH values close to neutrality,
a Kii value of 4 μM was obtained
for l-histidine. Pre-steady-state kinetic experiments indicate
that chemistry is not rate-limiting for the overall reaction and that l-histidine inhibition is caused by trapping the enzyme in an
inactive conformation. The pH dependence of binding, obtained by nuclear
magnetic resonance, indicates that l-histidine binds better
as the neutral α-amino group. The pH dependence of inhibition
(Kii), on the contrary, indicates that l-histidine better inhibits MtATP-phosphoribosytransferase with
a neutral imidazole and an ionized α-amino group. These results
are combined into a model that accounts for the allosteric inhibition
of MtATP-phosphoribosyltransferase.
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Affiliation(s)
- Sònia Pedreño
- Mycobacterial Research Division, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
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Meziane-Cherif D, Saul FA, Haouz A, Courvalin P. Structural and functional characterization of VanG D-Ala:D-Ser ligase associated with vancomycin resistance in Enterococcus faecalis. J Biol Chem 2012; 287:37583-92. [PMID: 22969085 DOI: 10.1074/jbc.m112.405522] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
d-Alanyl:d-lactate (d-Ala:d-Lac) and d-alanyl:d-serine ligases are key enzymes in vancomycin resistance of Gram-positive cocci. They catalyze a critical step in the synthesis of modified peptidoglycan precursors that are low binding affinity targets for vancomycin. The structure of the d-Ala:d-Lac ligase VanA led to the understanding of the molecular basis for its specificity, but that of d-Ala:d-Ser ligases had not been determined. We have investigated the enzymatic kinetics of the d-Ala:d-Ser ligase VanG from Enterococcus faecalis and solved its crystal structure in complex with ADP. The overall structure of VanG is similar to that of VanA but has significant differences mainly in the N-terminal and central domains. Based on reported mutagenesis data and comparison of the VanG and VanA structures, we show that residues Asp-243, Phe-252, and Arg-324 are molecular determinants for d-Ser selectivity. These residues are conserved in both enzymes and explain why VanA also displays d-Ala:d-Ser ligase activity, albeit with low catalytic efficiency in comparison with VanG. These observations suggest that d-Ala:d-Lac and d-Ala:d-Ser enzymes have evolved from a common ancestral d-Ala:d-X ligase. The crystal structure of VanG showed an unusual interaction between two dimers involving residues of the omega loop that are deeply anchored in the active site. We constructed an octapeptide mimicking the omega loop and found that it selectively inhibits VanG and VanA but not Staphylococcus aureus d-Ala:d-Ala ligase. This study provides additional insight into the molecular evolution of d-Ala:d-X ligases and could contribute to the development of new structure-based inhibitors of vancomycin resistance enzymes.
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Molecular docking studies on analogues of quercetin with d-alanine:d-alanine ligase of Helicobacter pylori. Med Chem Res 2012. [DOI: 10.1007/s00044-012-0207-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Abstract
Hepsin is a type II transmembrane serine protease that is expressed in several human tissues. Overexpression of hepsin has been found to correlate with tumour progression and metastasis, which is so far best studied for prostate cancer, where more than 90% of such tumours show this characteristic. To enable improved future patient treatment, we have developed a monoclonal humanized antibody that selectively inhibits human hepsin and does not inhibit other related proteases. We found that our antibody, hH35, potently inhibits hepsin enzymatic activity at nanomolar concentrations. Kinetic characterization revealed non-linear, slow, tight-binding inhibition. This correlates with the crystal structure we obtained for the human hepsin-hH35 antibody Fab fragment complex, which showed that the antibody binds hepsin around α3-helix, located far from the active centre. The unique allosteric mode of inhibition of hH35 is distinct from the recently described HGFA (hepatocyte growth factor activator) allosteric antibody inhibition. We further explain how a small change in the antibody design induces dramatic structural rearrangements in the hepsin antigen upon binding, leading to complete enzyme inactivation.
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Lin YL, Chen YS, Hsu YM, Yao CH, Chang TJ. PROTEOMIC ANALYSIS AND ANTIBACTERIAL EFFECTS OF LITHOSPERMI RADIX AGAINST COMMON BACTERIA FROM HUMAN INFECTED WOUNDS. BIOMEDICAL ENGINEERING-APPLICATIONS BASIS COMMUNICATIONS 2012. [DOI: 10.4015/s1016237212002937] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The prevention and treatment of infections of human wounds are an important issue. In this investigation five herbal plants were selected, and their antibacterial effects were elucidated. Of these five herbal plants, the morphological changes of the one with the strongest antibacterial effects were observed using a scanning electron microscope (SEM) and the differential expression of bacterial proteins treated with them was determined by two-dimensional gel electrophoresis (2D-GE). Two proteins of weakly expressed spots from the highest matching percentage of 2D-GE were identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF/TOF). The results indicated that the Lithospermi radix have the best minimal inhibitory concentration (MIC) and minimal bactericidal concentration (MBC). The SEM examination reveals different bactericidal morphological changes and colony distributions obtained using Lithospermi radix. 2D-GE reveals that Staphylococcus aureus treated with Lithospermi radix has the highest matching percentage (90.93%). Then identification of two proteins that are weakly expressed in Staphylococcus aureus by MALDI-TOF/TOF reveals that they are Holliday junction ATP-dependent DNA helicase RuvB and D-alanine: D-alanine ligase (DDI). These results are noteworthy to suggest that Lithospermi radix may be used as an antibacterial medicine to treatment of human wound infection.
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Affiliation(s)
- Yu-Li Lin
- Division of Pediatric Surgery, Department of Surgery, Cheng Ching General Hospital, Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Yueh-Sheng Chen
- School of Chinese Medicine, China Medical University, Taichung, Taiwan
- Department of Biomedical Imaging and Radiological Science, China Medical University, Taichung, Taiwan
| | - Yua-Man Hsu
- Department of Biological Science & Technology, College of Life Sciences, China Medical University, Taichung, Taiwan
| | - Chun-Hsu Yao
- School of Chinese Medicine, China Medical University, Taichung, Taiwan
- Department of Biomedical Imaging and Radiological Science, China Medical University, Taichung, Taiwan
| | - Tien-Jye Chang
- Department of Veterinary Medicine, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
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Vehar B, Hrast M, Kovač A, Konc J, Mariner K, Chopra I, O'Neill A, Janežič D, Gobec S. Ellipticines and 9-acridinylamines as inhibitors of D-alanine:D-alanine ligase. Bioorg Med Chem 2011; 19:5137-46. [PMID: 21831641 DOI: 10.1016/j.bmc.2011.07.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Revised: 07/11/2011] [Accepted: 07/12/2011] [Indexed: 11/29/2022]
Abstract
D-Alanine:D-alanine ligase (Ddl), an intracellular bacterial enzyme essential for cell wall biosynthesis, is an attractive target for development of novel antimicrobial drugs. This study focused on an extensive evaluation of two families of Ddl inhibitors encountered in our previous research. New members of both families were obtained through similarity search and synthesis. Ellipticines and 9-acridinylamines were both found to possess inhibitory activity against Ddl from Escherichia coli and antimicrobial activity against E. coli and Staphylococcus aureus. Ellipticines with a quaternary methylpyridinium moiety were the most potent among all studied compounds, with MIC values as low as 2 mg/L in strains with intact efflux mechanisms. Antimicrobial activity of the studied compounds was connected to membrane damage, making their development as antibacterial drug candidates unlikely unless analogues devoid of this nonspecific effect can be discovered.
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Affiliation(s)
- Blaž Vehar
- National Institute of Chemistry, Ljubljana, Slovenia
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Neuhaus FC. Role of the omega loop in specificity determination in subsite 2 of the D-alanine:D-alanine (D-lactate) ligase from Leuconostoc mesenteroides: a molecular docking study. J Mol Graph Model 2011; 30:31-7. [PMID: 21727015 DOI: 10.1016/j.jmgm.2011.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Revised: 05/26/2011] [Accepted: 06/02/2011] [Indexed: 11/25/2022]
Abstract
The synthesis of D-ala-D-lactate in Leuconostoc mesenteroides is catalyzed by D-alanine:D-alanine (D-lactate) ligase (ADP). The ability to assemble this depsipeptide as well as D-ala-D-ala provides a mechanism for the organism's intrinsic resistance to vancomycin. Mutation of Phe261 to Tyr261 in the Ω-loop of this ligase showed a complete loss of the ability to make D-ala-D-lactate (Park and Walsh, J. Biol. Chem. 272 (1997) 9210-9214). Phe261 is a key specificity determinant in the α-helical cap of the Ω-loop when folded into the closed conformation. A molecular docking study of the closed ligase using AutoDock 4.2 defines additional specificity constraints promoted by the Ω-loop capping the catalytic center. Attaining productive orientations of D-lactate with favorable ligation chemistry requires the flexibilities of Phe261 and Arg301 in the docking protocol. These are in addition to the optimization of van der Waals contacts with Lys260, Met326, and Ser327. The location of Phe261 and Lys260 in the α-helical cap of the Ω-loop over subsite 2 is an essential part of the folding process ensuring depsipeptide formation in the hydrophobic environment of the catalytic center. The importance of the F261Y mutation suggests that the hydroxyl of Tyr261 plays an instrumental role in determining non-productive docking orientations of D-lactate. Two of these are presented: (A) D-lactate-OH as an H-bond donor to the Tyr261-OH; (B) D-lactate as an H-bond donor to the phosphoryl of the intermediate D-alanyl phosphate, and the D-lactate-COO- as an H-bond acceptor for the Tyr261-OH. Neither orientation, A or B, show the bifurcated H-bonding with Arg301 recently proposed for the activation of the nucleophilic D-lactate for D-ala-D-lactate formation. Insights into the role of the Ω-loop and its K(F/Y) signature provide additional background for inhibitor design targeted to subsite 2 of the D-alanine:D-alanine (D-X) ligases.
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Affiliation(s)
- Francis C Neuhaus
- Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208-3500, USA.
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Bromberg L, Chang EP, Hatton TA, Concheiro A, Magariños B, Alvarez-Lorenzo C. Bactericidal core-shell paramagnetic nanoparticles functionalized with poly(hexamethylene biguanide). LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:420-429. [PMID: 21138282 DOI: 10.1021/la1039909] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Bactericidal paramagnetic particles were obtained either through the attachment of a conjugate of poly(ethyleneimine) (PEI) and poly(hexamethylene biguanide) (PHMBG) to the surface of magnetite (Fe(3)O(4)) particles, or via the sol-gel encapsulation of magnetite particles with a functional silane (3-glycidoxypropyl trimethoxysilane) and subsequent binding of the polysiloxane shell by the amine/imine groups of PHMBG. The encapsulated core-shell particles possess a high saturation magnetization, which is preserved for more than 10 months while in contact with air in aqueous suspensions. The minimum inhibitory concentration (MIC) of the encapsulated particles for eight types of bacteria was size-dependent, with polydisperse submillimeter particles possessing a several-fold higher MIC than analogous particles sized below 250 nm. The encapsulated particles are biocompatible and nontoxic to mammalian cells such as mouse fibroblasts. The particles efficiently bind both glycopeptide components mimicking the gram-positive bacteria membranes and whole bacteria, and possess broad-range bactericidal activity. The cell-particle complexes can be captured, manipulated, and removed by means of a magnet.
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Affiliation(s)
- Lev Bromberg
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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Structure of the Mycobacterium tuberculosis D-alanine:D-alanine ligase, a target of the antituberculosis drug D-cycloserine. Antimicrob Agents Chemother 2010; 55:291-301. [PMID: 20956591 DOI: 10.1128/aac.00558-10] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
D-alanine:D-alanine ligase (EC 6.3.2.4; Ddl) catalyzes the ATP-driven ligation of two D-alanine (D-Ala) molecules to form the D-alanyl:D-alanine dipeptide. This molecule is a key building block in peptidoglycan biosynthesis, making Ddl an attractive target for drug development. D-Cycloserine (DCS), an analog of D-Ala and a prototype Ddl inhibitor, has shown promise for the treatment of tuberculosis. Here, we report the crystal structure of Mycobacterium tuberculosis Ddl at a resolution of 2.1 Å. This structure indicates that Ddl is a dimer and consists of three discrete domains; the ligand binding cavity is at the intersection of all three domains and conjoined by several loop regions. The M. tuberculosis apo Ddl structure shows a novel conformation that has not yet been observed in Ddl enzymes from other species. The nucleotide and D-alanine binding pockets are flexible, requiring significant structural rearrangement of the bordering regions for entry and binding of both ATP and D-Ala molecules. Solution affinity and kinetic studies showed that DCS interacts with Ddl in a manner similar to that observed for D-Ala. Each ligand binds to two binding sites that have significant differences in affinity, with the first binding site exhibiting high affinity. DCS inhibits the enzyme, with a 50% inhibitory concentration (IC(50)) of 0.37 mM under standard assay conditions, implicating a preferential and weak inhibition at the second, lower-affinity binding site. Moreover, DCS binding is tighter at higher ATP concentrations. The crystal structure illustrates potential drugable sites that may result in the development of more-effective Ddl inhibitors.
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