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Aribisala JO, S'thebe NW, Sabiu S. In silico exploration of phenolics as modulators of penicillin binding protein (PBP) 2× of Streptococcus pneumoniae. Sci Rep 2024; 14:8788. [PMID: 38627456 PMCID: PMC11021432 DOI: 10.1038/s41598-024-59489-3] [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: 02/03/2024] [Accepted: 04/11/2024] [Indexed: 04/19/2024] Open
Abstract
Infections caused by multidrug-resistant Streptococcus pneumoniae remain the leading cause of pneumonia-related deaths in children < 5 years globally, and mutations in penicillin-binding protein (PBP) 2 × have been identified as the major cause of resistance in the organism to beta-lactams. Thus, the development of new modulators with enhanced binding of PBP2x is highly encouraged. In this study, phenolics, due to their reported antibacterial activities, were screened against the active site of PBP2x using structure-based pharmacophore and molecular docking techniques, and the ability of the top-hit phenolics to inhibit the active and allosteric sites of PBP2x was refined through 120 ns molecular dynamic simulation. Except for gallocatechin gallate and lysidicichin, respectively, at the active and allosteric sites of PBP2x, the top-hit phenolics had higher negative binding free energy (ΔGbind) than amoxicillin [active site (- 19.23 kcal/mol), allosteric site (- 33.75 kcal/mol)]. Although silicristin had the best broad-spectrum effects at the active (- 38.41 kcal/mol) and allosteric (- 50.54 kcal/mol) sites of PBP2x, the high thermodynamic entropy (4.90 Å) of the resulting complex might suggest the need for its possible structural refinement for enhanced potency. Interestingly, silicristin had a predicted synthetic feasibility score of < 5 and quantum calculations using the DFT B3LYP/6-31G+ (dp) revealed that silicristin is less stable and more reactive than amoxicillin. These findings point to the possible benefits of the top-hit phenolics, and most especially silicristin, in the direct and synergistic treatment of infections caused by S. pneumoniae. Accordingly, silicristin is currently the subject of further confirmatory in vitro research.
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Affiliation(s)
- Jamiu Olaseni Aribisala
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa
| | - Nosipho Wendy S'thebe
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa
| | - Saheed Sabiu
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa.
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2
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Bon CG, Grigg JC, Lee J, Robb CS, Caveney NA, Eltis LD, Strynadka NCJ. Structural and kinetic analysis of the monofunctional Staphylococcus aureus PBP1. J Struct Biol 2024; 216:108086. [PMID: 38527711 DOI: 10.1016/j.jsb.2024.108086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/13/2024] [Accepted: 03/14/2024] [Indexed: 03/27/2024]
Abstract
Staphylococcus aureus, an ESKAPE pathogen, is a major clinical concern due to its pathogenicity and manifold antimicrobial resistance mechanisms. The commonly used β-lactam antibiotics target bacterial penicillin-binding proteins (PBPs) and inhibit crosslinking of peptidoglycan strands that comprise the bacterial cell wall mesh, initiating a cascade of effects leading to bacterial cell death. S. aureus PBP1 is involved in synthesis of the bacterial cell wall during division and its presence is essential for survival of both antibiotic susceptible and resistant S. aureus strains. Here, we present X-ray crystallographic data for S. aureus PBP1 in its apo form as well as acyl-enzyme structures with distinct classes of β-lactam antibiotics representing the penicillins, carbapenems, and cephalosporins, respectively: oxacillin, ertapenem and cephalexin. Our structural data suggest that the PBP1 active site is readily accessible for substrate, with little conformational change in key structural elements required for its covalent acylation of β-lactam inhibitors. Stopped-flow kinetic analysis and gel-based competition assays support the structural observations, with even the weakest performing β-lactams still having comparatively high acylation rates and affinities for PBP1. Our structural and kinetic analysis sheds insight into the ligand-PBP interactions that drive antibiotic efficacy against these historically useful antimicrobial targets and expands on current knowledge for future drug design and treatment of S. aureus infections.
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Affiliation(s)
- Christopher G Bon
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Jason C Grigg
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Jaeyong Lee
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Craig S Robb
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Nathanael A Caveney
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Lindsay D Eltis
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada; Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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3
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Aribisala JO, Sabiu S. Cheminformatics identification of phenolics as modulators of penicillin-binding protein-3 of Pseudomonas aeruginosa towards interventive antibacterial therapy. J Biomol Struct Dyn 2024; 42:298-313. [PMID: 36974951 DOI: 10.1080/07391102.2023.2192808] [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: 11/29/2022] [Accepted: 03/11/2023] [Indexed: 03/29/2023]
Abstract
Antibacterial resistance to β-lactams in microorganisms has been attributed majorly to alterations in penicillin-binding proteins (PBPs) coupled with β-lactams' inactivation by β-lactamase. Consequently, the identification of a novel class of therapeutics with improved modulatory action on the PBPs is imperative and plant secondary metabolites, including phenolics, have found relevance in this regard. For the first time in this study, the over 10,000 phenolics currently known were computationally evaluated against PBP3 of Pseudomonas aeruginosa, a superbug implicated in several nosocomial infections. In doing this, a library of phenolics with an affinity for PBP3 of P. aeruginosa was screened using structure-activity relationship-based pharmacophore and molecular docking approaches. Subsequent thermodynamic screening of the top five phenolics with higher docking scores, more drug-likeness attributes, and feasible synthetic accessibility was achieved through a 120 ns molecular dynamic (MD) simulation. Four of the top five hits had higher binding free energy than cefotaxime (-18.72 kcal/mol), with catechin-3-rhamside having the highest affinity (-28.99 kcal/mol). All the hits were stable at the active site of the PBP3, with catechin-3-rhamside being the most stable (2.14 Å), and established important interactions with Ser294, implicated in the catalytic activity of PBP3. Also, PBP3 became more compact with less fluctuation of the active site amino acid residues following the binding of the hits. These observations are indicative of the potential of the test compounds as PBP3 inhibitors, with catechin-3-rhamside being the most prominent of the compounds that could be further improved for enhanced druggability against PBP3 in vitro and in vivo.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jamiu Olaseni Aribisala
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, Durban, South Africa
| | - Saheed Sabiu
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, Durban, South Africa
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4
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Bertonha AF, Silva CCL, Shirakawa KT, Trindade DM, Dessen A. Penicillin-binding protein (PBP) inhibitor development: A 10-year chemical perspective. Exp Biol Med (Maywood) 2023; 248:1657-1670. [PMID: 38030964 PMCID: PMC10723023 DOI: 10.1177/15353702231208407] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023] Open
Abstract
Bacterial cell wall formation is essential for cellular survival and morphogenesis. The peptidoglycan (PG), a heteropolymer that surrounds the bacterial membrane, is a key component of the cell wall, and its multistep biosynthetic process is an attractive antibacterial development target. Penicillin-binding proteins (PBPs) are responsible for cross-linking PG stem peptides, and their central role in bacterial cell wall synthesis has made them the target of successful antibiotics, including β-lactams, that have been used worldwide for decades. Following the discovery of penicillin, several other compounds with antibiotic activity have been discovered and, since then, have saved millions of lives. However, since pathogens inevitably become resistant to antibiotics, the search for new active compounds is continuous. The present review highlights the ongoing development of inhibitors acting mainly in the transpeptidase domain of PBPs with potential therapeutic applications for the development of new antibiotic agents. Both the critical aspects of the strategy, design, and structure-activity relationships (SAR) are discussed, covering the main published articles over the last 10 years. Some of the molecules described display activities against main bacterial pathogens and could open avenues toward the development of new, efficient antibacterial drugs.
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Affiliation(s)
- Ariane F Bertonha
- Brazilian Biosciences National Laboratory (LNBio), CNPEM, Campinas 13084-971, Brazil
| | - Caio C L Silva
- Brazilian Biosciences National Laboratory (LNBio), CNPEM, Campinas 13084-971, Brazil
| | - Karina T Shirakawa
- Brazilian Biosciences National Laboratory (LNBio), CNPEM, Campinas 13084-971, Brazil
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-862, Brazil
| | - Daniel M Trindade
- Brazilian Biosciences National Laboratory (LNBio), CNPEM, Campinas 13084-971, Brazil
| | - Andréa Dessen
- Brazilian Biosciences National Laboratory (LNBio), CNPEM, Campinas 13084-971, Brazil
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), F-38044 Grenoble, France
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5
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G S, K D, P S, N B. DFT calculations, molecular docking, in vitro antimicrobial and antidiabetic studies of green synthesized Schiff bases: as Covid-19 inhibitor. J Biomol Struct Dyn 2023; 41:12997-13014. [PMID: 36752337 DOI: 10.1080/07391102.2023.2175039] [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: 11/29/2022] [Accepted: 01/11/2023] [Indexed: 02/09/2023]
Abstract
In this investigation, we synthesized Schiff bases 2-(2-methoxyphenoxy)-N-(4-methylbenzylidene)ethanamine, N-(4-methoxybenzylidene)-2-(2-methoxyphenoxy)ethanamine and 2-(2-methoxyphenoxy)-N-(4-nitrobenzylidene)ethanamine from 2-(2-methoxyphenoxy)ethanamine and various aromatic aldehydes by the environmentally friendly sonication method. The B3LYP method with a 6-311++G (d, p) basis set was used in the DFT calculation to obtain the optimized structure of the Schiff base MPEA-NIT. The compounds were tested in vitro for inhibition of bacterial growth (disc well method) and inhibition of α-amylase (starch-iodine method). The compounds tested showed inhibitory activities. In addition, they were subjected to PASS analysis, drug likeness, and bioactivity score predictions using online software. To confirm the experimental findings, molecular docking analyses of synthesized compounds on α-amylase (PDB ID: 1SMD), tRNA threonylcarbamoyladenosine (PDB ID: 5MVR), glycosyl transferase (PDB ID: 6D9T), and peptididoglycan D,D-transpeptidase (PDB ID: 6HZQ) were performed. The emergence of a new coronavirus epidemic necessitates the development of antiviral medications (SARS-CoV-2). Docking active site interactions were investigated to predict compounds' activity against COVID-19 by binding with the SARS-CoV-2 (PDB ID: 6Y84).Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Saranya G
- Department of Chemistry, Chikkaiah Naicker College, Erode, India
| | | | - Shanmugapriya P
- Department of Chemistry, KSR College of Engineering, Thiruchengode, India
| | - Bhuvaneshwari N
- Department of Chemistry, Chikkaiah Naicker College, Erode, India
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6
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McLaughlin HP, Gulvik CA, Sue D. In silico analyses of penicillin binding proteins in Burkholderia pseudomallei uncovers SNPs with utility for phylogeography, species differentiation, and sequence typing. PLoS Negl Trop Dis 2022; 16:e0009882. [PMID: 35417451 PMCID: PMC9037935 DOI: 10.1371/journal.pntd.0009882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 04/25/2022] [Accepted: 03/15/2022] [Indexed: 11/26/2022] Open
Abstract
Burkholderia pseudomallei causes melioidosis. Sequence typing this pathogen can reveal geographical origin and uncover epidemiological associations. Here, we describe B. pseudomallei genes encoding putative penicillin binding proteins (PBPs) and investigate their utility for determining phylogeography and differentiating closely related species. We performed in silico analysis to characterize 10 PBP homologs in B. pseudomallei 1026b. As PBP active site mutations can confer β-lactam resistance in Gram-negative bacteria, PBP sequences in two resistant B. pseudomallei strains were examined for similar alterations. Sequence alignments revealed single amino acid polymorphisms (SAAPs) unique to the multidrug resistant strain Bp1651 in the transpeptidase domains of two PBPs, but not directly within the active sites. Using BLASTn analyses of complete assembled genomes in the NCBI database, we determined genes encoding PBPs were conserved among B. pseudomallei (n = 101) and Burkholderia mallei (n = 26) strains. Within these genes, single nucleotide polymorphisms (SNPs) useful for predicting geographic origin of B. pseudomallei were uncovered. SNPs unique to B. mallei were also identified. Based on 11 SNPs identified in two genes encoding predicted PBP-3s, a dual-locus sequence typing (DLST) scheme was developed. The robustness of this typing scheme was assessed using 1,523 RefSeq genomes from B. pseudomallei (n = 1,442) and B. mallei (n = 81) strains, resulting in 32 sequence types (STs). Compared to multi-locus sequence typing (MLST), the DLST scheme demonstrated less resolution to support the continental separation of Australian B. pseudomallei strains. However, several STs were unique to strains originating from a specific country or region. The phylogeography of Western Hemisphere B. pseudomallei strains was more highly resolved by DLST compared to internal transcribed spacer (ITS) typing, and all B. mallei strains formed a single ST. Conserved genes encoding PBPs in B. pseudomallei are useful for strain typing, can enhance predictions of geographic origin, and differentiate strains of closely related Burkholderia species. Burkholderia pseudomallei causes the life-threatening disease melioidosis and is considered a biological threat and select agent by the United States government. This soil-dwelling bacterium is commonly found in regions of southeast Asia and northern Australia, but it is also detected in other tropical and sub-tropical areas around the world. With a predicted global burden of 165,000 annual cases and mortality rate that can exceed 40% without prompt and appropriate antibiotic treatment, understanding the epidemiology of melioidosis and mechanisms of antibiotic resistance in B. pseudomallei can benefit public health and safety. Recently, we identified ten conserved genes encoding putative penicillin binding proteins (PBPs) in B. pseudomallei. Here, we examined B. pseudomallei PBP sequences for amino acid mutations that may contribute to β-lactam resistance. We also uncovered nucleotide mutations with utility to predict the geographical origin of B. pseudomallei strains and to differentiate closely related Burkholderia species. Based on 11 informative single nucleotide polymorphisms in two genes each encoding a PBP-3, we developed a simple, targeted dual-locus typing approach.
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Affiliation(s)
- Heather P. McLaughlin
- Biodefense Research and Development Laboratory, Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- * E-mail:
| | - Christopher A. Gulvik
- Zoonoses and Select Agent Laboratory, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - David Sue
- Biodefense Research and Development Laboratory, Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
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7
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Abo-Bakr AM, Alsoghier HM, Abdelmonsef AH. Molecular docking, modeling, semiempirical calculations studies and in vitro evaluation of new synthesized pyrimidin-imide derivatives. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131548] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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8
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β-lactam Resistance in Pseudomonas aeruginosa: Current Status, Future Prospects. Pathogens 2021; 10:pathogens10121638. [PMID: 34959593 PMCID: PMC8706265 DOI: 10.3390/pathogens10121638] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/06/2021] [Accepted: 12/16/2021] [Indexed: 12/12/2022] Open
Abstract
Pseudomonas aeruginosa is a major opportunistic pathogen, causing a wide range of acute and chronic infections. β-lactam antibiotics including penicillins, carbapenems, monobactams, and cephalosporins play a key role in the treatment of P. aeruginosa infections. However, a significant number of isolates of these bacteria are resistant to β-lactams, complicating treatment of infections and leading to worse outcomes for patients. In this review, we summarize studies demonstrating the health and economic impacts associated with β-lactam-resistant P. aeruginosa. We then describe how β-lactams bind to and inhibit P. aeruginosa penicillin-binding proteins that are required for synthesis and remodelling of peptidoglycan. Resistance to β-lactams is multifactorial and can involve changes to a key target protein, penicillin-binding protein 3, that is essential for cell division; reduced uptake or increased efflux of β-lactams; degradation of β-lactam antibiotics by increased expression or altered substrate specificity of an AmpC β-lactamase, or by the acquisition of β-lactamases through horizontal gene transfer; and changes to biofilm formation and metabolism. The current understanding of these mechanisms is discussed. Lastly, important knowledge gaps are identified, and possible strategies for enhancing the effectiveness of β-lactam antibiotics in treating P. aeruginosa infections are considered.
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9
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Ninh The S, Le Tuan A, Dinh Thi Thu T, Nguyen Dinh L, Tran Thi T, Pham-The H. Essential oils of Uvaria boniana - chemical composition, in vitro bioactivity, docking, and in silico ADMET profiling of selective major compounds. Z NATURFORSCH C 2021; 77:207-218. [PMID: 34761648 DOI: 10.1515/znc-2021-0111] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 10/16/2021] [Indexed: 02/07/2023]
Abstract
Phytochemical investigation applying GC (gas chromatography)-MS (mass spectrometry)/GC-FID (flame ionization detection) on the hydro-distilled essential oils of the Vietnamese medicinal plant Uvaria boniana leaf and twig lead to the detection of 35 constituents (97.36%) in the leaf oil and 52 constituents (98.75%) in the twig oil. Monoterpenes, monoterpenoids, sesquiterpenes, and sesquiterpenoids were characteristic of U. boniana essential oils. The leaf oil was represented by major components (E)-caryophyllene (16.90%), bicyclogermacrene (15.95%), α-humulene (14.96%), and linalool (12.40%), whereas four compounds α-cadinol (16.16%), epi-α-muurolol (10.19%), α-pinene (11.01%), and β-pinene (8.08%) were the main ones in the twig oil. As compared with the leaf oil, the twig oil was better in antimicrobial activity. With the same MIC value of 40 mg/mL, the twig oil successfully controlled the growth of Gram (+) bacterium Bacillus subtilis, Gram (-) bacterium Escherichia coli, fungus Aspergillus niger, and yeast Saccharomyces cerevisiae. In addition, both two oil samples have induced antiinflammatory activity with the IC50 values of 223.7-240.6 mg/mL in NO productive inhibition when BV2 cells had been stimulated by LPS. Docking simulations of four major compounds of U. boniana twig oil on eight relevant antibacterial targets revealed that epi-α-muurolol and α-cadinol are moderate inhibitors of E. coli DNA gyrase subunit B, penicillin binding protein 2X and penicillin binding protein 3 of Pseudomonas aeruginosa with similar free binding energies of -30.1, -29.3, and -29.3 kJ/mol, respectively. Furthermore, in silico ADMET studies indicated that all four docked compounds have acceptable oral absorption, low metabolism, and appropriated toxicological profile to be considered further as drug candidates.
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Affiliation(s)
- Son Ninh The
- Institute of Chemistry, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Caugiay, Hanoi, Vietnam
| | - Anh Le Tuan
- Mien Trung Institute for Scientific Research, VAST, Hanoi, Vietnam
| | | | | | - Tuyen Tran Thi
- Institute of Natural Products Chemistry, VAST, Hanoi, Vietnam.,Graduate University of Science and Technology, VAST, Hanoi, Vietnam
| | - Hai Pham-The
- Hanoi University of Pharmacy, 13-15 Le Thanh Tong, Hoan Kiem, Hanoi, Vietnam
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10
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Newman H, Krajnc A, Bellini D, Eyermann CJ, Boyle GA, Paterson NG, McAuley KE, Lesniak R, Gangar M, von Delft F, Brem J, Chibale K, Schofield CJ, Dowson CG. High-Throughput Crystallography Reveals Boron-Containing Inhibitors of a Penicillin-Binding Protein with Di- and Tricovalent Binding Modes. J Med Chem 2021; 64:11379-11394. [PMID: 34337941 PMCID: PMC9282634 DOI: 10.1021/acs.jmedchem.1c00717] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The effectiveness of β-lactam antibiotics is increasingly compromised by β-lactamases. Boron-containing inhibitors are potent serine-β-lactamase inhibitors, but the interactions of boron-based compounds with the penicillin-binding protein (PBP) β-lactam targets have not been extensively studied. We used high-throughput X-ray crystallography to explore reactions of a boron-containing fragment set with the Pseudomonas aeruginosa PBP3 (PaPBP3). Multiple crystal structures reveal that boronic acids react with PBPs to give tricovalently linked complexes bonded to Ser294, Ser349, and Lys484 of PaPBP3; benzoxaboroles react with PaPBP3 via reaction with two nucleophilic serines (Ser294 and Ser349) to give dicovalently linked complexes; and vaborbactam reacts to give a monocovalently linked complex. Modifications of the benzoxaborole scaffold resulted in a moderately potent inhibition of PaPBP3, though no antibacterial activity was observed. Overall, the results further evidence the potential for the development of new classes of boron-based antibiotics, which are not compromised by β-lactamase-driven resistance.
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Affiliation(s)
- Hector Newman
- School
of Life Sciences, University of Warwick, Coventry CV4 7AL, U.K.
- Diamond
Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, U.K.
| | - Alen Krajnc
- Department
of Chemistry and the Ineos Oxford Institute of Antimicrobial Research, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Dom Bellini
- School
of Life Sciences, University of Warwick, Coventry CV4 7AL, U.K.
| | - Charles J. Eyermann
- Drug
Discovery and Development Centre (H3D), University of Cape Town, Rondebosch 7701, South Africa
| | - Grant A. Boyle
- Drug
Discovery and Development Centre (H3D), University of Cape Town, Rondebosch 7701, South Africa
| | - Neil G. Paterson
- Diamond
Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, U.K.
| | - Katherine E. McAuley
- Diamond
Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, U.K.
| | - Robert Lesniak
- Department
of Chemistry and the Ineos Oxford Institute of Antimicrobial Research, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Mukesh Gangar
- Drug
Discovery and Development Centre (H3D), University of Cape Town, Rondebosch 7701, South Africa
| | - Frank von Delft
- Diamond
Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, U.K.
- Structural
Genomics Consortium (SGC), University of
Oxford, Oxford, U.K.
- Department
of Biochemistry, University of Johannesburg, Auckland Park 2006, South Africa
- Research
Complex at Harwell, Harwell
Science and Innovation Campus, Didcot OX11 0FA, U.K.
| | - Jürgen Brem
- Department
of Chemistry and the Ineos Oxford Institute of Antimicrobial Research, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Kelly Chibale
- Drug
Discovery and Development Centre (H3D), University of Cape Town, Rondebosch 7701, South Africa
- South
African Medical Research Council Drug Discovery and Development Research
Unit, Department of Chemistry and Institute of Infectious Disease
and Molecular Medicine, University of Cape
Town, Rondebosch 7701, South Africa
| | - Christopher J. Schofield
- Department
of Chemistry and the Ineos Oxford Institute of Antimicrobial Research, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, U.K.
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11
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Freischem S, Grimm I, López-Pérez A, Willbold D, Klenke B, Vuong C, Dingley AJ, Weiergräber OH. Interaction Mode of the Novel Monobactam AIC499 Targeting Penicillin Binding Protein 3 of Gram-Negative Bacteria. Biomolecules 2021; 11:biom11071057. [PMID: 34356681 PMCID: PMC8301747 DOI: 10.3390/biom11071057] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/12/2021] [Accepted: 07/14/2021] [Indexed: 01/05/2023] Open
Abstract
Novel antimicrobial strategies are urgently required because of the rising threat of multi drug resistant bacterial strains and the infections caused by them. Among the available target structures, the so-called penicillin binding proteins are of particular interest, owing to their good accessibility in the periplasmic space, and the lack of homologous proteins in humans, reducing the risk of side effects of potential drugs. In this report, we focus on the interaction of the innovative β-lactam antibiotic AIC499 with penicillin binding protein 3 (PBP3) from Escherichia coli and Pseudomonas aeruginosa. This recently developed monobactam displays broad antimicrobial activity, against Gram-negative strains, and improved resistance to most classes of β-lactamases. By analyzing crystal structures of the respective complexes, we were able to explore the binding mode of AIC499 to its target proteins. In addition, the apo structures determined for PBP3, from P. aeruginosa and the catalytic transpeptidase domain of the E. coli orthologue, provide new insights into the dynamics of these proteins and the impact of drug binding.
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Affiliation(s)
- Stefan Freischem
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, 52425 Jülich, Germany; (S.F.); (D.W.); (A.J.D.)
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Immanuel Grimm
- AiCuris Anti-Infective Cures AG, 42117 Wuppertal, Germany; (I.G.); (A.L.-P.); (B.K.); (C.V.)
| | - Arancha López-Pérez
- AiCuris Anti-Infective Cures AG, 42117 Wuppertal, Germany; (I.G.); (A.L.-P.); (B.K.); (C.V.)
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Type NE2 4AX, UK
| | - Dieter Willbold
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, 52425 Jülich, Germany; (S.F.); (D.W.); (A.J.D.)
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Burkhard Klenke
- AiCuris Anti-Infective Cures AG, 42117 Wuppertal, Germany; (I.G.); (A.L.-P.); (B.K.); (C.V.)
| | - Cuong Vuong
- AiCuris Anti-Infective Cures AG, 42117 Wuppertal, Germany; (I.G.); (A.L.-P.); (B.K.); (C.V.)
| | - Andrew J. Dingley
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, 52425 Jülich, Germany; (S.F.); (D.W.); (A.J.D.)
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Oliver H. Weiergräber
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, 52425 Jülich, Germany; (S.F.); (D.W.); (A.J.D.)
- Correspondence:
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12
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Rout UK, Sanket AS, Sisodia BS, Mohapatra PK, Pati S, Kant R, Dwivedi GR. A Comparative Review on Current and Future Drug Targets Against Bacteria & Malaria. Curr Drug Targets 2021; 21:736-775. [PMID: 31995004 DOI: 10.2174/1389450121666200129103618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 12/13/2019] [Accepted: 12/20/2019] [Indexed: 11/22/2022]
Abstract
Long before the discovery of drugs like 'antibiotic and anti-parasitic drugs', the infectious diseases caused by pathogenic bacteria and parasites remain as one of the major causes of morbidity and mortality in developing and underdeveloped countries. The phenomenon by which the organism exerts resistance against two or more structurally unrelated drugs is called multidrug resistance (MDR) and its emergence has further complicated the treatment scenario of infectious diseases. Resistance towards the available set of treatment options and poor pipeline of novel drug development puts an alarming situation. A universal goal in the post-genomic era is to identify novel targets/drugs for various life-threatening diseases caused by such pathogens. This review is conceptualized in the backdrop of drug resistance in two major pathogens i.e. "Pseudomonas aeruginosa" and "Plasmodium falciparum". In this review, the available targets and key mechanisms of resistance of these pathogens have been discussed in detail. An attempt has also been made to analyze the common drug targets of bacteria and malaria parasite to overcome the current drug resistance scenario. The solution is also hypothesized in terms of a present pipeline of drugs and efforts made by scientific community.
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Affiliation(s)
- Usha K Rout
- Microbiology Department, ICMR-Regional Medical Research Centre, Bhubaneswar-751023, India
| | | | - Brijesh S Sisodia
- Regional Ayurveda Research Institute for Drug Development, Gwalior-474 009, India
| | | | - Sanghamitra Pati
- Microbiology Department, ICMR-Regional Medical Research Centre, Bhubaneswar-751023, India
| | - Rajni Kant
- ICMR-Regional Medical Research Centre, Gorakhpur, Uttar Pradesh- 273013, India
| | - Gaurav R Dwivedi
- ICMR-Regional Medical Research Centre, Gorakhpur, Uttar Pradesh- 273013, India
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13
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K R, Kakkassery JT, Raphael VP, Johnson R, K VT. In vitro antibacterial and in silico docking studies of two Schiff bases on Staphylococcus aureus and its target proteins. FUTURE JOURNAL OF PHARMACEUTICAL SCIENCES 2021. [DOI: 10.1186/s43094-021-00225-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Schiff base compounds have extensive applications in various fields such as analytical, inorganic, organic, and biological fields. They have excellent pharmacology application prospects in the modern era and are widely used in the pharmaceutical industry. In the present work in vitro antibacterial and in silico docking studies of two Schiff base compounds 2,2’-(5,5-dimethylcyclohexane-1,3-diylidene)bis(azan-1-yl-1-ylidene)diphenol (DmChDp) and N,N’-(5,5-dimethylcyclohexane-1,3-diylidene)dianiline (DmChDa) were carried out against the bacterial strain Staphylococcus aureus and its target proteins.
Results
The tests proved that the ligands have potential antibacterial activity. In the computational analysis, the drug-like properties of the compounds were first pre-filtered using the Lipinski rule of five. Then, molecular docking study was conducted using the AutoDock 4.2 program, to establish the mechanism by which the molecules inhibit the growth of S. aureus. For this purpose, 6 different target proteins (PDB ID: 1T2P, 3U2D, 2W9S, 1N67, 2ZCO, and 4H8E) of S. aureus were selected. Both the Schiff bases showed a good binding affinity with the target protein dihydrofolate reductase enzyme (PDB ID: 2W9S) but in different sites. Maximum binding energies of about − 10.3 and − 10.2 kcal/mol were observed when DmChDp and DmChDa were docked with 2W9S.
Conclusion
Schiff base compounds DmChDp and DmChDa have appreciable growth-inhibitory power against S. aureus, which can be attributed to the deactivation of the enzyme, dihydrofolate reductase.
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14
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Structural Characterization of Diazabicyclooctane β-Lactam "Enhancers" in Complex with Penicillin-Binding Proteins PBP2 and PBP3 of Pseudomonas aeruginosa. mBio 2021; 12:mBio.03058-20. [PMID: 33593978 PMCID: PMC8545096 DOI: 10.1128/mbio.03058-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Multidrug-resistant (MDR) pathogens pose a significant public health threat. A major mechanism of resistance expressed by MDR pathogens is β-lactamase-mediated degradation of β-lactam antibiotics. The diazabicyclooctane (DBO) compounds zidebactam and WCK 5153, recognized as β-lactam “enhancers” due to inhibition of Pseudomonas aeruginosa penicillin-binding protein 2 (PBP2), are also class A and C β-lactamase inhibitors. To structurally probe their mode of PBP2 inhibition as well as investigate why P. aeruginosa PBP2 is less susceptible to inhibition by β-lactam antibiotics compared to the Escherichia coli PBP2, we determined the crystal structure of P. aeruginosa PBP2 in complex with WCK 5153. WCK 5153 forms an inhibitory covalent bond with the catalytic S327 of PBP2. The structure suggests a significant role for the diacylhydrazide moiety of WCK 5153 in interacting with the aspartate in the S-X-N/D PBP motif. Modeling of zidebactam in the active site of PBP2 reveals a similar binding mode. Both DBOs increase the melting temperature of PBP2, affirming their stabilizing interactions. To aid in the design of DBOs that can inhibit multiple PBPs, the ability of three DBOs to interact with P. aeruginosa PBP3 was explored crystallographically. Even though the DBOs show covalent binding to PBP3, they destabilized PBP3. Overall, the studies provide insights into zidebactam and WCK 5153 inhibition of PBP2 compared to their inhibition of PBP3 and the evolutionarily related KPC-2 β-lactamase. These molecular insights into the dual-target DBOs advance our knowledge regarding further DBO optimization efforts to develop novel potent β-lactamase-resistant, non-β-lactam PBP inhibitors.
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15
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Laser-Irradiated Chlorpromazine as a Potent Anti-Biofilm Agent for Coating of Biomedical Devices. COATINGS 2020. [DOI: 10.3390/coatings10121230] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Nowadays, antibiotic resistance has become increasingly common, triggering a global health crisis, immediately needing alternative, including repurposed drugs with potent bactericidal effects. We demonstrated that chlorpromazine aqueous solutions exposed to laser radiation exhibited visible activity against various microorganisms. The aim of this study was to investigate the quantitative antimicrobial activity of chlorpromazine in non-irradiated and 4-h laser irradiated form. Also, we examined the effect of both solutions impregnated on a cotton patch, cannula, and urinary catheter against Gram-positive Staphylococcus aureus and Gram-negative Pseudomonas aeruginosa and Escherichia coli. In all experimental versions, the chlorpromazine antimicrobial activity was enhanced by laser exposure. Besides the experimental results, the in silico analyses using molecular docking proved that the improved antimicrobial activity of the irradiated compound was a result of the combined action of the photoproducts on the biological target (s). Our results show that laser radiation could alter the molecular structure of various drugs and their effects, proving to be a promising strategy to halt antibiotic resistance, by repurposing current medicines for new antimicrobial strategies, thereby decreasing the costs and time for the development of more efficient drugs.
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16
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Miller LM, Herman R, Gyulev I, Krauss TF, Thomas GH, Duhme-Klair AK. Synthesis and biochemical evaluation of cephalosporin analogues equipped with chemical tethers. RSC Adv 2020; 10:36485-36494. [PMID: 35517937 PMCID: PMC9056950 DOI: 10.1039/d0ra04893c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 09/25/2020] [Indexed: 02/04/2023] Open
Abstract
Molecular probes typically require structural modifications to allow for the immobilisation or bioconjugation with a desired substrate but the effects of these changes are often not evaluated. Here, we set out to determine the effects of attaching functional handles to a first-generation cephalosporin. A series of cephalexin derivatives was prepared, equipped with chemical tethers suitable for the site-selective conjugation of antibiotics to functionalised surfaces. The tethers were positioned remotely from the β-lactam ring to ensure minimal effect to the antibiotic's pharmacophore. Herein, the activity of the modified antibiotics was evaluated for binding to the therapeutic target, the penicillin binding proteins, and shown to maintain binding interactions. In addition, the deactivation of the modified drugs by four β-lactamases (TEM-1, CTX-M-15, AmpC, NDM-1) was investigated and the effect of the tethers on the catalytic efficiencies determined. CTX-M-15 was found to favour hydrolysis of the parent antibiotic without a tether, whereas AmpC and NDM-1 were found to favour the modified analogues. Furthermore, the antimicrobial activity of the derivatives was evaluated to investigate the effect of the structural modifications on the antimicrobial activity of the parent drug, cephalexin. Tethered β-lactam antibiotics provide insights into designing chemical tools to target specific β-lactamases.![]()
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Affiliation(s)
- Lisa M Miller
- Department of Chemistry, University of York Heslington York YO10 5DD UK
| | - Reyme Herman
- Department of Biology, University of York Heslington York YO10 5DD UK
| | - Ivan Gyulev
- Department of Biology, University of York Heslington York YO10 5DD UK
| | - Thomas F Krauss
- Department of Physics, University of York Heslington York YO10 5DD UK
| | - Gavin H Thomas
- Department of Biology, University of York Heslington York YO10 5DD UK
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17
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Lu Z, Wang H, Zhang A, Liu X, Zhou W, Yang C, Guddat L, Yang H, Schofield CJ, Rao Z. Structures of Mycobacterium tuberculosis Penicillin-Binding Protein 3 in Complex with Five β-Lactam Antibiotics Reveal Mechanism of Inactivation. Mol Pharmacol 2020; 97:287-294. [DOI: 10.1124/mol.119.118042] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 01/14/2020] [Indexed: 11/22/2022] Open
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18
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New compounds for a good old class: Synthesis of two Β-lactam bearing cephalosporins and their evaluation with a multidisciplinary approach. Bioorg Med Chem 2020; 28:115302. [PMID: 31932194 DOI: 10.1016/j.bmc.2019.115302] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 12/13/2019] [Accepted: 12/31/2019] [Indexed: 11/21/2022]
Abstract
Antimicrobial resistance is spreading massively in the world and is becoming one of the main health threats of the 21st century. One of the possible strategies to overcome this problem is to modify the known classes of antibiotics in a rational way, with the aim of tuning their efficacy. In this paper, we present the synthesis and the evaluation of the biological activity of a series of two β-lactam bearing cephalosporin derivatives, in which an additional isolated azetidinone ring, bearing different substituents, is joined to the classical cephalosporanic nucleus by a chain of variable length. A computational approach has been also applied in order to predict the molecular interactions between some representative derivatives and selected penicillin-binding proteins, the natural targets of β-lactam antibiotics. All these derivatives are active against Gram-positive bacteria, with MIC100 comparable or even better than that of the reference antibiotic ceftriaxone, and show no or very low cytotoxic activity on different cell lines. Overall, these molecules appear to be able to exert their activity in particular against microorganisms belonging to some of the species more involved in the development of multidrug resistance.
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19
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Kim Y, Maltseva N, Wilamowski M, Tesar C, Endres M, Joachimiak A. Structural and biochemical analysis of the metallo-β-lactamase L1 from emerging pathogen Stenotrophomonas maltophilia revealed the subtle but distinct di-metal scaffold for catalytic activity. Protein Sci 2019; 29:723-743. [PMID: 31846104 PMCID: PMC7020990 DOI: 10.1002/pro.3804] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 12/10/2019] [Accepted: 12/11/2019] [Indexed: 01/05/2023]
Abstract
Emergence of Enterobacteriaceae harboring metallo‐β‐lactamases (MBL) has raised global threats due to their broad antibiotic resistance profiles and the lack of effective inhibitors against them. We have been studied one of the emerging environmental MBL, the L1 from Stenotrophomonas maltophilia K279a. We determined several crystal structures of L1 complexes with three different classes of β‐lactam antibiotics (penicillin G, moxalactam, meropenem, and imipenem), with the inhibitor captopril and different metal ions (Zn+2, Cd+2, and Cu+2). All hydrolyzed antibiotics and the inhibitor were found binding to two Zn+2 ions mainly through the opened lactam ring and some hydrophobic interactions with the binding pocket atoms. Without a metal ion, the active site is very similarly maintained as that of the native form with two Zn+2 ions, however, the protein does not bind the substrate moxalactam. When two Zn+2 ions were replaced with other metal ions, the same di‐metal scaffold was maintained and the added moxalactam was found hydrolyzed in the active site. Differential scanning fluorimetry and isothermal titration calorimetry were used to study thermodynamic properties of L1 MBL compared with New Deli Metallo‐β‐lactamase‐1 (NDM‐1). Both enzymes are significantly stabilized by Zn+2 and other divalent metals but showed different dependency. These studies also suggest that moxalactam and its hydrolyzed form may bind and dissociate with different kinetic modes with or without Zn+2 for each of L1 and NDM‐1. Our analysis implicates metal ions, in forming a distinct di‐metal scaffold, which is central to the enzyme stability, promiscuous substrate binding and versatile catalytic activity. Statement The L1 metallo‐β‐lactamase from an environmental multidrug‐resistant opportunistic pathogen Stenotrophomonas maltophilia K279a has been studied by determining 3D structures of L1 enzyme in the complexes with several β‐lactam antibiotics and different divalent metals and characterizing its biochemical and ligand binding properties. We found that the two‐metal center in the active site is critical in the enzymatic process including antibiotics recognition and binding, which explains the enzyme's activity toward diverse antibiotic substrates. This study provides the critical information for understanding the ligand recognition and for advanced drug development.
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Affiliation(s)
- Youngchang Kim
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, the University of Chicago, Chicago, Illinois.,Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois
| | - Natalia Maltseva
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, the University of Chicago, Chicago, Illinois
| | - Mateusz Wilamowski
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, the University of Chicago, Chicago, Illinois
| | - Christine Tesar
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois
| | - Michael Endres
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, the University of Chicago, Chicago, Illinois.,Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois
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20
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Influence of the α-Methoxy Group on the Reaction of Temocillin with Pseudomonas aeruginosa PBP3 and CTX-M-14 β-Lactamase. Antimicrob Agents Chemother 2019; 64:AAC.01473-19. [PMID: 31685462 DOI: 10.1128/aac.01473-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 10/14/2019] [Indexed: 12/26/2022] Open
Abstract
The prevalence of multidrug-resistant Pseudomonas aeruginosa has led to the reexamination of older "forgotten" drugs, such as temocillin, for their ability to combat resistant microbes. Temocillin is the 6-α-methoxy analogue of ticarcillin, a carboxypenicillin with well-characterized antipseudomonal properties. The α-methoxy modification confers resistance to serine β-lactamases, yet temocillin is ineffective against P. aeruginosa growth. The origins of temocillin's inferior antibacterial properties against P. aeruginosa have remained relatively unexplored. Here, we analyze the reaction kinetics, protein stability, and binding conformations of temocillin and ticarcillin with penicillin-binding protein 3 (PBP3), an essential PBP in P. aeruginosa We show that the 6-α-methoxy group perturbs the stability of the PBP3 acyl-enzyme, which manifests in an elevated off-rate constant (k off) in biochemical assays comparing temocillin with ticarcillin. Complex crystal structures with PBP3 reveal similar binding modes of the two drugs but with important differences. Most notably, the 6-α-methoxy group disrupts a high-quality hydrogen bond with a conserved residue important for ligand binding while also being inserted into a crowded active site, possibly destabilizing the active site and enabling water molecule from bulk solvent to access and cleave the acyl-enzyme bond. This hypothesis is supported by the observation that the acyl-enzyme complex of temocillin has reduced thermal stability compared with ticarcillin. Furthermore, we explore temocillin's mechanism of β-lactamase inhibition with a high-resolution complex structure of CTX-M-14 class A serine β-lactamase. The results suggest that the α-methoxy group prevents hydrolysis by locking the compound into an unexpected conformation that impedes access of the catalytic water to the acyl-enzyme adduct.
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21
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Singh A, Tomberg J, Nicholas RA, Davies C. Recognition of the β-lactam carboxylate triggers acylation of Neisseria gonorrhoeae penicillin-binding protein 2. J Biol Chem 2019; 294:14020-14032. [PMID: 31362987 PMCID: PMC6755799 DOI: 10.1074/jbc.ra119.009942] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 07/25/2019] [Indexed: 01/07/2023] Open
Abstract
Resistance of Neisseria gonorrhoeae to extended-spectrum cephalosporins (ESCs) has become a major threat to human health. The primary mechanism by which N. gonorrhoeae becomes resistant to ESCs is by acquiring a mosaic penA allele, encoding penicillin-binding protein 2 (PBP2) variants containing up to 62 mutations compared with WT, of which a subset contribute to resistance. To interpret molecular mechanisms underpinning cephalosporin resistance, it is necessary to know how PBP2 is acylated by ESCs. Here, we report the crystal structures of the transpeptidase domain of WT PBP2 in complex with cefixime and ceftriaxone, along with structures of PBP2 in the apo form and with a phosphate ion bound in the active site at resolutions of 1-7-1.9 Å. These structures reveal that acylation of PBP2 by ESCs is accompanied by rotation of the Thr-498 side chain in the KTG motif to contact the cephalosporin carboxylate, twisting of the β3 strand to form the oxyanion hole, and rolling of the β3-β4 loop toward the active site. Recognition of the cephalosporin carboxylate appears to be the key trigger for formation of an acylation-competent state of PBP2. The structures also begin to explain the impact of mutations implicated in ESC resistance. In particular, a G545S mutation may hinder twisting of β3 because its side chain hydroxyl forms a hydrogen bond with Thr-498. Overall, our data suggest that acylation is initiated by conformational changes elicited or trapped by binding of ESCs and that these movements are restricted by mutations associated with resistance against ESCs.
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Affiliation(s)
- Avinash Singh
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425
| | - Joshua Tomberg
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Robert A. Nicholas
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Christopher Davies
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425, To whom correspondence should be addressed:
Dept. of Biochemistry and Molecular Biology, Medical University of South Carolina, 173 Ashley Ave., Charleston, SC 29425. Tel.:
843-876-2302; Fax:
843-792-8568; E-mail:
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22
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McLean K, Lee D, Holmes EA, Penewit K, Waalkes A, Ren M, Lee SA, Gasper J, Manoil C, Salipante SJ. Genomic Analysis Identifies Novel Pseudomonas aeruginosa Resistance Genes under Selection during Inhaled Aztreonam Therapy In Vivo. Antimicrob Agents Chemother 2019; 63:e00866-19. [PMID: 31285231 PMCID: PMC6709462 DOI: 10.1128/aac.00866-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 06/28/2019] [Indexed: 12/13/2022] Open
Abstract
Inhaled aztreonam is increasingly used for chronic Pseudomonas aeruginosa suppression in patients with cystic fibrosis (CF), but the potential for that organism to evolve aztreonam resistance remains incompletely explored. Here, we performed genomic analysis of clonally related pre- and posttreatment CF clinical isolate pairs to identify genes that are under positive selection during aztreonam therapy in vivo We identified 16 frequently mutated genes associated with aztreonam resistance, the most prevalent being ftsI and ampC, and 13 of which increased aztreonam resistance when introduced as single gene transposon mutants. Several previously implicated aztreonam resistance genes were found to be under positive selection in clinical isolates even in the absence of inhaled aztreonam exposure, indicating that other selective pressures in the cystic fibrosis airway can promote aztreonam resistance. Given its potential to confer plasmid-mediated resistance, we further characterized mutant ampC alleles and performed artificial evolution of ampC for maximal activity against aztreonam. We found that naturally occurring ampC mutants conferred variably increased resistance to aztreonam (2- to 64-fold) and other β-lactam agents but that its maximal evolutionary capacity for hydrolyzing aztreonam was considerably higher (512- to 1,024-fold increases) and was achieved while maintaining or increasing resistance to other drugs. These studies implicate novel chromosomal aztreonam resistance determinants while highlighting that different mutations are favored during selection in vivo and in vitro, show that ampC has a high maximal potential to hydrolyze aztreonam, and provide an approach to disambiguate mutations promoting specific resistance phenotypes from those more generally increasing bacterial fitness in vivo.
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Affiliation(s)
- Kathryn McLean
- Department of Laboratory Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Duankun Lee
- Department of Laboratory Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Elizabeth A Holmes
- Department of Laboratory Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Kelsi Penewit
- Department of Laboratory Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Adam Waalkes
- Department of Laboratory Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Mingxin Ren
- Department of Laboratory Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Samuel A Lee
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Joseph Gasper
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Colin Manoil
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Stephen J Salipante
- Department of Laboratory Medicine, University of Washington School of Medicine, Seattle, Washington, USA
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23
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Novel and Improved Crystal Structures of H. influenzae, E. coli and P. aeruginosa Penicillin-Binding Protein 3 (PBP3) and N. gonorrhoeae PBP2: Toward a Better Understanding of β-Lactam Target-Mediated Resistance. J Mol Biol 2019; 431:3501-3519. [PMID: 31301409 DOI: 10.1016/j.jmb.2019.07.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 07/02/2019] [Accepted: 07/02/2019] [Indexed: 01/26/2023]
Abstract
Even with the emergence of antibiotic resistance, penicillin and the wider family of β-lactams have remained the single most important family of antibiotics. The periplasmic/extra-cytoplasmic targets of penicillin are a family of enzymes with a highly conserved catalytic activity involved in the final stage of bacterial cell wall (peptidoglycan) biosynthesis. Named after their ability to bind penicillin, rather than their catalytic activity, these key targets are called penicillin-binding proteins (PBPs). Resistance is predominantly mediated by reducing the target drug concentration via β-lactamases; however, naturally transformable bacteria have also acquired target-mediated resistance by inter-species recombination. Here we focus on structural based interpretations of amino acid alterations associated with the emergence of resistance within clinical isolates and include new PBP3 structures along with new, and improved, PBP-β-lactam co-structures.
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24
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Schmidt M. Time-Resolved Macromolecular Crystallography at Pulsed X-ray Sources. Int J Mol Sci 2019; 20:ijms20061401. [PMID: 30897736 PMCID: PMC6470897 DOI: 10.3390/ijms20061401] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 03/14/2019] [Accepted: 03/18/2019] [Indexed: 11/30/2022] Open
Abstract
The focus of structural biology is shifting from the determination of static structures to the investigation of dynamical aspects of macromolecular function. With time-resolved macromolecular crystallography (TRX), intermediates that form and decay during the macromolecular reaction can be investigated, as well as their reaction dynamics. Time-resolved crystallographic methods were initially developed at synchrotrons. However, about a decade ago, extremely brilliant, femtosecond-pulsed X-ray sources, the free electron lasers for hard X-rays, became available to a wider community. TRX is now possible with femtosecond temporal resolution. This review provides an overview of methodological aspects of TRX, and at the same time, aims to outline the frontiers of this method at modern pulsed X-ray sources.
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Affiliation(s)
- Marius Schmidt
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA.
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25
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Clark ST, Sinha U, Zhang Y, Wang PW, Donaldson SL, Coburn B, Waters VJ, Yau YCW, Tullis DE, Guttman DS, Hwang DM. Penicillin-binding protein 3 is a common adaptive target among Pseudomonas aeruginosa isolates from adult cystic fibrosis patients treated with β-lactams. Int J Antimicrob Agents 2019; 53:620-628. [PMID: 30664925 DOI: 10.1016/j.ijantimicag.2019.01.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 12/03/2018] [Accepted: 01/16/2019] [Indexed: 11/28/2022]
Abstract
OBJECTIVE Determining the mechanisms that modulate β-lactam resistance in clinical Pseudomonas aeruginosa (P. aeruginosa) isolates can be challenging, as the molecular profiles identified in mutation-based or expression-based resistance determinant screens may not correlate with in vitro phenotypes. One of the lesser studied resistance mechanisms in P. aeruginosa is the modification of penicillin-binding protein 3 (pbpB/ftsI). This study reported that nonsynonymous polymorphisms within pbpB frequently occur among β-lactam resistant sputum isolates, and are associated with unique antibiotic susceptibility patterns. METHODS Longitudinally collected isolates (n = 126) from cystic fibrosis (CF) patients with or without recent β-lactam therapy or of non-clinical origin were tested for susceptibility to six β-lactams (aztreonam, ceftazidime, cefsulodin, cefepime, meropenem, and piperacillin). Known β-lactam resistance mechanisms were characterised by polymerase chain reaction (PCR)-based methods, and polymorphisms in the transpeptidase-encoding domain of pbpB identified by sequencing. RESULTS Twelve nonsynonymous polymorphisms were detected among 86 isolates (67%) from five CF patients with a history of β-lactam therapy, compared with one polymorphism in 30 (3.3%) from three patients who had not received β-lactam treatments. No nonsynonymous polymorphisms were found in ten environmental isolates. Multiple pbpB alleles, often with different combinations of polymorphisms, were detected within the population of strains from each CF patient for up to 2.6 years. Traditional patterns of ampC or mexA de-repression reduced expression of oprD or the presence of extended-spectrum β-lactamases were not observed in resistant isolates with nonsynonymous polymorphisms in pbpB. CONCLUSION This study's findings suggest that pbpB is a common adaptive target, and may contribute to the development of β-lactam resistance in P. aeruginosa.
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Affiliation(s)
- Shawn T Clark
- Toronto General Hospital Research Institute, University Health Network, Toronto, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Utkarshna Sinha
- Toronto General Hospital Research Institute, University Health Network, Toronto, Canada
| | - Yu Zhang
- Toronto General Hospital Research Institute, University Health Network, Toronto, Canada
| | - Pauline W Wang
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada
| | - Sylva L Donaldson
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada
| | - Bryan Coburn
- Toronto General Hospital Research Institute, University Health Network, Toronto, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Valerie J Waters
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada; Department of Pediatrics, Division of Infectious Diseases, The Hospital for Sick Children, Toronto, Canada
| | - Yvonne C W Yau
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada; Department of Pediatric Laboratory Medicine, Division of Microbiology, The Hospital for Sick Children, Toronto, Canada
| | - D Elizabeth Tullis
- Toronto Adult Cystic Fibrosis Centre, St Michael's Hospital, Toronto, Canada
| | - David S Guttman
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada; Department of Cell & Systems Biology, University of Toronto, Toronto, Canada
| | - David M Hwang
- Toronto General Hospital Research Institute, University Health Network, Toronto, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada; Department of Laboratory Medicine & Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, Canada.
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Anti-pathogens constituents and novel ergosterol derivatives with the broad-spectrum germicidal substances from earthworm, Pheretima aspergillum. Tetrahedron 2018. [DOI: 10.1016/j.tet.2018.07.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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27
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Dean CR, Barkan DT, Bermingham A, Blais J, Casey F, Casarez A, Colvin R, Fuller J, Jones AK, Li C, Lopez S, Metzger LE, Mostafavi M, Prathapam R, Rasper D, Reck F, Ruzin A, Shaul J, Shen X, Simmons RL, Skewes-Cox P, Takeoka KT, Tamrakar P, Uehara T, Wei JR. Mode of Action of the Monobactam LYS228 and Mechanisms Decreasing In Vitro Susceptibility in Escherichia coli and Klebsiella pneumoniae. Antimicrob Agents Chemother 2018; 62:e01200-18. [PMID: 30061293 PMCID: PMC6153799 DOI: 10.1128/aac.01200-18] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 07/25/2018] [Indexed: 12/14/2022] Open
Abstract
The monobactam scaffold is attractive for the development of new agents to treat infections caused by drug-resistant Gram-negative bacteria because it is stable to metallo-β-lactamases (MBLs). However, the clinically used monobactam aztreonam lacks stability to serine β-lactamases (SBLs) that are often coexpressed with MBLs. LYS228 is stable to MBLs and most SBLs. LYS228 bound purified Escherichia coli penicillin binding protein 3 (PBP3) similarly to aztreonam (derived acylation rate/equilibrium dissociation constant [k2/Kd ] of 367,504 s-1 M-1 and 409,229 s-1 M-1, respectively) according to stopped-flow fluorimetry. A gel-based assay showed that LYS228 bound mainly to E. coli PBP3, with weaker binding to PBP1a and PBP1b. Exposing E. coli cells to LYS228 caused filamentation consistent with impaired cell division. No single-step mutants were selected from 12 Enterobacteriaceae strains expressing different classes of β-lactamases at 8× the MIC of LYS228 (frequency, <2.5 × 10-9). At 4× the MIC, mutants were selected from 2 of 12 strains at frequencies of 1.8 × 10-7 and 4.2 × 10-9 LYS228 MICs were ≤2 μg/ml against all mutants. These frequencies compared favorably to those for meropenem and tigecycline. Mutations decreasing LYS228 susceptibility occurred in ramR and cpxA (Klebsiella pneumoniae) and baeS (E. coli and K. pneumoniae). Susceptibility of E. coli ATCC 25922 to LYS228 decreased 256-fold (MIC, 0.125 to 32 μg/ml) after 20 serial passages. Mutants accumulated mutations in ftsI (encoding the target, PBP3), baeR, acrD, envZ, sucB, and rfaI These results support the continued development of LYS228, which is currently undergoing phase II clinical trials for complicated intraabdominal infection and complicated urinary tract infection (registered at ClinicalTrials.gov under identifiers NCT03377426 and NCT03354754).
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Affiliation(s)
- Charles R Dean
- Novartis Institutes for BioMedical Research, Emeryville, California, USA
| | - David T Barkan
- Novartis Institutes for BioMedical Research, Emeryville, California, USA
| | - Alun Bermingham
- Novartis Institutes for BioMedical Research, Emeryville, California, USA
| | - Johanne Blais
- Novartis Institutes for BioMedical Research, Emeryville, California, USA
| | - Fergal Casey
- Novartis Institutes for BioMedical Research, Emeryville, California, USA
| | - Anthony Casarez
- Novartis Institutes for BioMedical Research, Emeryville, California, USA
| | - Richard Colvin
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, USA
| | - John Fuller
- Novartis Institutes for BioMedical Research, Emeryville, California, USA
| | - Adriana K Jones
- Novartis Institutes for BioMedical Research, Emeryville, California, USA
| | - Cindy Li
- Novartis Institutes for BioMedical Research, Emeryville, California, USA
| | - Sara Lopez
- Novartis Institutes for BioMedical Research, Emeryville, California, USA
| | - Louis E Metzger
- Novartis Institutes for BioMedical Research, Emeryville, California, USA
| | - Mina Mostafavi
- Novartis Institutes for BioMedical Research, Emeryville, California, USA
| | - Ramadevi Prathapam
- Novartis Institutes for BioMedical Research, Emeryville, California, USA
| | - Dita Rasper
- Novartis Institutes for BioMedical Research, Emeryville, California, USA
| | - Folkert Reck
- Novartis Institutes for BioMedical Research, Emeryville, California, USA
| | - Alexey Ruzin
- Novartis Institutes for BioMedical Research, Emeryville, California, USA
| | - Jacob Shaul
- Novartis Institutes for BioMedical Research, Emeryville, California, USA
| | - Xiaoyu Shen
- Novartis Institutes for BioMedical Research, Emeryville, California, USA
| | - Robert L Simmons
- Novartis Institutes for BioMedical Research, Emeryville, California, USA
| | - Peter Skewes-Cox
- Novartis Institutes for BioMedical Research, Emeryville, California, USA
| | - Kenneth T Takeoka
- Novartis Institutes for BioMedical Research, Emeryville, California, USA
| | - Pramila Tamrakar
- Novartis Institutes for BioMedical Research, Emeryville, California, USA
| | - Tsuyoshi Uehara
- Novartis Institutes for BioMedical Research, Emeryville, California, USA
| | - Jun-Rong Wei
- Novartis Institutes for BioMedical Research, Emeryville, California, USA
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Wee BA, Tai AS, Sherrard LJ, Ben Zakour NL, Hanks KR, Kidd TJ, Ramsay KA, Lamont I, Whiley DM, Bell SC, Beatson SA. Whole genome sequencing reveals the emergence of a Pseudomonas aeruginosa shared strain sub-lineage among patients treated within a single cystic fibrosis centre. BMC Genomics 2018; 19:644. [PMID: 30165811 PMCID: PMC6117919 DOI: 10.1186/s12864-018-5018-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 08/14/2018] [Indexed: 11/18/2022] Open
Abstract
Background Chronic lung infections caused by Pseudomonas aeruginosa are a significant cause of morbidity and mortality in people with cystic fibrosis (CF). Shared P. aeruginosa strains, that can be transmitted between patients, are of concern and in Australia the AUST-02 shared strain is predominant in individuals attending CF centres in Queensland and Western Australia. M3L7 is a multidrug resistant sub-type of AUST-02 that was recently identified in a Queensland CF centre and was shown to be associated with poorer clinical outcomes. The main aim of this study was to resolve the relationship of the emergent M3L7 sub-type within the AUST-02 group of strains using whole genome sequencing. Results A whole genome core phylogeny of 63 isolates indicated that M3L7 is a monophyletic sub-lineage within the context of the broader AUST-02 group. Relatively short branch lengths connected all of the M3L7 isolates. A phylogeny based on nucleotide polymorphisms present across the genome showed that the chronological estimation of the most recent common ancestor was around 2001 (± 3 years). SNP differences between sequential non-hypermutator M3L7 isolates collected 3–4 years apart from five patients suggested both continuous infection of the same strain and cross-infection of some M3L7 variants between patients. The majority of polymorphisms that were characteristic of M3L7 (i.e. acquired after divergence from all other AUST-02 isolates sequenced) were found to produce non-synonymous mutations in virulence and antibiotic resistance genes. Conclusions M3L7 has recently diverged from a common ancestor, indicating descent from a single carrier at a CF treatment centre in Australia. Both adaptation to the lung and transmission of M3L7 between adults attending this centre may have contributed to its rapid dissemination. Further genomic investigations are required on multiple intra-sample isolates of this sub-type to decipher potential mechanisms which facilitates its epidemiological success. Electronic supplementary material The online version of this article (10.1186/s12864-018-5018-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bryan A Wee
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.,Present Address: Usher Institute of Population Health Sciences & Informatics, University of Edinburgh, Edinburgh, United Kingdom
| | - Anna S Tai
- Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia.,Adult Cystic Fibrosis Centre, Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, QLD, Australia.,Department of Respiratory Medicine, Western Australia Adult Cystic Fibrosis Centre, Sir Charles Gairdner Hospital, Nedlands, WA, Australia
| | - Laura J Sherrard
- Lung Bacteria Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,Present Address: School of Pharmacy, Queen's University Belfast, Belfast, United Kingdom
| | - Nouri L Ben Zakour
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Kirt R Hanks
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Timothy J Kidd
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.,Centre for Experimental Medicine, Queen's University Belfast, Belfast, UK.,Child Health Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Kay A Ramsay
- Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia.,Lung Bacteria Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,Present Address: Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Iain Lamont
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - David M Whiley
- Faculty of Medicine, UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia.,Microbiology Department, Pathology Queensland Central Laboratory, Brisbane, QLD, Australia
| | - Scott C Bell
- Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia.,Adult Cystic Fibrosis Centre, Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, QLD, Australia.,Lung Bacteria Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Scott A Beatson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia. .,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia. .,Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia.
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Nguyen L, Garcia J, Gruenberg K, MacDougall C. Multidrug-Resistant Pseudomonas Infections: Hard to Treat, But Hope on the Horizon? Curr Infect Dis Rep 2018; 20:23. [PMID: 29876674 DOI: 10.1007/s11908-018-0629-6] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
PURPOSE OF REVIEW As the sixth most common nosocomial pathogen in the USA, Pseudomonas aeruginosa poses a significant threat to patients within the healthcare system. Its intrinsic and acquired resistance mechanisms also significantly limit the choices for antimicrobial therapy, prompting an increase in the research and development of antibacterial agents with enhanced activity against multidrug-resistant (MDR) P. aeruginosa. While many approved and pipeline antibiotics have activity against wild-type P. aeruginosa, only four new antibiotics have promising activity against MDR P. aeruginosa: ceftazidime-avibactam (Avycaz®), ceftolozane-tazobactam (Zerbaxa®), cefiderocol, and imipenem-cilastatin/relebactam. The goal of this paper is to review the epidemiology and mechanisms of resistance in P. aeruginosa as well as explore the newly approved and pipeline agents that overcome these mechanisms of resistance. RECENT FINDINGS Ceftazidime-avibactam and ceftolozane-tazobactam are currently FDA-approved and available for use, while cefiderocol and imipenem-cilastatin/relebactam are in development. Current evidence suggests ceftazidime-avibactam and ceftolozane-tazobactam both may have a role in treatment of MDR P. aeruginosa infections. Ceftolozane-tazobactam appears to be modestly more potent against P. aeruginosa, but emergence of resistance has been noted in various reported cases. Trials are ongoing for cefiderocol and imipenem-cilastatin/relebactam and early results appear promising. The aforementioned agents fill important gaps in the antibiotic armamentarium, particularly for patients with MDR P. aeruginosa infections who otherwise have extremely limited and often toxic antibiotic options. However, resistance to all of these agents will likely emerge, and additional antibiotic development is warranted to provide sufficient options to successfully manage MDR P. aeruginosa infections.
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Affiliation(s)
- Lynn Nguyen
- Department of Clinical Pharmacy, University of California San Francisco School of Pharmacy, 533 Parnassus Ave, U-585, Box 0622, San Francisco, CA, 94143-0622, USA
| | - Joshua Garcia
- Department of Pharmacy Practice, Marshall B. Ketchum University College of Pharmacy, Fullerton, CA, USA
| | - Katherine Gruenberg
- Department of Clinical Pharmacy, University of California San Francisco School of Pharmacy, 533 Parnassus Ave, U-585, Box 0622, San Francisco, CA, 94143-0622, USA
| | - Conan MacDougall
- Department of Clinical Pharmacy, University of California San Francisco School of Pharmacy, 533 Parnassus Ave, U-585, Box 0622, San Francisco, CA, 94143-0622, USA.
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Yeh CH, Walsh SI, Craney A, Tabor MG, Voica AF, Adhikary R, Morris SE, Romesberg FE. Optimization of a β-Lactam Scaffold for Antibacterial Activity via the Inhibition of Bacterial Type I Signal Peptidase. ACS Med Chem Lett 2018; 9:376-380. [PMID: 29670704 DOI: 10.1021/acsmedchemlett.8b00064] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 03/07/2018] [Indexed: 11/30/2022] Open
Abstract
β-Lactam antibiotics, one of the most important class of human therapeutics, act via the inhibition of penicillin-binding proteins (PBPs). The unparalleled success in their development has inspired efforts to develop them as inhibitors of other targets. Bacterial type I signal peptidase is evolutionarily related to the PBPs, but the stereochemistry of its substrates and its catalytic mechanism suggest that β-lactams with the 5S stereochemistry, as opposed to the 5R stereochemistry of the traditional β-lactams, would be required for inhibition. We report the synthesis and evaluation of a variety of 5S penem derivatives and identify several with promising activity against both a Gram-positive and a Gram-negative bacterial pathogen. To our knowledge these are the first 5S β-lactams to possess significant antibacterial activity and the first β-lactams imparted with antibacterial activity via optimization of the inhibition of a target other than a PBP. Along with the privileged status of their scaffold and the promise of bacterial signal peptidase I (SPase) as a target, this activity makes these compounds promising leads for development as novel therapeutics.
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Affiliation(s)
- Chien-Hung Yeh
- Department of Chemistry, The Scripps Research Institute, La Jolla California 92037 United States
| | - Shawn I. Walsh
- Department of Chemistry, The Scripps Research Institute, La Jolla California 92037 United States
| | - Arryn Craney
- Department of Chemistry, The Scripps Research Institute, La Jolla California 92037 United States
| | - M. Greg Tabor
- Department of Chemistry, The Scripps Research Institute, La Jolla California 92037 United States
| | - Ana-Florina Voica
- Department of Chemistry, The Scripps Research Institute, La Jolla California 92037 United States
| | - Ramkrishna Adhikary
- Department of Chemistry, The Scripps Research Institute, La Jolla California 92037 United States
| | - Sydney E. Morris
- Department of Chemistry, The Scripps Research Institute, La Jolla California 92037 United States
| | - Floyd E. Romesberg
- Department of Chemistry, The Scripps Research Institute, La Jolla California 92037 United States
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Wagh MA, Baravkar SB, Jedhe GS, Borkute R, Choudhari AS, Sarkar D, Sanjayan GJ. Design and Synthesis of 2-Amino-thiophene-Tethered Ureidopenicillin Analogs with Potent Antibacterial and Antitubercular activity. ChemistrySelect 2018. [DOI: 10.1002/slct.201800027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Mahendra A. Wagh
- Division of Organic Chemistry; CSIR-National Chemical Laboratory; Dr. HomiBhabha Road, Pune 411 008 Maharashtra India
| | - Sachin B. Baravkar
- Division of Organic Chemistry; CSIR-National Chemical Laboratory; Dr. HomiBhabha Road, Pune 411 008 Maharashtra India
| | - Ganesh S. Jedhe
- Division of Organic Chemistry; CSIR-National Chemical Laboratory; Dr. HomiBhabha Road, Pune 411 008 Maharashtra India
| | - Rachna Borkute
- Combi-Chem Resource Centre; CSIR-National Chemical Laboratory; Dr. HomiBhabha Road Pune 411 008 Maharashtra India
| | - Amit S. Choudhari
- Combi-Chem Resource Centre; CSIR-National Chemical Laboratory; Dr. HomiBhabha Road Pune 411 008 Maharashtra India
| | - Dhiman Sarkar
- Combi-Chem Resource Centre; CSIR-National Chemical Laboratory; Dr. HomiBhabha Road Pune 411 008 Maharashtra India
| | - Gangadhar J. Sanjayan
- Division of Organic Chemistry; CSIR-National Chemical Laboratory; Dr. HomiBhabha Road, Pune 411 008 Maharashtra India
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Verdino A, Vigliotta G, Giordano D, Caputo I, Soriente A, De Rosa M, Marabotti A. Synthesis and biological evaluation of the progenitor of a new class of cephalosporin analogues, with a particular focus on structure-based computational analysis. PLoS One 2017; 12:e0181563. [PMID: 28749999 PMCID: PMC5531512 DOI: 10.1371/journal.pone.0181563] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Accepted: 07/03/2017] [Indexed: 02/04/2023] Open
Abstract
We present the synthesis and biological evaluation of the prototype of a new class of cephalosporins, containing an additional isolated beta lactam ring with two phenyl substituents. This new compound is effective against Gram positive microorganisms, with a potency similar to that of ceftriaxone, a cephalosporin widely used in clinics and taken as a reference, and with no cytotoxicity against two different human cell lines, even at a concentration much higher than the minimal inhibitory concentration tested. Additionally, a deep computational analysis has been conducted with the aim of understanding the contribution of its moieties to the binding energy towards several penicillin-binding proteins from both Gram positive and Gram negative bacteria. All these results will help us developing derivatives of this compound with improved chemical and biological properties, such as a broader spectrum of action and/or an increased affinity towards their molecular targets.
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Affiliation(s)
- Anna Verdino
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, Fisciano (SA), Italy
| | - Giovanni Vigliotta
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, Fisciano (SA), Italy
| | - Deborah Giordano
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, Fisciano (SA), Italy
| | - Ivana Caputo
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, Fisciano (SA), Italy
| | - Annunziata Soriente
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, Fisciano (SA), Italy
| | - Margherita De Rosa
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, Fisciano (SA), Italy
- * E-mail: (MDR); (AM)
| | - Anna Marabotti
- Department of Chemistry and Biology "A. Zambelli", University of Salerno, Fisciano (SA), Italy
- * E-mail: (MDR); (AM)
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Okumu A, McCarthy K, Orwa J, Williamson J, Musau S, Alexander H, Cavanaugh S, Modi S, Cain K. Comparison of Mycobacterium tuberculosis complex Yield and Contamination Rates using Lowenstein-Jensen with and without Antibiotics in Western Kenya. JOURNAL OF MEDICAL SCIENCE AND CLINICAL RESEARCH 2017; 5:10.18535/jmscr/v5i8.86. [PMID: 35979512 PMCID: PMC9380436 DOI: 10.18535/jmscr/v5i8.86] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
BACKGROUND While molecular methods have been recently endorsed for diagnosis of tuberculosis (TB), mycobacterial culture remains the gold standard. Lowenstein-Jensen (LJ) is often used for the cultivation of Mycobacterium tuberculosis complex (MTBC); however contamination often renders a subset of cultures useless. We compared the MTBC yield and contamination rate of processed sputum inoculated on LJ with antibiotics (LJ PACT) to LJ without antibiotics (LJ). METHODOLOGY Sputum samples were obtained from people living with HIV enrolled in a TB screening study in western Kenya, processed using NALC/NaOH-Na citrate, then inoculated on LJ PACT and LJ media. Cultures were evaluated weekly with growth identified as acid-fast bacilli by Ziehl-Neelsen bright-field microscopy. MTBC and nontuberculous mycobacteria (NTM) were identified by immunochromatographic and line probe assays. RESULTS A total of 700 sputum samples were cultured on both LJ PACT and LJ between March and June 2012. Of those cultured on LJ PACT, 29 (4.1%) grew MTBC, 613 (87.6%) were negative, 12 (1.7%) grew NTM, and 46 (6.6%) were contaminated; on LJ, 28 (4%) grew MTBC, 553 (79%) were negative, 9 (1.3%) grew NTM, and 110 (15.7%) were contaminated. The difference in contamination on LJ PACT and LJ was statistically significant (p<0.0001), while the difference in MTBC growth was not (p=0.566).
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Affiliation(s)
- A Okumu
- Kenya Medical Research Institute (KEMRI) Center for Global Health Research, Kisumu, Kenya
| | - K McCarthy
- Division of Tuberculosis Elimination (DTBE), CDC, Atlanta, GA
| | - J Orwa
- Kenya Medical Research Institute (KEMRI) Center for Global Health Research, Kisumu, Kenya
| | - J Williamson
- Division of Parasitic Diseases and Malaria (DPDM), CDC, Atlanta, GA
| | - S Musau
- Kenya Medical Research Institute (KEMRI) Center for Global Health Research, Kisumu, Kenya
| | - H Alexander
- Division of Tuberculosis Elimination (DTBE), CDC, Atlanta, GA
| | - S Cavanaugh
- Division of Tuberculosis Elimination (DTBE), CDC, Atlanta, GA
| | - S Modi
- Division of Global HIV/AIDS (DGHA), Centers for Disease Control and Prevention (CDC), Atlanta, GA
| | - K Cain
- Kenya Medical Research Institute (KEMRI) Center for Global Health Research, Kisumu, Kenya
- Division of Tuberculosis Elimination (DTBE), CDC, Atlanta, GA
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Biochemical and Structural Analysis of a Novel Esterase from Caulobacter crescentus related to Penicillin-Binding Protein (PBP). Sci Rep 2016; 6:37978. [PMID: 27905486 PMCID: PMC5131357 DOI: 10.1038/srep37978] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 11/03/2016] [Indexed: 01/16/2023] Open
Abstract
Considering that the prevalence of antibiotic-resistant pathogenic bacteria is largely increasing, a thorough understanding of penicillin-binding proteins (PBPs) is of great importance and crucial significance because this enzyme family is a main target of β-lactam-based antibiotics. In this work, combining biochemical and structural analysis, we present new findings that provide novel insights into PBPs. Here, a novel PBP homologue (CcEstA) from Caulobacter crescentus CB15 was characterized using native-PAGE, mass spectrometry, gel filtration, CD spectroscopy, fluorescence, reaction kinetics, and enzyme assays toward various substrates including nitrocefin. Furthermore, the crystal structure of CcEstA was determined at a 1.9 Å resolution. Structural analyses showed that CcEstA has two domains: a large α/β domain and a small α-helix domain. A nucleophilic serine (Ser68) residue is located in a hydrophobic groove between the two domains along with other catalytic residues (Lys71 and Try157). Two large flexible loops (UL and LL) of CcEstA are proposed to be involved in the binding of incoming substrates. In conclusion, CcEstA could be described as a paralog of the group that contains PBPs and β-lactamases. Therefore, this study could provide new structural and functional insights into the understanding this protein family.
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Genome scale identification, structural analysis, and classification of periplasmic binding proteins from Mycobacterium tuberculosis. Curr Genet 2016; 63:553-576. [DOI: 10.1007/s00294-016-0664-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 11/04/2016] [Accepted: 11/05/2016] [Indexed: 01/26/2023]
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Aguilera Rossi CG, Gómez-Puertas P, Ayala Serrano JA. In vivo functional and molecular characterization of the Penicillin-Binding Protein 4 (DacB) of Pseudomonas aeruginosa. BMC Microbiol 2016; 16:234. [PMID: 27716106 PMCID: PMC5054556 DOI: 10.1186/s12866-016-0853-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 09/27/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Community and nosocomial infections by Pseudomonas aeruginosa still create a major therapeutic challenge. The resistance of this opportunist pathogen to β-lactam antibiotics is determined mainly by production of the inactivating enzyme AmpC, a class C cephalosporinase with a regulation system more complex than those found in members of the Enterobacteriaceae family. This regulatory system also participates directly in peptidoglycan turnover and recycling. One of the regulatory mechanisms for AmpC expression, recently identified in clinical isolates, is the inactivation of LMM-PBP4 (Low-Molecular-Mass Penicillin-Binding Protein 4), a protein whose catalytic activity on natural substrates has remained uncharacterized until now. RESULTS We carried out in vivo activity trials for LMM-PBP4 of Pseudomonas aeruginosa on macromolecular peptidoglycan of Escherichia coli and Pseudomonas aeruginosa. The results showed a decrease in the relative quantity of dimeric, trimeric and anhydrous units, and a smaller reduction in monomer disaccharide pentapeptide (M5) levels, validating the occurrence of D,D-carboxypeptidase and D,D-endopeptidase activities. Under conditions of induction for this protein and cefoxitin treatment, the reduction in M5 is not fully efficient, implying that LMM-PBP4 of Pseudomonas aeruginosa presents better behaviour as a D,D-endopeptidase. Kinetic evaluation of the direct D,D-peptidase activity of this protein on natural muropeptides M5 and D45 confirmed this bifunctionality and the greater affinity of LMM-PBP4 for its dimeric substrate. A three-dimensional model for the monomeric unit of LMM-PBP4 provided structural information which supports its catalytic performance. CONCLUSIONS LMM-PBP4 of Pseudomonas aeruginosa is a bifunctional enzyme presenting both D,D-carboxypeptidase and D,D-endopeptidase activities; the D,D-endopeptidase function is predominant. Our study provides unprecedented functional and structural information which supports the proposal of this protein as a potential hydrolase-autolysin associated with peptidoglycan maturation and recycling. The fact that mutant PBP4 induces AmpC, may indicate that a putative muropeptide-subunit product of the DD-EPase activity of PBP4 could be a negative regulator of the pathway. This data contributes to understanding of the regulatory aspects of resistance to β-lactam antibiotics in this bacterial model.
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Affiliation(s)
- Cristian Gustavo Aguilera Rossi
- Departamento de Ciencias Preclínicas, Facultad de Medicina, Universidad de La Frontera, Temuco, Chile.,Laboratorio de División Celular Bacteriana y Resistencia a Antibióticos, Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid-CSIC, Madrid, Spain
| | - Paulino Gómez-Puertas
- Grupo de Modelado Molecular, Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid-CSIC, Madrid, Spain
| | - Juan Alfonso Ayala Serrano
- Laboratorio de División Celular Bacteriana y Resistencia a Antibióticos, Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid-CSIC, Madrid, Spain.
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Docking optimization, variance and promiscuity for large-scale drug-like chemical space using high performance computing architectures. Drug Discov Today 2016; 21:1672-1680. [DOI: 10.1016/j.drudis.2016.06.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 05/12/2016] [Accepted: 06/21/2016] [Indexed: 12/27/2022]
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Wang X, Jiang F, Zheng J, Chen L, Dong J, Sun L, Zhu Y, Liu B, Yang J, Yang G, Jin Q. The outer membrane phospholipase A is essential for membrane integrity and type III secretion in Shigella flexneri. Open Biol 2016; 6:rsob.160073. [PMID: 27655730 PMCID: PMC5043575 DOI: 10.1098/rsob.160073] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Accepted: 08/31/2016] [Indexed: 12/11/2022] Open
Abstract
Outer membrane phospholipase A (OMPLA) is an enzyme located in the outer membrane of Gram-negative bacteria. OMPLA exhibits broad substrate specificity, and some of its substrates are located in the cellular envelope. Generally, the enzymatic activity can only be induced by perturbation of the cell envelope integrity through diverse methods. Although OMPLA has been thoroughly studied as a membrane protein in Escherichia coli and is constitutively expressed in many other bacterial pathogens, little is known regarding the functions of OMPLA during the process of bacterial infection. In this study, the proteomic and transcriptomic data indicated that OMPLA in Shigella flexneri, termed PldA, both stabilizes the bacterial membrane and is involved in bacterial infection under ordinary culture conditions. A series of physiological assays substantiated the disorganization of the bacterial outer membrane and the periplasmic space in the ΔpldA mutant strain. Furthermore, the ΔpldA mutant strain showed decreased levels of type III secretion system expression, contributing to the reduced internalization efficiency in host cells. The results of this study support that PldA, which is widespread across Gram-negative bacteria, is an important factor for the bacterial life cycle, particularly in human pathogens.
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Affiliation(s)
- Xia Wang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, People's Republic of China
| | - Feng Jiang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, People's Republic of China
| | - Jianhua Zheng
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, People's Republic of China
| | - Lihong Chen
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, People's Republic of China
| | - Jie Dong
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, People's Republic of China
| | - Lilian Sun
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, People's Republic of China
| | - Yafang Zhu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, People's Republic of China
| | - Bo Liu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, People's Republic of China
| | - Jian Yang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, People's Republic of China
| | - Guowei Yang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, People's Republic of China
| | - Qi Jin
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, People's Republic of China
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Filippova EV, Kieser KJ, Luan CH, Wawrzak Z, Kiryukhina O, Rubin EJ, Anderson WF. Crystal structures of the transpeptidase domain of the Mycobacterium tuberculosis penicillin-binding protein PonA1 reveal potential mechanisms of antibiotic resistance. FEBS J 2016; 283:2206-18. [PMID: 27101811 PMCID: PMC5245116 DOI: 10.1111/febs.13738] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 03/30/2016] [Accepted: 04/15/2016] [Indexed: 01/21/2023]
Abstract
UNLABELLED Mycobacterium tuberculosis is a human respiratory pathogen that causes the deadly disease tuberculosis. The rapid global spread of antibiotic-resistant M. tuberculosis makes tuberculosis infections difficult to treat. To overcome this problem new effective antimicrobial strategies are urgently needed. One promising target for new therapeutic approaches is PonA1, a class A penicillin-binding protein, which is required for maintaining physiological cell wall synthesis and cell shape during growth in mycobacteria. Here, crystal structures of the transpeptidase domain, the enzymatic domain responsible for penicillin binding, of PonA1 from M. tuberculosis in the inhibitor-free form and in complex with penicillin V are reported. We used site-directed mutagenesis, antibiotic profiling experiments, and fluorescence thermal shift assays to measure PonA1's sensitivity to different classes of β-lactams. Structural comparison of the PonA1 apo-form and the antibiotic-bound form shows that binding of penicillin V induces conformational changes in the position of the loop β4'-α3 surrounding the penicillin-binding site. We have also found that binding of different antibiotics including penicillin V positively impacts protein stability, while other tested β-lactams such as clavulanate or meropenem resulted in destabilization of PonA1. Our antibiotic profiling experiments indicate that the transpeptidase activity of PonA1 in both M. tuberculosis and M. smegmatis mediates tolerance to specific cell wall-targeting antibiotics, particularly to penicillin V and meropenem. Because M. tuberculosis is an important human pathogen, these structural data provide a template to design novel transpeptidase inhibitors to treat tuberculosis infections. DATABASE Structural data are available in the PDB database under the accession numbers 5CRF and 5CXW.
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Affiliation(s)
- Ekaterina V Filippova
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Midwest Center for Structural Genomics (MCSG), Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Karen J Kieser
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Chi-Hao Luan
- Midwest Center for Structural Genomics (MCSG), Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
- High Throughput Analysis Laboratory and Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Zdzislaw Wawrzak
- Life Science Collaborative Access Team, Synchrotron Research Center, Northwestern University, Evanston, IL, USA
| | - Olga Kiryukhina
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Midwest Center for Structural Genomics (MCSG), Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Eric J Rubin
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Wayne F Anderson
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Midwest Center for Structural Genomics (MCSG), Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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Elucidation of Mechanisms of Ceftazidime Resistance among Clinical Isolates of Pseudomonas aeruginosa by Using Genomic Data. Antimicrob Agents Chemother 2016; 60:3856-61. [PMID: 27067331 DOI: 10.1128/aac.03113-15] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 04/05/2016] [Indexed: 11/20/2022] Open
Abstract
Ceftazidime is one of the few cephalosporins with activity against Pseudomonas aeruginosa Using whole-genome comparative analysis, we set out to determine the prevalent mechanism(s) of resistance to ceftazidime (CAZ) using a set of 181 clinical isolates. These isolates represented various multilocus sequence types that consisted of both ceftazidime-susceptible and -resistant populations. A presumptive resistance mechanism against ceftazidime was identified in 88% of the nonsusceptible isolates using this approach.
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41
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Glycosyltransferases and Transpeptidases/Penicillin-Binding Proteins: Valuable Targets for New Antibacterials. Antibiotics (Basel) 2016; 5:antibiotics5010012. [PMID: 27025527 PMCID: PMC4810414 DOI: 10.3390/antibiotics5010012] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 01/27/2016] [Accepted: 02/03/2016] [Indexed: 12/29/2022] Open
Abstract
Peptidoglycan (PG) is an essential macromolecular sacculus surrounding most bacteria. It is assembled by the glycosyltransferase (GT) and transpeptidase (TP) activities of multimodular penicillin-binding proteins (PBPs) within multiprotein complex machineries. Both activities are essential for the synthesis of a functional stress-bearing PG shell. Although good progress has been made in terms of the functional and structural understanding of GT, finding a clinically useful antibiotic against them has been challenging until now. In contrast, the TP/PBP module has been successfully targeted by β-lactam derivatives, but the extensive use of these antibiotics has selected resistant bacterial strains that employ a wide variety of mechanisms to escape the lethal action of these antibiotics. In addition to traditional β-lactams, other classes of molecules (non-β-lactams) that inhibit PBPs are now emerging, opening new perspectives for tackling the resistance problem while taking advantage of these valuable targets, for which a wealth of structural and functional knowledge has been accumulated. The overall evidence shows that PBPs are part of multiprotein machineries whose activities are modulated by cofactors. Perturbation of these systems could lead to lethal effects. Developing screening strategies to take advantage of these mechanisms could lead to new inhibitors of PG assembly. In this paper, we present a general background on the GTs and TPs/PBPs, a survey of recent issues of bacterial resistance and a review of recent works describing new inhibitors of these enzymes.
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Ren J, Nettleship JE, Males A, Stuart DI, Owens RJ. Crystal structures of penicillin-binding protein 3 in complexes with azlocillin and cefoperazone in both acylated and deacylated forms. FEBS Lett 2016; 590:288-97. [PMID: 26823174 PMCID: PMC4764023 DOI: 10.1002/1873-3468.12054] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 12/18/2015] [Accepted: 01/01/2016] [Indexed: 11/10/2022]
Abstract
Penicillin‐binding protein 3 (PBP3) from Pseudomonas aeruginosa is the molecular target of β‐lactam‐based antibiotics. Structures of PBP3 in complexes with azlocillin and cefoperazone, which are in clinical use for the treatment of pseudomonad infections, have been determined to 2.0 Å resolution. Together with data from other complexes, these structures identify a common set of residues involved in the binding of β‐lactams to PBP3. Comparison of wild‐type and an active site mutant (S294A) showed that increased thermal stability of PBP3 following azlocillin binding was entirely due to covalent binding to S294, whereas cefoperazone binding produces some increase in stability without the covalent link. Consistent with this, a third crystal structure was determined in which the hydrolysis product of cefoperazone was noncovalently bound in the active site of PBP3. This is the first structure of a complex between a penicillin‐binding protein and cephalosporic acid and may be important in the design of new noncovalent PBP3 inhibitors.
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Affiliation(s)
- Jingshan Ren
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Oxford, UK
| | - Joanne E Nettleship
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Oxford, UK.,OPPF-UK, The Research Complex at Harwell, Rutherford Appleton Laboratory, Oxfordshire, UK
| | - Alexandra Males
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Oxford, UK.,OPPF-UK, The Research Complex at Harwell, Rutherford Appleton Laboratory, Oxfordshire, UK
| | - David I Stuart
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Oxford, UK.,Diamond Light Sources, Harwell Science and Innovation Campus, Didcot, UK
| | - Raymond J Owens
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Oxford, UK.,OPPF-UK, The Research Complex at Harwell, Rutherford Appleton Laboratory, Oxfordshire, UK
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43
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Adeniyi AA, Muthusamy R, Soliman MES. New drug design with covalent modifiers. Expert Opin Drug Discov 2016; 11:79-90. [DOI: 10.1517/17460441.2016.1115478] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Adebayo A Adeniyi
- School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Ramesh Muthusamy
- School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Mahmoud ES Soliman
- School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa
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44
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Li LM, Li J, Zhang XY. Antimicrobial and molecular interaction studies on derivatives of curcumin against Streptococcus pneumoniae which caused pneumonia. ELECTRON J BIOTECHN 2016. [DOI: 10.1016/j.ejbt.2015.09.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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45
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Ding H, Guo M, Vidhyasagar V, Talwar T, Wu Y. The Q Motif Is Involved in DNA Binding but Not ATP Binding in ChlR1 Helicase. PLoS One 2015; 10:e0140755. [PMID: 26474416 PMCID: PMC4608764 DOI: 10.1371/journal.pone.0140755] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 09/30/2015] [Indexed: 01/08/2023] Open
Abstract
Helicases are molecular motors that couple the energy of ATP hydrolysis to the unwinding of structured DNA or RNA and chromatin remodeling. The conversion of energy derived from ATP hydrolysis into unwinding and remodeling is coordinated by seven sequence motifs (I, Ia, II, III, IV, V, and VI). The Q motif, consisting of nine amino acids (GFXXPXPIQ) with an invariant glutamine (Q) residue, has been identified in some, but not all helicases. Compared to the seven well-recognized conserved helicase motifs, the role of the Q motif is less acknowledged. Mutations in the human ChlR1 (DDX11) gene are associated with a unique genetic disorder known as Warsaw Breakage Syndrome, which is characterized by cellular defects in genome maintenance. To examine the roles of the Q motif in ChlR1 helicase, we performed site directed mutagenesis of glutamine to alanine at residue 23 in the Q motif of ChlR1. ChlR1 recombinant protein was overexpressed and purified from HEK293T cells. ChlR1-Q23A mutant abolished the helicase activity of ChlR1 and displayed reduced DNA binding ability. The mutant showed impaired ATPase activity but normal ATP binding. A thermal shift assay revealed that ChlR1-Q23A has a melting point value similar to ChlR1-WT. Partial proteolysis mapping demonstrated that ChlR1-WT and Q23A have a similar globular structure, although some subtle conformational differences in these two proteins are evident. Finally, we found ChlR1 exists and functions as a monomer in solution, which is different from FANCJ, in which the Q motif is involved in protein dimerization. Taken together, our results suggest that the Q motif is involved in DNA binding but not ATP binding in ChlR1 helicase.
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Affiliation(s)
- Hao Ding
- Department of Biochemistry, University of Saskatchewan, Health Sciences Building, 107 Wiggins Road, Saskatoon, Saskatchewan, Canada
| | - Manhong Guo
- Department of Biochemistry, University of Saskatchewan, Health Sciences Building, 107 Wiggins Road, Saskatoon, Saskatchewan, Canada
| | - Venkatasubramanian Vidhyasagar
- Department of Biochemistry, University of Saskatchewan, Health Sciences Building, 107 Wiggins Road, Saskatoon, Saskatchewan, Canada
| | - Tanu Talwar
- Department of Biochemistry, University of Saskatchewan, Health Sciences Building, 107 Wiggins Road, Saskatoon, Saskatchewan, Canada
| | - Yuliang Wu
- Department of Biochemistry, University of Saskatchewan, Health Sciences Building, 107 Wiggins Road, Saskatoon, Saskatchewan, Canada
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Meiyazhagan G, Raju R, Winfred SB, Mannivanan B, Bhoopalan H, Shankar V, Sekar S, Venkatachalam DP, Pitani R, Nagendrababu V, Thaiman M, Devivanayagam K, Jayaraman J, Ragavachary R, Venkatraman G. Bioactivity Studies of β-Lactam Derived Polycyclic Fused Pyrroli-Dine/Pyrrolizidine Derivatives in Dentistry: In Vitro, In Vivo and In Silico Studies. PLoS One 2015; 10:e0131433. [PMID: 26185985 PMCID: PMC4505899 DOI: 10.1371/journal.pone.0131433] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 06/02/2015] [Indexed: 11/22/2022] Open
Abstract
The antibacterial activity of β-lactam derived polycyclic fused pyrrolidine/pyrrolizidine derivatives synthesized by 1, 3-dipolar cycloaddition reaction was evaluated against microbes involved in dental infection. Fifteen compounds were screened; among them compound 3 showed efficient antibacterial activity in an ex vivo dentinal tubule model and in vivo mice infectious model. In silico docking studies showed greater affinity to penicillin binding protein. Cell damage was observed under Scanning Electron Microscopy (SEM) which was further proved by Confocal Laser Scanning Microscope (CLSM) and quantified using Flow Cytometry by PI up-take. Compound 3 treated E. faecalis showed ROS generation and loss of membrane integrity was quantified by flow cytometry. Compound 3 was also found to be active against resistant E. faecalis strains isolated from failed root canal treatment cases. Further, compound 3 was found to be hemocompatible, not cytotoxic to normal mammalian NIH 3T3 cells and non mutagenic. It was concluded that β-lactam compound 3 exhibited promising antibacterial activity against E. faecalis involved in root canal infections and the mechanism of action was deciphered. The results of this research can be further implicated in the development of potent antibacterial medicaments with applications in dentistry.
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Affiliation(s)
- Gowri Meiyazhagan
- Department of Human Genetics, Sri Ramachandra University, Porur, Chennai, Tamilnadu, India
| | - Rajesh Raju
- Department of Organic Chemistry, University of Madras, Guindy Campus, Chennai, Tamilnadu, India
| | - Sofi Beaula Winfred
- Department of Human Genetics, Sri Ramachandra University, Porur, Chennai, Tamilnadu, India
| | - Bhavani Mannivanan
- Department of Human Genetics, Sri Ramachandra University, Porur, Chennai, Tamilnadu, India
| | - Hemadev Bhoopalan
- Department of Human Genetics, Sri Ramachandra University, Porur, Chennai, Tamilnadu, India
| | - Venkatesh Shankar
- Department of Bioinformatics, Alagappa University, Karaikudi, Tamilnadu, India
| | - Sathiya Sekar
- Center for Toxicology and Developmental Research, Sri Ramachandra University, Porur, Chennai, Tamilnadu, India
| | | | - Ravishankar Pitani
- Department of Community Medicine, Sri Ramachandra University, Porur, Chennai Tamilnadu, India
| | - Venkateshbabu Nagendrababu
- Department of Conservative Dentistry and Endodontics, Sri Ramachandra University, Porur, Chennai, Tamilnadu, India
| | - Malini Thaiman
- Central Research Facility, Sri Ramachandra University, Porur, Chennai, Tamilnadu, India
| | - Kandaswamy Devivanayagam
- Department of Conservative Dentistry and Endodontics, Sri Ramachandra University, Porur, Chennai, Tamilnadu, India
| | | | - Raghunathan Ragavachary
- Department of Organic Chemistry, University of Madras, Guindy Campus, Chennai, Tamilnadu, India
- * E-mail: (RRag); (GV)
| | - Ganesh Venkatraman
- Department of Human Genetics, Sri Ramachandra University, Porur, Chennai, Tamilnadu, India
- * E-mail: (RRag); (GV)
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Sun YT, Huang PY, Lin CH, Lee KR, Lee MT. Studying antibiotic-membrane interactions via X-ray diffraction and fluorescence microscopy. FEBS Open Bio 2015; 5:515-21. [PMID: 26155459 PMCID: PMC4491592 DOI: 10.1016/j.fob.2015.06.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 06/10/2015] [Accepted: 06/11/2015] [Indexed: 11/25/2022] Open
Abstract
Antibiotic drug resistance is a serious issue for the treatment of bacterial infection. Understanding the resistance to antibiotics is a key issue for developing new drugs. We used penicillin and sulbactam as model antibiotics to study their interaction with model membranes. Cholesterol was used to target the membrane for comparison with the well-known insertion model. Lamellar X-ray diffraction (LXD) was used to determine membrane thickness using successive drug-to-lipid molar ratios. The aspiration method for a single giant unilamellar vesicle (GUV) was used to monitor the kinetic binding process of antibiotic-membrane interactions in an aqueous solution. Both penicillin and sulbactam are found positioned outside the model membrane, while cholesterol inserts perpendicularly into the hydrophobic region of the membrane in aqueous solution. This result provides structural insights for understanding the antibiotic-membrane interaction and the mechanism of antibiotics.
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Affiliation(s)
- Yi-Ting Sun
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu 30013, Taiwan ; National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Ping-Yuan Huang
- National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Cheng-Hao Lin
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Kuan-Rong Lee
- Institute of Molecular Medicine, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Ming-Tao Lee
- National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan ; Department of Physics, National Central University, Jhongli 32001, Taiwan
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48
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Kino R, Araya T, Arai T, Sohma Y, Kanai M. Covalent modifier-type aggregation inhibitor of amyloid-β based on a cyclo-KLVFF motif. Bioorg Med Chem Lett 2015; 25:2972-5. [PMID: 26045033 DOI: 10.1016/j.bmcl.2015.05.027] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 05/10/2015] [Accepted: 05/12/2015] [Indexed: 11/18/2022]
Abstract
Inhibition of amyloid-β (Aβ) aggregation could be a drug development target for treating Alzheimer disease. Insufficient activity to inhibit aggregation, however, remains a key issue. Here, we report a covalent modifier-type aggregation inhibitor of Aβ, diazirine-equipped cyclo-KLVF(β-Ph)F (2). Due to the affinity of the cyclo-KLVFF motif for Aβ, 2 selectively reacted with Aβ1-42 under UV-light irradiation to form an irreversible covalent bond. The Tyr-10 residue of Aβ1-42 was identified as the covalent modification site with 2. The extent of cross-β-sheet structure, characteristics of amyloid aggregation, and toxicity of Aβ1-42 were strongly attenuated by this chemical modification.
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Affiliation(s)
- Ryuto Kino
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takushi Araya
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Tadamasa Arai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; ERATO (Japan) Science and Technology Agency (JST), Kanai Life Science Catalysis Project, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Youhei Sohma
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; ERATO (Japan) Science and Technology Agency (JST), Kanai Life Science Catalysis Project, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Motomu Kanai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; ERATO (Japan) Science and Technology Agency (JST), Kanai Life Science Catalysis Project, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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49
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Kim A, Wolf NM, Zhu T, Johnson ME, Deng J, Cook JL, Fung LWM. Identification of Bacillus anthracis PurE inhibitors with antimicrobial activity. Bioorg Med Chem 2015; 23:1492-9. [PMID: 25737087 DOI: 10.1016/j.bmc.2015.02.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 01/28/2015] [Accepted: 02/06/2015] [Indexed: 11/19/2022]
Abstract
N(5)-carboxy-amino-imidazole ribonucleotide (N(5)-CAIR) mutase (PurE), a bacterial enzyme in the de novo purine biosynthetic pathway, has been suggested to be a target for antimicrobial agent development. We have optimized a thermal shift method for high-throughput screening of compounds binding to Bacillus anthracis PurE. We used a low ionic strength buffer condition to accentuate the thermal shift stabilization induced by compound binding to Bacillus anthracis PurE. The compounds identified were then subjected to computational docking to the active site to further select compounds likely to be inhibitors. A UV-based enzymatic activity assay was then used to select inhibitory compounds. Minimum inhibitory concentration (MIC) values were subsequently obtained for the inhibitory compounds against Bacillus anthracis (ΔANR strain), Escherichia coli (BW25113 strain, wild-type and ΔTolC), Francisella tularensis, Staphylococcus aureus (both methicillin susceptible and methicillin-resistant strains) and Yersinia pestis. Several compounds exhibited excellent (0.05-0.15μg/mL) MIC values against Bacillus anthracis. A common core structure was identified for the compounds exhibiting low MIC values. The difference in concentrations for inhibition and MIC suggest that another enzyme(s) is also targeted by the compounds that we identified.
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Affiliation(s)
- Anna Kim
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, IL 60607, United States
| | - Nina M Wolf
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, IL 60607, United States
| | - Tian Zhu
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, Chicago, IL 60607, United States
| | - Michael E Johnson
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, Chicago, IL 60607, United States
| | - Jiangping Deng
- Loyola University Medical Center, Maywood, IL 60153, United States
| | - James L Cook
- Loyola University Medical Center, Maywood, IL 60153, United States
| | - Leslie W-M Fung
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, IL 60607, United States.
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50
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An YD, Du QZ, Tong LY, Yu ZW, Gong XW. Cloning, expression and purification of penicillin-binding protein 3 from Pseudomonas aeruginosa CMCC 10104. Protein Expr Purif 2014; 110:37-42. [PMID: 25514204 DOI: 10.1016/j.pep.2014.12.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Revised: 12/05/2014] [Accepted: 12/07/2014] [Indexed: 11/18/2022]
Abstract
Penicillin-binding protein 3 (PBP3) of Pseudomonas aeruginosa is the primary target of β-lactams used to treat pseudomonas infections. Meanwhile, structure change and overproduction of PBP3 play important roles in the drug resistance of P. aeruginosa. Therefore, studies on the gene and structure of PBP3 are urgently needed. P. aeruginosa CMCC 10104 is a type culture strain common used in China. However, there is no report on its genomic and proteomic profiles. In this study, based on ftsI of P. aeruginosa PAO1, the gene encoding PBP3 was cloned from CMCC 10104. A truncated version of the ftsI gene, omitting the bases encoding the hydrophobic leader peptide (amino acids 1-34), was amplified by PCR. The cloned DNA shared 99.76% identity with ftsI from PAO1. Only four bases were different (66 C-A, 1020 T-C, 1233 T-C, and 1527 T-C). However, there were no differences between their deduced amino acid sequences. The recombinant PBP3 (rPBP3), containing a 6-histidine tag, was expressed in Escherichia coli BL21 (DE3). Immobilized metal affinity chromatography (IMAC) with Ni(2+)-NTA agarose was used for its purification. The purified rPBP3 was identified by SDS-PAGE and western blot analysis, and showed a single band at about 60kDa with purity higher than 95%. The penicillin-binding assay indicated that the obtained rPBP3 was functional and not hindered by the presence of the C-terminal His-tag. The protocol described in this study offers a method for obtaining purified recombinant PBP3 from P. aeruginosa CMCC 10104.
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Affiliation(s)
- Yan Dong An
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Qi Zhen Du
- Zhejiang A&F University, Hangzhou 311300, China
| | - Li Yan Tong
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Zhao Wu Yu
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Xing Wen Gong
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China.
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