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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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Jacobs LMC, Consol P, Chen Y. Drug Discovery in the Field of β-Lactams: An Academic Perspective. Antibiotics (Basel) 2024; 13:59. [PMID: 38247618 PMCID: PMC10812508 DOI: 10.3390/antibiotics13010059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/21/2023] [Accepted: 12/23/2023] [Indexed: 01/23/2024] Open
Abstract
β-Lactams are the most widely prescribed class of antibiotics that inhibit penicillin-binding proteins (PBPs), particularly transpeptidases that function in peptidoglycan synthesis. A major mechanism of antibiotic resistance is the production of β-lactamase enzymes, which are capable of hydrolyzing β-lactam antibiotics. There have been many efforts to counter increasing bacterial resistance against β-lactams. These studies have mainly focused on three areas: discovering novel inhibitors against β-lactamases, developing new β-lactams less susceptible to existing resistance mechanisms, and identifying non-β-lactam inhibitors against cell wall transpeptidases. Drug discovery in the β-lactam field has afforded a range of research opportunities for academia. In this review, we summarize the recent new findings on both β-lactamases and cell wall transpeptidases because these two groups of enzymes are evolutionarily and functionally connected. Many efforts to develop new β-lactams have aimed to inhibit both transpeptidases and β-lactamases, while several promising novel β-lactamase inhibitors have shown the potential to be further developed into transpeptidase inhibitors. In addition, the drug discovery progress against each group of enzymes is presented in three aspects: understanding the targets, screening methodology, and new inhibitor chemotypes. This is to offer insights into not only the advancement in this field but also the challenges, opportunities, and resources for future research. In particular, cyclic boronate compounds are now capable of inhibiting all classes of β-lactamases, while the diazabicyclooctane (DBO) series of small molecules has led to not only new β-lactamase inhibitors but potentially a new class of antibiotics by directly targeting PBPs. With the cautiously optimistic successes of a number of new β-lactamase inhibitor chemotypes and many questions remaining to be answered about the structure and function of cell wall transpeptidases, non-β-lactam transpeptidase inhibitors may usher in the next exciting phase of drug discovery in this field.
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Affiliation(s)
| | | | - Yu Chen
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA; (L.M.C.J.); (P.C.)
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3
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Gibson PS, Veening JW. Gaps in the wall: understanding cell wall biology to tackle amoxicillin resistance in Streptococcus pneumoniae. Curr Opin Microbiol 2023; 72:102261. [PMID: 36638546 DOI: 10.1016/j.mib.2022.102261] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/05/2022] [Accepted: 12/09/2022] [Indexed: 01/13/2023]
Abstract
Streptococcus pneumoniae is the most common cause of community-acquired pneumonia, and one of the main pathogens responsible for otitis media infections in children. Amoxicillin (AMX) is a broad-spectrum β-lactam antibiotic, used frequently for the treatment of bacterial respiratory tract infections. Here, we discuss the pneumococcal response to AMX, including the mode of action of AMX, the effects on autolysin regulation, and the evolution of resistance through natural transformation. We discuss current knowledge gaps in the synthesis and translocation of peptidoglycan and teichoic acids, major constituents of the pneumococcal cell wall and critical to AMX activity. Furthermore, an outlook of AMX resistance research is presented, including the development of natural competence inhibitors to block evolution via horizontal gene transfer, and the use of high-throughput essentiality screens for the discovery of novel cotherapeutics.
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Affiliation(s)
- Paddy S Gibson
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland
| | - Jan-Willem Veening
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland.
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4
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Synthesis, Photophysical Characterization and Evaluation of Biological Properties of C7, a Novel Symmetric Tetra-Imidazolium- Bis-Heterocycle. Microorganisms 2023; 11:microorganisms11020495. [PMID: 36838459 PMCID: PMC9959923 DOI: 10.3390/microorganisms11020495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/02/2023] [Accepted: 02/10/2023] [Indexed: 02/18/2023] Open
Abstract
A novel symmetric tetra-imidazolium-bis-heterocycle, called C7, was designed and synthesized in a quick two-step pathway, with the objective to synthesize biologically active supramolecular assembly. The synthesized compound was then analyzed for its photophysical properties, for a potential application in theragnostic (fluorescence) or phototherapy (photodynamic therapy, with the production of reactive oxygen species, such as singlet oxygen 1O2). C7 was thus screened for its biological activity, in particular against important human pathogens of viral origin (respiratory viruses such as adenovirus type 2 and human coronavirus 229E) and of fungal and bacterial origin. The compound showed limited antiviral activity, combined with very good antiproliferative activity against breast cancer, and head and neck squamous cell carcinoma models. Interestingly, the selected compound showed excellent antibacterial activity against a large array of Gram-positive and Gram-negative clinically isolated pathogenic bacteria, with a possible inhibitory mechanism on the bacterial cell wall synthesis studied with electron microscopy and molecular docking tools. Collectively, the newly synthesized compound C7 could be considered as a potential lead for the development of new antibacterial treatment, endowed with basic photophysical properties, opening the door towards the future development of phototherapy approaches.
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5
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Diessner EM, Takahashi GR, Martin RW, Butts CT. Comparative Modeling and Analysis of Extremophilic D-Ala-D-Ala Carboxypeptidases. Biomolecules 2023; 13:biom13020328. [PMID: 36830697 PMCID: PMC9953012 DOI: 10.3390/biom13020328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/21/2023] [Accepted: 02/02/2023] [Indexed: 02/11/2023] Open
Abstract
Understanding the molecular adaptations of organisms to extreme environments requires a comparative analysis of protein structure, function, and dynamics across species found in different environmental conditions. Computational studies can be particularly useful in this pursuit, allowing exploratory studies of large numbers of proteins under different thermal and chemical conditions that would be infeasible to carry out experimentally. Here, we perform such a study of the MEROPS family S11, S12, and S13 proteases from psychophilic, mesophilic, and thermophilic bacteria. Using a combination of protein structure prediction, atomistic molecular dynamics, and trajectory analysis, we examine both conserved features and trends across thermal groups. Our findings suggest a number of hypotheses for experimental investigation.
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Affiliation(s)
| | - Gemma R. Takahashi
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
| | - Rachel W. Martin
- Department of Chemistry, University of California, Irvine, CA 92697, USA
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
- Correspondence: (R.W.M.); (C.T.B.)
| | - Carter T. Butts
- Departments of Sociology, Statistics, Electrical Engineering and Computer Science, University of California, Irvine, CA 92697, USA
- Correspondence: (R.W.M.); (C.T.B.)
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6
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Uruén C, García C, Fraile L, Tommassen J, Arenas J. How Streptococcus suis escapes antibiotic treatments. Vet Res 2022; 53:91. [DOI: 10.1186/s13567-022-01111-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
AbstractStreptococcus suis is a zoonotic agent that causes sepsis and meningitis in pigs and humans. S. suis infections are responsible for large economic losses in pig production. The lack of effective vaccines to prevent the disease has promoted the extensive use of antibiotics worldwide. This has been followed by the emergence of resistance against different classes of antibiotics. The rates of resistance to tetracyclines, lincosamides, and macrolides are extremely high, and resistance has spread worldwide. The genetic origin of S. suis resistance is multiple and includes the production of target-modifying and antibiotic-inactivating enzymes and mutations in antibiotic targets. S. suis genomes contain traits of horizontal gene transfer. Many mobile genetic elements carry a variety of genes that confer resistance to antibiotics as well as genes for autonomous DNA transfer and, thus, S. suis can rapidly acquire multiresistance. In addition, S. suis forms microcolonies on host tissues, which are associations of microorganisms that generate tolerance to antibiotics through a variety of mechanisms and favor the exchange of genetic material. Thus, alternatives to currently used antibiotics are highly demanded. A deep understanding of the mechanisms by which S. suis becomes resistant or tolerant to antibiotics may help to develop novel molecules or combinations of antimicrobials to fight these infections. Meanwhile, phage therapy and vaccination are promising alternative strategies, which could alleviate disease pressure and, thereby, antibiotic use.
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Chochua S, Metcalf B, Li Z, Mathis S, Tran T, Rivers J, Fleming-Dutra KE, Li Y, McGee L, Beall B. Invasive Group A Streptococcal Penicillin Binding Protein 2× Variants Associated with Reduced Susceptibility to β-Lactam Antibiotics in the United States, 2015-2021. Antimicrob Agents Chemother 2022; 66:e0080222. [PMID: 35969070 PMCID: PMC9487518 DOI: 10.1128/aac.00802-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 07/18/2022] [Indexed: 11/20/2022] Open
Abstract
All known group A streptococci [GAS] are susceptible to β-lactam antibiotics. We recently identified an invasive GAS (iGAS) variant (emm43.4/PBP2x-T553K) with unusually high minimum inhibitory concentrations (MICs) for ampicillin and amoxicillin, although clinically susceptible to β-lactams. We aimed to quantitate PBP2x variants, small changes in β-lactam MICs, and lineages within contemporary population-based iGAS. PBP2x substitutions were comprehensively identified among 13,727 iGAS recovered during 2015-2021, in the USA. Isolates were subjected to antimicrobial susceptibility testing employing low range agar diffusion and PBP2x variants were subjected to phylogenetic analyses. Fifty-five variants were defined based upon substitutions within an assigned PBP2x transpeptidase domain. Twenty-nine of these variants, representing 338/13,727 (2.5%) isolates and 16 emm types, exhibited slightly elevated β-lactam MICs, none of which were above clinical breakpoints. The emm43.4/PBP2x-T553K variant, comprised of two isolates, displayed the most significant phenotype (ampicillin MIC 0.25 μg/ml) and harbored missense mutations within 3 non-PBP genes with known involvement in antibiotic efflux, membrane insertion of PBP2x, and peptidoglycan remodeling. The proportion of all PBP2x variants with elevated MICs remained stable throughout 2015-2021 (<3.0%). The predominant lineage (emm4/PBP2x-M593T/ermT) was resistant to macrolides/lincosamides and comprised 129/340 (37.9%) of isolates with elevated β-lactam MICs. Continuing β-lactam selective pressure is likely to have selected PBP2x variants that had escaped scrutiny due to MICs that remain below clinical cutoffs. Higher MICs exhibited by emm43.4/PBP2x-T553K are probably rare due to the requirement of additional mutations. Although elevated β-lactam MICs remain uncommon, emm43.4/PBP2x-T553K and emm4/PBP2x-M593T/ermT lineages indicate that antibiotic stewardship and strain monitoring is necessary.
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Affiliation(s)
- Sopio Chochua
- Respiratory Disease Branch, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Benjamin Metcalf
- Respiratory Disease Branch, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Zhongya Li
- ASRT Inc., Contractor to Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Saundra Mathis
- ASRT Inc., Contractor to Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Theresa Tran
- ASRT Inc., Contractor to Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Joy Rivers
- Respiratory Disease Branch, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Katherine E. Fleming-Dutra
- Respiratory Disease Branch, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Yuan Li
- Respiratory Disease Branch, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lesley McGee
- Respiratory Disease Branch, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Bernard Beall
- Respiratory Disease Branch, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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8
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Photodynamic inactivation (PDI) as a promising alternative to current pharmaceuticals for the treatment of resistant microorganisms. ADVANCES IN INORGANIC CHEMISTRY 2022; 79:65-103. [PMID: 35095189 PMCID: PMC8787646 DOI: 10.1016/bs.adioch.2021.12.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Although the whole world is currently observing the global battle against COVID-19, it should not be underestimated that in the next 30 years, approximately 10 million people per year could be exposed to infections caused by multi-drug resistant bacteria. As new antibiotics come under pressure from unpredictable resistance patterns and relegation to last-line therapy, immediate action is needed to establish a radically different approach to countering resistant microorganisms. Among the most widely explored alternative methods for combating bacterial infections are metal complexes and nanoparticles, often in combination with light, but strategies using monoclonal antibodies and bacteriophages are increasingly gaining acceptance. Photodynamic inactivation (PDI) uses light and a dye termed a photosensitizer (PS) in the presence of oxygen to generate reactive oxygen species (ROS) in the field of illumination that eventually kill microorganisms. Over the past few years, hundreds of photomaterials have been investigated, seeking ideal strategies based either on single molecules (e.g., tetrapyrroles, metal complexes) or in combination with various delivery systems. The present work describes some of the most recent advances of PDI, focusing on the design of suitable photosensitizers, their formulations, and their potential to inactivate bacteria, viruses, and fungi. Particular attention is focused on the compounds and materials developed in our laboratories that are capable of killing in the exponential growth phase (up to seven logarithmic units) of bacteria without loss of efficacy or resistance, while being completely safe for human cells. Prospectively, PDI using these photomaterials could potentially cure infected wounds and oral infections caused by various multidrug-resistant bacteria. It is also possible to treat the surfaces of medical equipment with the materials described, in order to disinfect them with light, and reduce the risk of nosocomial infections.
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Verma T, Aggarwal A, Singh S, Sharma S, Sarma SJ. Current challenges and advancements towards discovery and resistance of antibiotics. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131380] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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10
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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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11
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Martínez-Caballero S, Mahasenan KV, Kim C, Molina R, Feltzer R, Lee M, Bouley R, Hesek D, Fisher JF, Muñoz IG, Chang M, Mobashery S, Hermoso JA. Integrative structural biology of the penicillin-binding protein-1 from Staphylococcus aureus, an essential component of the divisome machinery. Comput Struct Biotechnol J 2021; 19:5392-5405. [PMID: 34667534 PMCID: PMC8493512 DOI: 10.1016/j.csbj.2021.09.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/13/2021] [Accepted: 09/15/2021] [Indexed: 12/18/2022] Open
Abstract
The penicillin-binding proteins are the enzyme catalysts of the critical transpeptidation crosslinking polymerization reaction of bacterial peptidoglycan synthesis and the molecular targets of the penicillin antibiotics. Here, we report a combined crystallographic, small-angle X-ray scattering (SAXS) in-solution structure, computational and biophysical analysis of PBP1 of Staphylococcus aureus (saPBP1), providing mechanistic clues about its function and regulation during cell division. The structure reveals the pedestal domain, the transpeptidase domain, and most of the linker connecting to the "penicillin-binding protein and serine/threonine kinase associated" (PASTA) domains, but not its two PASTA domains, despite their presence in the construct. To address this absence, the structure of the PASTA domains was determined at 1.5 Å resolution. Extensive molecular-dynamics simulations interpret the PASTA domains of saPBP1 as conformationally mobile and separated from the transpeptidase domain. This conclusion was confirmed by SAXS experiments on the full-length protein in solution. A series of crystallographic complexes with β-lactam antibiotics (as inhibitors) and penta-Gly (as a substrate mimetic) allowed the molecular characterization of both inhibition by antibiotics and binding for the donor and acceptor peptidoglycan strands. Mass-spectrometry experiments with synthetic peptidoglycan fragments revealed binding by PASTA domains in coordination with the remaining domains. The observed mobility of the PASTA domain in saPBP1 could play a crucial role for in vivo interaction with its glycosyltransferase partner in the membrane or with other components of the divisome machinery, as well as for coordination of transpeptidation and polymerization processes in the bacterial divisome.
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Affiliation(s)
- Siseth Martínez-Caballero
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry "Rocasolano", CSIC, 28006 Madrid, Spain
| | - Kiran V Mahasenan
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Choon Kim
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Rafael Molina
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry "Rocasolano", CSIC, 28006 Madrid, Spain
| | - Rhona Feltzer
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Mijoon Lee
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Renee Bouley
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Dusan Hesek
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Jed F Fisher
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Inés G Muñoz
- Structural Biology Programme, Spanish National Cancer Research Center (CNIO), 28029 Madrid, Spain
| | - Mayland Chang
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry "Rocasolano", CSIC, 28006 Madrid, Spain
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12
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Vannice KS, Ricaldi J, Nanduri S, Fang FC, Lynch JB, Bryson-Cahn C, Wright T, Duchin J, Kay M, Chochua S, Van Beneden CA, Beall B. Streptococcus pyogenes pbp2x Mutation Confers Reduced Susceptibility to β-Lactam Antibiotics. Clin Infect Dis 2021; 71:201-204. [PMID: 31630171 DOI: 10.1093/cid/ciz1000] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 10/14/2019] [Indexed: 11/14/2022] Open
Abstract
Two near-identical clinical Streptococcus pyogenes isolates of emm subtype emm43.4 with a pbp2x missense mutation (T553K) were detected. Minimum inhibitory concentrations (MICs) for ampicillin and amoxicillin were 8-fold higher, and the MIC for cefotaxime was 3-fold higher than for near-isogenic control isolates, consistent with a first step in developing β-lactam resistance.
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Affiliation(s)
- Kirsten S Vannice
- Epidemiology Workforce Branch, Division of Scientific Education and Professional Development, Epidemic Intelligence Service, Center for Surveillance, Epidemiology, and Laboratory Services, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Communicable Disease Epidemiology and Immunization, Prevention Division, Public Health-Seattle & King County, Seattle, Washington, USA
| | - Jessica Ricaldi
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Srinivas Nanduri
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - John B Lynch
- Harborview Medical Center, Seattle, Washington, USA
| | | | | | - Jeff Duchin
- Communicable Disease Epidemiology and Immunization, Prevention Division, Public Health-Seattle & King County, Seattle, Washington, USA
| | - Meagan Kay
- Communicable Disease Epidemiology and Immunization, Prevention Division, Public Health-Seattle & King County, Seattle, Washington, USA
| | - Sopio Chochua
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Chris A Van Beneden
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Bernard Beall
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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13
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Waglechner N, Culp EJ, Wright GD. Ancient Antibiotics, Ancient Resistance. EcoSal Plus 2021; 9:eESP-0027-2020. [PMID: 33734062 PMCID: PMC11163840 DOI: 10.1128/ecosalplus.esp-0027-2020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/26/2021] [Indexed: 02/06/2023]
Abstract
As the spread of antibiotic resistance threatens our ability to treat infections, avoiding the return of a preantibiotic era requires the discovery of new drugs. While therapeutic use of antibiotics followed by the inevitable selection of resistance is a modern phenomenon, these molecules and the genetic determinants of resistance were in use by environmental microbes long before humans discovered them. In this review, we discuss evidence that antibiotics and resistance were present in the environment before anthropogenic use, describing techniques including direct sampling of ancient DNA and phylogenetic analyses that are used to reconstruct the past. We also pay special attention to the ecological and evolutionary forces that have shaped the natural history of antibiotic biosynthesis, including a discussion of competitive versus signaling roles for antibiotics, proto-resistance, and substrate promiscuity of biosynthetic and resistance enzymes. Finally, by applying an evolutionary lens, we describe concepts governing the origins and evolution of biosynthetic gene clusters and cluster-associated resistance determinants. These insights into microbes' use of antibiotics in nature, a game they have been playing for millennia, can provide inspiration for discovery technologies and management strategies to combat the growing resistance crisis.
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Affiliation(s)
- Nicholas Waglechner
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Elizabeth J. Culp
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Gerard D. Wright
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
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14
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Sargun A, Johnstone TC, Zhi H, Raffatellu M, Nolan EM. Enterobactin- and salmochelin-β-lactam conjugates induce cell morphologies consistent with inhibition of penicillin-binding proteins in uropathogenic Escherichia coli CFT073. Chem Sci 2021; 12:4041-4056. [PMID: 34163675 PMCID: PMC8179508 DOI: 10.1039/d0sc04337k] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 12/31/2020] [Indexed: 12/15/2022] Open
Abstract
The design and synthesis of narrow-spectrum antibiotics that target a specific bacterial strain, species, or group of species is a promising strategy for treating bacterial infections when the causative agent is known. In this work, we report the synthesis and evaluation of four new siderophore-β-lactam conjugates where the broad-spectrum β-lactam antibiotics cephalexin (Lex) and meropenem (Mem) are covalently attached to either enterobactin (Ent) or diglucosylated Ent (DGE) via a stable polyethylene glycol (PEG3) linker. These siderophore-β-lactam conjugates showed enhanced minimum inhibitory concentrations against Escherichia coli compared to the parent antibiotics. Uptake studies with uropathogenic E. coli CFT073 demonstrated that the DGE-β-lactams target the pathogen-associated catecholate siderophore receptor IroN. A comparative analysis of siderophore-β-lactams harboring ampicillin (Amp), Lex and Mem indicated that the DGE-Mem conjugate is advantageous because it targets IroN and exhibits low minimum inhibitory concentrations, fast time-kill kinetics, and enhanced stability to serine β-lactamases. Phase-contrast and fluorescence imaging of E. coli treated with the siderophore-β-lactam conjugates revealed cellular morphologies consistent with the inhibition of penicillin-binding proteins PBP3 (Ent/DGE-Amp/Lex) and PBP2 (Ent/DGE-Mem). Overall, this work illuminates the uptake and cell-killing activity of Ent- and DGE-β-lactam conjugates against E. coli and supports that native siderophore scaffolds provide the opportunity for narrowing the activity spectrum of antibiotics in clinical use and targeting pathogenicity.
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Affiliation(s)
- Artur Sargun
- Department of Chemistry, Massachusetts Institute of Technology Cambridge MA 02139 USA +1-617-452-2495
| | - Timothy C Johnstone
- Department of Chemistry, Massachusetts Institute of Technology Cambridge MA 02139 USA +1-617-452-2495
| | - Hui Zhi
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California San Diego La Jolla CA 92093 USA
| | - Manuela Raffatellu
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California San Diego La Jolla CA 92093 USA
- Center for Microbiome Innovation, University of California San Diego La Jolla CA 92093 USA
- Chiba University-UC San Diego Center for Mucosal Immunology, Allergy, and Vaccines La Jolla CA 92093 USA
| | - Elizabeth M Nolan
- Department of Chemistry, Massachusetts Institute of Technology Cambridge MA 02139 USA +1-617-452-2495
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15
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Liu X, Biboy J, Consoli E, Vollmer W, den Blaauwen T. MreC and MreD balance the interaction between the elongasome proteins PBP2 and RodA. PLoS Genet 2020; 16:e1009276. [PMID: 33370261 PMCID: PMC7793260 DOI: 10.1371/journal.pgen.1009276] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 01/08/2021] [Accepted: 11/12/2020] [Indexed: 12/23/2022] Open
Abstract
Rod-shape of most bacteria is maintained by the elongasome, which mediates the synthesis and insertion of peptidoglycan into the cylindrical part of the cell wall. The elongasome contains several essential proteins, such as RodA, PBP2, and the MreBCD proteins, but how its activities are regulated remains poorly understood. Using E. coli as a model system, we investigated the interactions between core elongasome proteins in vivo. Our results show that PBP2 and RodA form a complex mediated by their transmembrane and periplasmic parts and independent of their catalytic activity. MreC and MreD also interact directly with PBP2. MreC elicits a change in the interaction between PBP2 and RodA, which is suppressed by MreD. The cytoplasmic domain of PBP2 is required for this suppression. We hypothesize that the in vivo measured PBP2-RodA interaction change induced by MreC corresponds to the conformational change in PBP2 as observed in the MreC-PBP2 crystal structure, which was suggested to be the "on state" of PBP2. Our results indicate that the balance between MreC and MreD determines the activity of PBP2, which could open new strategies for antibiotic drug development.
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Affiliation(s)
- Xiaolong Liu
- Bacterial Cell Biology & Physiology, Swammerdam Institute for Life Science, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - Jacob Biboy
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Elisa Consoli
- Bacterial Cell Biology & Physiology, Swammerdam Institute for Life Science, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Tanneke den Blaauwen
- Bacterial Cell Biology & Physiology, Swammerdam Institute for Life Science, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
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16
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Hernández-Avilés C, Love CC, Serafini R, Ramírez-Agámez L, Kelley DE, de Andino EM, Teague SR, LaCaze KA, Brinsko SP, Varner DD. Inclusion of supplemental antibiotics (amikacin - penicillin) in a commercial extender for stallion semen: Effects on sperm quality, bacterial growth, and fertility following cooled storage. Theriogenology 2020; 158:209-217. [PMID: 32971438 DOI: 10.1016/j.theriogenology.2020.09.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 09/08/2020] [Accepted: 09/14/2020] [Indexed: 01/17/2023]
Abstract
In this study, the effectiveness of supplementing INRA-96® extender (INRA-Control; original antibiotic formulation: potassium penicillin G = 38 μg/mL; gentamicin sulfate = 105 μg/mL; amphotericin B = 0.315 μg/mL) with amikacin sulfate and potassium penicillin G (AP) was determined. In Exp. 1, two sources of amikacin (INRA-AP-Sigma or INRA-AP-GoldBio) in combination with penicillin G were compared with ticarcillin/clavulanate (INRA-Tim) or no-supplemental antibiotics (INRA-Control) to examine effects on sperm quality and commensal bacterial growth. No differences were detected in semen quality among treatments after 30 min of exposure (Time 30min) or 24 h of cooled storage (Time 24 h; P > 0.05). At both time periods, commensal bacterial growth was significantly lower in Groups INRA-AP-GoldBio and INRA-AP-Sigma than in INRA-Tim or INRA-Control (P < 0.05). In Exp. 2, increasing doses of amikacin sulfate (GoldBio) plus potassium penicillin G (Sigma) - AP (AP-1000, 2000, 3000, 4000 or 5000 μg-IU/mL, respectively) were added to INRA-96® extender and their effects on sperm quality and commensal bacterial growth were evaluated at Time 30min and Time 24 h. Slight reductions in progressive motility and viability were observed at Time 30min in Groups AP-4000 and AP-5000 as compared to other treatment groups (P < 0.05); however, no differences in sperm quality were detected among treatment groups at Time 24 h (P > 0.05). At both time periods, commensal bacterial growth was significantly lower in Groups AP-3000, AP-4000 and AP-5000 than in AP-1000 and AP-2000 (P < 0.05). In Exp. 3, a breeding trial was conducted to determine the effect of adding a high dose of AP (AP-5000) to INRA-96® extender on resulting pregnancy rates of mares bred with cool-stored semen (Time 24 h). Numerical, but not statistical differences, were observed in pregnancy rates between the mares bred with INRA-Control (6/11; 55%) or INRA-AP-5000 (9/11; 82%; P > 0.05). Supplementation of INRA-96® extender with two different concentrations of AP (AP-1000 or AP-5000) was tested in two clinical cases of stallions where semen was moderately to heavily contaminated with Pseudomonas aeruginosa, or both Klebsiella pneumoniae and Pseudomonas aeruginosa. In both cases, addition of AP resulted in a considerable decrease on bacterial growth in cool-stored semen when compared to the use of the original INRA-96® extender without supplemental antibiotics. In conclusion, the addition of amikacin sulfate and potassium penicillin G to INRA-96® extender allowed for effective control of commensal bacteria without affecting sperm quality. Higher doses of amikacin and penicillin can be safely added to INRA-96® extender to improve the antibacterial activity of this extender against commensal, and potentially pathogenic bacteria, while sperm quality and fertility of cooled semen remains unaffected. Based on the results of the present study, we currently recommend that INRA-96® extender can be safely supplemented with amikacin/penicillin by using a conventional dose of 1000 μg/mL - 1000 IU/mL as a prophylactic measure in cases where contamination of the ejaculates with commensal bacteria is evident. Alternatively, a high dose (5000 μg/mL - 5000 IU/mL) can be used as a control method for potentially pathogenic bacteria.
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Affiliation(s)
- Camilo Hernández-Avilés
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, 77845-4475, TX, USA.
| | - Charles C Love
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, 77845-4475, TX, USA
| | - Rosanna Serafini
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, 77845-4475, TX, USA
| | - Luisa Ramírez-Agámez
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, 77845-4475, TX, USA
| | - Dale E Kelley
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, 77845-4475, TX, USA
| | - Elena Martínez de Andino
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, 77845-4475, TX, USA
| | - Sheila R Teague
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, 77845-4475, TX, USA
| | - Katrina A LaCaze
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, 77845-4475, TX, USA
| | - Steven P Brinsko
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, 77845-4475, TX, USA
| | - Dickson D Varner
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, 77845-4475, TX, USA
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17
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Lopez Quezada L, Smith R, Lupoli TJ, Edoo Z, Li X, Gold B, Roberts J, Ling Y, Park SW, Nguyen Q, Schoenen FJ, Li K, Hugonnet JE, Arthur M, Sacchettini JC, Nathan C, Aubé J. Activity-Based Protein Profiling Reveals That Cephalosporins Selectively Active on Non-replicating Mycobacterium tuberculosis Bind Multiple Protein Families and Spare Peptidoglycan Transpeptidases. Front Microbiol 2020; 11:1248. [PMID: 32655524 PMCID: PMC7324553 DOI: 10.3389/fmicb.2020.01248] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 05/15/2020] [Indexed: 11/13/2022] Open
Abstract
As β-lactams are reconsidered for the treatment of tuberculosis (TB), their targets are assumed to be peptidoglycan transpeptidases, as verified by adduct formation and kinetic inhibition of Mycobacterium tuberculosis (Mtb) transpeptidases by carbapenems active against replicating Mtb. Here, we investigated the targets of recently described cephalosporins that are selectively active against non-replicating (NR) Mtb. NR-active cephalosporins failed to inhibit recombinant Mtb transpeptidases. Accordingly, we used alkyne analogs of NR-active cephalosporins to pull down potential targets through unbiased activity-based protein profiling and identified over 30 protein binders. None was a transpeptidase. Several of the target candidates are plausibly related to Mtb's survival in an NR state. However, biochemical tests and studies of loss of function mutants did not identify a unique target that accounts for the bactericidal activity of these beta-lactams against NR Mtb. Instead, NR-active cephalosporins appear to kill Mtb by collective action on multiple targets. These results highlight the ability of these β-lactams to target diverse classes of proteins.
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Affiliation(s)
- Landys Lopez Quezada
- Department of Microbiology & Immunology, Weill Cornell Medical College, New York, NY, United States
| | - Robert Smith
- Chemical Methodologies & Library Development Center, The University of Kansas, Lawrence, KS, United States
| | - Tania J. Lupoli
- Department of Microbiology & Immunology, Weill Cornell Medical College, New York, NY, United States
| | - Zainab Edoo
- Sorbonne Université, Sorbonne Paris Cité, Université de Paris, INSERM, Centre de Recherche des Cordeliers, CRC, Paris, France
| | - Xiaojun Li
- Departments of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Ben Gold
- Department of Microbiology & Immunology, Weill Cornell Medical College, New York, NY, United States
| | - Julia Roberts
- Department of Microbiology & Immunology, Weill Cornell Medical College, New York, NY, United States
| | - Yan Ling
- Department of Microbiology & Immunology, Weill Cornell Medical College, New York, NY, United States
| | - Sae Woong Park
- Department of Microbiology & Immunology, Weill Cornell Medical College, New York, NY, United States
| | - Quyen Nguyen
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Frank J. Schoenen
- Chemical Methodologies & Library Development Center, The University of Kansas, Lawrence, KS, United States
| | - Kelin Li
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jean-Emmanuel Hugonnet
- Sorbonne Université, Sorbonne Paris Cité, Université de Paris, INSERM, Centre de Recherche des Cordeliers, CRC, Paris, France
| | - Michel Arthur
- Sorbonne Université, Sorbonne Paris Cité, Université de Paris, INSERM, Centre de Recherche des Cordeliers, CRC, Paris, France
| | - James C. Sacchettini
- Departments of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Carl Nathan
- Department of Microbiology & Immunology, Weill Cornell Medical College, New York, NY, United States
| | - Jeffrey Aubé
- Chemical Methodologies & Library Development Center, The University of Kansas, Lawrence, KS, United States
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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18
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Singh A, Turner JM, Tomberg J, Fedarovich A, Unemo M, Nicholas RA, Davies C. Mutations in penicillin-binding protein 2 from cephalosporin-resistant Neisseria gonorrhoeae hinder ceftriaxone acylation by restricting protein dynamics. J Biol Chem 2020; 295:7529-7543. [PMID: 32253235 PMCID: PMC7247294 DOI: 10.1074/jbc.ra120.012617] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 04/06/2020] [Indexed: 01/07/2023] Open
Abstract
The global incidence of the sexually transmitted disease gonorrhea is expected to rise due to the spread of Neisseria gonorrhoeae strains with decreased susceptibility to extended-spectrum cephalosporins (ESCs). ESC resistance is conferred by mosaic variants of penicillin-binding protein 2 (PBP2) that have diminished capacity to form acylated adducts with cephalosporins. To elucidate the molecular mechanisms of ESC resistance, we conducted a biochemical and high-resolution structural analysis of PBP2 variants derived from the decreased-susceptibility N. gonorrhoeae strain 35/02 and ESC-resistant strain H041. Our data reveal that mutations both lower affinity of PBP2 for ceftriaxone and restrict conformational changes that normally accompany acylation. Specifically, we observe that a G545S substitution hinders rotation of the β3 strand necessary to form the oxyanion hole for acylation and also traps ceftriaxone in a noncanonical configuration. In addition, F504L and N512Y substitutions appear to prevent bending of the β3-β4 loop that is required to contact the R1 group of ceftriaxone in the active site. Other mutations also appear to act by reducing flexibility in the protein. Overall, our findings reveal that restriction of protein dynamics in PBP2 underpins the ESC resistance of N. gonorrhoeae.
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Affiliation(s)
- Avinash Singh
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425
| | - Jonathan M Turner
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425
| | - Joshua Tomberg
- Departments of Pharmacology and Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Alena Fedarovich
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425
| | - Magnus Unemo
- WHO Collaborating Centre for Gonorrhoea and other STIs, Department of Laboratory Medicine, Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Robert A Nicholas
- Departments of Pharmacology and 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.
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19
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Olsen RJ, Zhu L, Musser JM. A Single Amino Acid Replacement in Penicillin-Binding Protein 2X in Streptococcus pyogenes Significantly Increases Fitness on Subtherapeutic Benzylpenicillin Treatment in a Mouse Model of Necrotizing Myositis. THE AMERICAN JOURNAL OF PATHOLOGY 2020; 190:1625-1631. [PMID: 32407732 DOI: 10.1016/j.ajpath.2020.04.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/14/2020] [Accepted: 04/21/2020] [Indexed: 12/15/2022]
Abstract
Invasive strains of Streptococcus pyogenes with significantly reduced susceptibility to β-lactam antibiotics have been recently described. These reports have caused considerable concern in the international infectious disease, medical microbiology, and public health communities because S. pyogenes has remained universally susceptible to β-lactam antibiotics for 70 years. Virtually all analyzed strains had single amino acid replacements in penicillin-binding protein 2X (PBP2X), a major target of β-lactam antibiotics in pathogenic bacteria. We used isogenic strains to test the hypothesis that a single amino acid replacement in PBP2X conferred a fitness advantage in a mouse model of necrotizing myositis. We determined that when mice were administered intermittent subtherapeutic dosing of benzylpenicillin, the strain with a Pro601Leu amino acid replacement in PBP2X that confers reduced β-lactam susceptibility in vitro was more fit, as assessed by the magnitude of colony-forming units recovered from disease tissue. These data provide important pathogenesis information that bears on this emerging global infectious disease problem.
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Affiliation(s)
- Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, Texas; Clinical Microbiology Laboratory, Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Luchang Zhu
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, Texas
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, Texas; Clinical Microbiology Laboratory, Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York.
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20
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Fiuza TS, Lima JPMS, de Souza GA. EpitoCore: Mining Conserved Epitope Vaccine Candidates in the Core Proteome of Multiple Bacteria Strains. Front Immunol 2020; 11:816. [PMID: 32431712 PMCID: PMC7214623 DOI: 10.3389/fimmu.2020.00816] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 04/09/2020] [Indexed: 12/30/2022] Open
Abstract
In reverse vaccinology approaches, complete proteomes of bacteria are submitted to multiple computational prediction steps in order to filter proteins that are possible vaccine candidates. Most available tools perform such analysis only in a single strain, or a very limited number of strains. But the vast amount of genomic data had shown that most bacteria contain pangenomes, i.e., their genomic information contains core, conserved genes, and random accessory genes specific to each strain. Therefore, in reverse vaccinology methods it is of the utmost importance to define core proteins and core epitopes. EpitoCore is a decision-tree pipeline developed to fulfill that need. It provides surfaceome prediction of proteins from related strains, defines core proteins within those, calculate their immunogenicity, predicts epitopes for a given set of MHC alleles defined by the user, and then reports if epitopes are located extracellularly and if they are conserved among the core homologs. Pipeline performance is illustrated by mining peptide vaccine candidates in Mycobacterium avium hominissuis strains. From a total proteome of ~4,800 proteins per strain, EpitoCore predicted 103 highly immunogenic core homologs located at cell surface, many of those related to virulence and drug resistance. Conserved epitopes identified among these homologs allows the users to define sets of peptides with potential to immunize the largest coverage of tested HLA alleles using peptide-based vaccines. Therefore, EpitoCore is able to provide automated identification of conserved epitopes in bacterial pangenomic datasets.
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Affiliation(s)
- Tayna S. Fiuza
- Bioinformatics Multidisciplinary Environment, Universidade Federal do Rio Grande Do Norte-UFRN, Natal, Brazil
| | - João P. M. S. Lima
- Bioinformatics Multidisciplinary Environment, Universidade Federal do Rio Grande Do Norte-UFRN, Natal, Brazil
- Department of Biochemistry, Universidade Federal do Rio Grande do Norte-UFRN, Natal, Brazil
| | - Gustavo A. de Souza
- Bioinformatics Multidisciplinary Environment, Universidade Federal do Rio Grande Do Norte-UFRN, Natal, Brazil
- Department of Biochemistry, Universidade Federal do Rio Grande do Norte-UFRN, Natal, Brazil
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21
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Hayes K, O'Halloran F, Cotter L. A review of antibiotic resistance in Group B Streptococcus: the story so far. Crit Rev Microbiol 2020; 46:253-269. [PMID: 32363979 DOI: 10.1080/1040841x.2020.1758626] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Group B Streptococcus (GBS) is the leading cause of neonatal disease worldwide, and invasive disease in adults is becoming more prevalent. Currently, some countries adopt an intrapartum antibiotic prophylaxis regime to help prevent the transmission of GBS from mother to neonate during delivery. This precaution has reduced the incidence of GBS-associated early-onset disease; however, rates of late-onset disease and stillbirths associated with GBS infections remain unchanged. GBS is still recognized as being universally susceptible to beta-lactam antibiotics; however, there have been reports of reduced susceptibility to beta-lactams, including penicillin, in some countries. Resistance to second-line antibiotics, such as erythromycin and clindamycin, remains high amongst GBS, with several countries noting increased resistance rates in recent years. Moreover, resistance to other antibiotic classes, such as fluoroquinolones and aminoglycosides, also continues to rise. In instances where patients are allergic to penicillin and second-line antibiotics are ineffective, vancomycin is administered. While vancomycin, a last resort antibiotic, still remains largely effective, there have been two documented cases of vancomycin resistance in GBS. This review provides a comprehensive analysis of the prevalence of antibiotic resistance in GBS and outlines the specific resistance mechanisms identified in GBS isolates to date.
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22
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Leonard A, Möhlis K, Schlüter R, Taylor E, Lalk M, Methling K. Exploring metabolic adaptation of Streptococcus pneumoniae to antibiotics. J Antibiot (Tokyo) 2020; 73:441-454. [PMID: 32210362 PMCID: PMC7292801 DOI: 10.1038/s41429-020-0296-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 01/31/2020] [Accepted: 02/09/2020] [Indexed: 02/07/2023]
Abstract
The Gram-positive bacterium Streptococcus pneumoniae is one of the common causes of community acquired pneumonia, meningitis, and otitis media. Analyzing the metabolic adaptation toward environmental stress conditions improves our understanding of its pathophysiology and its dependency on host-derived nutrients. In this study, extra- and intracellular metabolic profiles were evaluated to investigate the impact of antimicrobial compounds targeting different pathways of the metabolome of S. pneumoniae TIGR4Δcps. For the metabolomics approach, we analyzed the complex variety of metabolites by using 1H NMR, HPLC-MS, and GC–MS as different analytical techniques. Through this combination, we detected nearly 120 metabolites. For each antimicrobial compound, individual metabolic effects were detected that often comprised global biosynthetic pathways. Cefotaxime altered amino acids metabolism and carbon metabolism. The purine and pyrimidine metabolic pathways were mostly affected by moxifloxacin treatment. The combination of cefotaxime and azithromycin intensified the stress response compared with the use of the single antibiotic. However, we observed that three cell wall metabolites were altered only by treatment with the combination of the two antibiotics. Only moxifloxacin stress-induced alternation in CDP-ribitol concentration. Teixobactin-Arg10 resulted in global changes of pneumococcal metabolism. To meet the growing requirements for new antibiotics, our metabolomics approach has shown to be a promising complement to other OMICs investigations allowing insights into the mode of action of novel antimicrobial compounds.
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Affiliation(s)
- Anne Leonard
- Institute for Biochemistry, Metabolomics, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Kevin Möhlis
- Institute for Biochemistry, Metabolomics, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Rabea Schlüter
- Imaging Center of the Department of Biology, University of Greifswald, F.-L-Jahn-Str. 15, 17489, Greifswald, Germany
| | - Edward Taylor
- University of Lincoln, School of Life Sciences, Green Lane, LN67DL, Lincoln, England, United Kingdom
| | - Michael Lalk
- Institute for Biochemistry, Metabolomics, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Karen Methling
- Institute for Biochemistry, Metabolomics, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany.
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23
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Reduced In Vitro Susceptibility of Streptococcus pyogenes to β-Lactam Antibiotics Associated with Mutations in the pbp2x Gene Is Geographically Widespread. J Clin Microbiol 2020; 58:JCM.01993-19. [PMID: 31996443 DOI: 10.1128/jcm.01993-19] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 01/15/2020] [Indexed: 12/31/2022] Open
Abstract
Recently, two related Streptococcus pyogenes strains with reduced susceptibility to ampicillin, amoxicillin, and cefotaxime, antibiotics commonly used to treat S. pyogenes infections, were reported. The two strains had the same nonsynonymous (amino acid-substituting) mutation in the pbp2x gene, encoding penicillin-binding protein 2X (PBP2X). This concerning report led us to investigate our library of 7,025 genome sequences of type emm1, emm28, and emm89 S. pyogenes clinical strains recovered from intercontinental sources for mutations in pbp2x We identified 137 strains that, combined, had 37 nonsynonymous mutations in 36 codons in pbp2x Although to a lesser magnitude than the two previously published isolates, many of our strains had decreased susceptibility in vitro to multiple beta-lactam antibiotics. Many pbp2x mutations were found only in single strains, but 16 groups of two or more isolates of the same emm type had an identical amino acid replacement. Phylogenetic analysis showed that, with one exception, strains of the same emm type with the same amino acid replacement were clonally related by descent. This finding indicates that strains with some amino acid changes in PBP2X can successfully spread to new human hosts and cause invasive infections. Mapping of the amino acid changes onto a three-dimensional structure of the related Streptococcus pneumoniae PBP2X suggests that some substitutions are located in regions functionally important in related pathogenic bacterial species. Decreased beta-lactam susceptibility is geographically widespread in strains of numerically common emm gene subtypes. Enhanced surveillance and further epidemiological and molecular genetic study of this potential emergent antimicrobial problem are warranted.
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Kazi A, Hisyam Ismail CMK, Anthony AA, Chuah C, Leow CH, Lim BH, Banga Singh KK, Leow CY. Designing and evaluation of an antibody-targeted chimeric recombinant vaccine encoding Shigella flexneri outer membrane antigens. INFECTION GENETICS AND EVOLUTION 2020; 80:104176. [PMID: 31923724 DOI: 10.1016/j.meegid.2020.104176] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 01/03/2020] [Accepted: 01/05/2020] [Indexed: 11/16/2022]
Abstract
Shigellosis is one of the most common diseases found in the developing countries, especially those countries that are prone flood. The causative agent for this disease is the Shigella species. This organism is one of the third most common enteropathogens responsible for childhood diarrhea. Since Shigella can survive gastric acidity and is an intracellular pathogen, it becomes difficult to treat. Also, uncontrolled use of antibiotics has led to development of resistant strains which poses a threat to public health. Therefore, there is a need for long term control of Shigella infection which can be achieved by designing a proper and effective vaccine. In this study, emphasis was made on designing a candidate that could elicit both B-cell and T-cell immune response. Hence B- and T-cell epitopes of outer membrane channel protein (OM) and putative lipoprotein (PL) from S. flexneri 2a were computationally predicted using immunoinformatics approach and a chimeric construct (chimeric-OP) containing the immunogenic epitopes selected from OM and PL was designed, cloned and expressed in E. coli system. The immunogenicity of the recombinant chimeric-OP was assessed using Shigella antigen infected rabbit antibody. The result showed that the chimeric-OP was a synthetic peptide candidate suitable for the development of vaccine and immunodiagnostics against Shigella infection.
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Affiliation(s)
- Ada Kazi
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Kelantan, Malaysia
| | | | - Amy Amilda Anthony
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Candy Chuah
- School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Chiuan Herng Leow
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia
| | - Boon Huat Lim
- School of Health Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | | | - Chiuan Yee Leow
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Kelantan, Malaysia.
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25
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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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26
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Lalge R, Thipsay P, Shankar VK, Maurya A, Pimparade M, Bandari S, Zhang F, Murthy SN, Repka MA. Preparation and evaluation of cefuroxime axetil gastro-retentive floating drug delivery system via hot melt extrusion technology. Int J Pharm 2019; 566:520-531. [PMID: 31185262 DOI: 10.1016/j.ijpharm.2019.06.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 06/06/2019] [Accepted: 06/07/2019] [Indexed: 10/26/2022]
Abstract
Cefuroxime Axetil (CA) is a poorly soluble, broad spectrum antibiotic which undergoes enzymatic degradation in gastrointestinal tract. The objective of the present study was to develop lipid-based gastro-retentive floating drug delivery systems containing CA using hot-melt extrusion (HME) to improve absorption. Selected formulations of CA and lipids were extruded using a twin screw hot-melt extruder. Milled extrudates were characterized for dissolution, floating strength, and micromeritic properties. Solid-state characterization was performed using differential scanning calorimetry (DSC), scanning electron microscopy (SEM), Fourier transform infrared (FTIR) spectroscopy, and hot-stage microscopy. In vitro characterization demonstrated that the formulations exhibited a sustained drug release profile for 12 h. All formulations showed desired floating and flow properties. Solid-state characterization revealed no phase separation and no chemical interactions between the drug and excipients. Based on in vitro study results, an optimized formulation (F8) was further evaluated for in vivo performance. Oral bioavailability (Cmax and AUC0-24h) of F8 was significantly higher than that of pure CA. This study describes the use of lipid-based gastro-retentive floating drug delivery systems to achieve desired sustained release profile for more complete dissolution which could potentially reduce enzymatic degradation. This study also highlights the effectiveness of HME technology to improve dissolution and bioavailability.
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Affiliation(s)
- Rahul Lalge
- Department of Pharmaceutics and Drug Delivery, School of Pharmacy, The University of Mississippi, University, MS 38677, USA
| | - Priyanka Thipsay
- Department of Pharmaceutics and Drug Delivery, School of Pharmacy, The University of Mississippi, University, MS 38677, USA
| | - Vijay Kumar Shankar
- Department of Pharmaceutics and Drug Delivery, School of Pharmacy, The University of Mississippi, University, MS 38677, USA
| | - Abhijeet Maurya
- Department of Pharmaceutics and Drug Delivery, School of Pharmacy, The University of Mississippi, University, MS 38677, USA
| | - Manjeet Pimparade
- Department of Pharmaceutics and Drug Delivery, School of Pharmacy, The University of Mississippi, University, MS 38677, USA
| | - Suresh Bandari
- Department of Pharmaceutics and Drug Delivery, School of Pharmacy, The University of Mississippi, University, MS 38677, USA
| | - Feng Zhang
- College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, USA
| | - S Narasimha Murthy
- Department of Pharmaceutics and Drug Delivery, School of Pharmacy, The University of Mississippi, University, MS 38677, USA; Institute for Drug Delivery and Biomedical Research, Bangalore, India
| | - Michael A Repka
- Department of Pharmaceutics and Drug Delivery, School of Pharmacy, The University of Mississippi, University, MS 38677, USA; Pii Center for Pharmaceutical Innovation & Instruction, The University of Mississippi, University, MS 38677, USA.
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27
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Calvanese L, Falcigno L, Squeglia F, Berisio R, D’Auria G. PASTA sequence composition is a predictive tool for protein class identification. Amino Acids 2018; 50:1441-1450. [DOI: 10.1007/s00726-018-2621-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 07/13/2018] [Indexed: 12/18/2022]
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28
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Kar D, Pandey SD, Mallick S, Dutta M, Ghosh AS. Substitution of Alanine at Position 184 with Glutamic Acid in Escherichia coli PBP5 Ω-Like Loop Introduces a Moderate Cephalosporinase Activity. Protein J 2018; 37:122-131. [DOI: 10.1007/s10930-018-9765-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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29
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Bernardo-García N, Mahasenan KV, Batuecas MT, Lee M, Hesek D, Petráčková D, Doubravová L, Branny P, Mobashery S, Hermoso JA. Allostery, Recognition of Nascent Peptidoglycan, and Cross-linking of the Cell Wall by the Essential Penicillin-Binding Protein 2x of Streptococcus pneumoniae. ACS Chem Biol 2018; 13:694-702. [PMID: 29357220 DOI: 10.1021/acschembio.7b00817] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Transpeptidases, members of the penicillin-binding protein (PBP) families, catalyze cross-linking of the bacterial cell wall. This transformation is critical for the survival of bacteria, and it is the target of inhibition by β-lactam antibiotics. We report herein our structural insights into catalysis by the essential PBP2x of Streptococcus pneumoniae by disclosing a total of four X-ray structures, two computational models based on the crystal structures, and molecular-dynamics simulations. The X-ray structures are for the apo PBP2x, the enzyme modified covalently in the active site by oxacillin (a penicillin antibiotic), the enzyme modified by oxacillin in the presence of a synthetic tetrasaccharide surrogate for the cell-wall peptidoglycan, and a noncovalent complex of cefepime (a cephalosporin antibiotic) bound to the active site. A prerequisite for catalysis by transpeptidases, including PBP2x, is the molecular recognition of nascent peptidoglycan strands, which harbor pentapeptide stems. We disclose that the recognition of nascent peptidoglycan by PBP2x takes place by complexation of one pentapeptide stem at an allosteric site located in the PASTA domains of this enzyme. This binding predisposes the third pentapeptide stem in the same nascent peptidoglycan strand to penetration into the active site for the turnover events. The complexation of the two pentapeptide stems in the same peptidoglycan strand is a recognition motif for the nascent peptidoglycan, critical for the cell-wall cross-linking reaction.
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Affiliation(s)
- Noelia Bernardo-García
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry “Rocasolano,” CSIC, 28006 Madrid, Spain
| | - Kiran V. Mahasenan
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - María T. Batuecas
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry “Rocasolano,” CSIC, 28006 Madrid, Spain
| | - Mijoon Lee
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Dusan Hesek
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Denisa Petráčková
- Institute of Microbiology, v.v.i, Czech Academy of Sciences, Prague 4, 142 20, Czech Republic
| | - Linda Doubravová
- Institute of Microbiology, v.v.i, Czech Academy of Sciences, Prague 4, 142 20, Czech Republic
| | - Pavel Branny
- Institute of Microbiology, v.v.i, Czech Academy of Sciences, Prague 4, 142 20, Czech Republic
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Juan A. Hermoso
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry “Rocasolano,” CSIC, 28006 Madrid, Spain
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30
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Adediran SA, Sarkar KS, Pratt RF. Kinetic Evidence for a Second Ligand Binding Site on Streptococcus pneumoniae Penicillin-Binding Protein 2x. Biochemistry 2018; 57:1758-1766. [PMID: 29485264 DOI: 10.1021/acs.biochem.7b01209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
High molecular mass penicillin-binding proteins (PBPs, DD-peptidases) of class B, such as Streptococcus pneumoniae PBP2x, catalyze the cross-linking of peptidoglycan in bacterial cell wall biosynthesis and are thus important antibiotic targets. Despite their importance in this regard, structure-function studies of ligands of these enzymes have been impeded by the absence of useful substrates. In vitro, these enzymes do not catalyze peptide hydrolysis or aminolysis, their in vivo reaction, but some, such as PBP2x, do catalyze these reactions of certain thioesters such as PhCH2CONHCH2COSCH(D-Me)CO2- (2). We have now prepared several peptidoglycan-mimetic thioesters that we expected to more closely resemble the natural substrates of these enzymes. To our surprise, however, these compounds, although indeed substrates of PBP2x, did not, unlike 2, appear to form an acyl-enzyme intermediate during hydrolysis, and their turnover was inhibited by certain peptides and N-acylamino acids much more weakly than that of 2. An inhibitor of this type, N-benzyloxycarbonyl-d-glutamic acid, also quenched the fluorescence of PBP2x that had been labeled at the DD-peptidase active site by 6-dansylamidopenicillanic acid. These results were interpreted in terms of a model where the peptidoglycan-mimetic thioesters preferentially bound to and hydrolyzed at a site other than the classical DD-peptidase active site. This second site is likely to represent part of an extended binding site that accommodates a peptidoglycan substrate or regulator in vivo. Such a site may be a target for future inhibitor/antibiotic design.
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Affiliation(s)
- S A Adediran
- Department of Chemistry , Wesleyan University , Lawn Avenue , Middletown , Connecticut 06459 , United States
| | - Kumar Subarno Sarkar
- Department of Chemistry , Wesleyan University , Lawn Avenue , Middletown , Connecticut 06459 , United States
| | - R F Pratt
- Department of Chemistry , Wesleyan University , Lawn Avenue , Middletown , Connecticut 06459 , United States
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31
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Zucchini L, Mercy C, Garcia PS, Cluzel C, Gueguen-Chaignon V, Galisson F, Freton C, Guiral S, Brochier-Armanet C, Gouet P, Grangeasse C. PASTA repeats of the protein kinase StkP interconnect cell constriction and separation of Streptococcus pneumoniae. Nat Microbiol 2018; 3:197-209. [PMID: 29203882 DOI: 10.1038/s41564-017-0069-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 10/23/2017] [Indexed: 11/09/2022]
Abstract
Eukaryotic-like serine/threonine kinases (eSTKs) with extracellular PASTA repeats are key membrane regulators of bacterial cell division. How PASTA repeats govern eSTK activation and function remains elusive. Using evolution- and structural-guided approaches combined with cell imaging, we disentangle the role of each PASTA repeat of the eSTK StkP from Streptococcus pneumoniae. While the three membrane-proximal PASTA repeats behave as interchangeable modules required for the activation of StkP independently of cell wall binding, they also control the septal cell wall thickness. In contrast, the fourth and membrane-distal PASTA repeat directs StkP localization at the division septum and encompasses a specific motif that is critical for final cell separation through interaction with the cell wall hydrolase LytB. We propose a model in which the extracellular four-PASTA domain of StkP plays a dual function in interconnecting the phosphorylation of StkP endogenous targets along with septal cell wall remodelling to allow cell division of the pneumococcus.
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Affiliation(s)
- Laure Zucchini
- Molecular Microbiology and Structural Biochemistry, Unité Mixte de Recherche, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Lyon, France
| | - Chryslène Mercy
- Molecular Microbiology and Structural Biochemistry, Unité Mixte de Recherche, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Lyon, France
| | - Pierre Simon Garcia
- Molecular Microbiology and Structural Biochemistry, Unité Mixte de Recherche, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Lyon, France
- Laboratoire de Biométrie et Biologie Evolutive, Unité Mixte de Recherche, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Villeurbanne, France
| | - Caroline Cluzel
- Laboratoire de Biologie Tissulaire et d'Ingénierie Thérapeutique, Unité Mixte de Recherche, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Lyon, France
| | - Virginie Gueguen-Chaignon
- Protein Science Facility, Structure Fédérative de Recherche Biosciences/UMS3444/US8, Université Claude Bernard Lyon 1, Ecole Normale Supérieur de Lyon, INSERM, Centre National de la Recherche Scientifique, Lyon, France
| | - Frédéric Galisson
- Molecular Microbiology and Structural Biochemistry, Unité Mixte de Recherche, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Lyon, France
| | - Céline Freton
- Molecular Microbiology and Structural Biochemistry, Unité Mixte de Recherche, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Lyon, France
| | - Sébastien Guiral
- Molecular Microbiology and Structural Biochemistry, Unité Mixte de Recherche, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Lyon, France
| | - Céline Brochier-Armanet
- Laboratoire de Biométrie et Biologie Evolutive, Unité Mixte de Recherche, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Villeurbanne, France
| | - Patrice Gouet
- Molecular Microbiology and Structural Biochemistry, Unité Mixte de Recherche, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Lyon, France
| | - Christophe Grangeasse
- Molecular Microbiology and Structural Biochemistry, Unité Mixte de Recherche, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Lyon, France.
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32
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Diversity of Mosaic pbp2x Families in Penicillin-Resistant Streptococcus pneumoniae from Iran and Romania. Antimicrob Agents Chemother 2017; 61:AAC.01535-17. [PMID: 28971878 PMCID: PMC5700355 DOI: 10.1128/aac.01535-17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 09/19/2017] [Indexed: 11/20/2022] Open
Abstract
Penicillin-resistant Streptococcus pneumoniae strains are found at high rates in Romania and Iran. The mosaic structure of PBP2x was investigated in 9 strains from Iran and in 15 strains from Romania to understand their evolutionary history. Mutations potentially important for β-lactam resistance were identified by comparison of the PBP2x sequences with the sequence of the related PBP2x of reference penicillin-sensitive S. mitis strains. Two main PBP2x mosaic gene families were recognized. Eight Iranian strains expressed PBP2x variants in group 1, which had a mosaic block highly related to PBP2x of the Spain23F-1 clone, which is widespread among international penicillin-resistant S. pneumoniae clones. A second unique PBP2x group was observed in Romanian strains; furthermore, three PBP2x single mosaic variants were found. Sequence blocks of penicillin-sensitive strain S. mitis 658 were common among PBP2x variants from strains from both countries. Each PBP2x group contained specific signature mutations within the transpeptidase domain, documenting the existence of distinct mutational pathways for the development of penicillin resistance.
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33
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Sharifzadeh S, Boersma MJ, Kocaoglu O, Shokri A, Brown CL, Shirley JD, Winkler ME, Carlson EE. Novel Electrophilic Scaffold for Imaging of Essential Penicillin-Binding Proteins in Streptococcus pneumoniae. ACS Chem Biol 2017; 12:2849-2857. [PMID: 28990753 DOI: 10.1021/acschembio.7b00614] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptidoglycan (PG) is a mesh-like heteropolymer made up of glycan chains cross-linked by short peptides and is the major scaffold of eubacterial cell walls, determining cell shape, size, and chaining. This structure, which is required for growth and survival, is located outside of the cytoplasmic membrane of bacterial cells, making it highly accessible to antibiotics. Penicillin-binding proteins (PBPs) are essential for construction of PG and perform transglycosylase activities to generate the glycan strands and transpeptidation to cross-link the appended peptides. The β-lactam antibiotics, which are among the most clinically effective antibiotics for the treatment of bacterial infections, inhibit PBP transpeptidation, ultimately leading to cell lysis. Despite this importance, the discrete functions of individual PBP homologues have been difficult to determine. These major gaps in understanding of PBP activation and macromolecular interactions largely result from a lack of tools to assess the functional state of specific PBPs in bacterial cells. We have identified β-lactones as a privileged scaffold for the generation of PBP-selective probes and utilized these compounds for imaging of the essential proteins, PBP2x and PBP2b, in Streptococcus pneumoniae. We demonstrated that while PBP2b activity is restricted to a ring surrounding the division sites, PBP2x activity is present both at the septal center and at the surrounding ring. These spatially separate regions of PBP2x activity could not be detected by previous activity-based approaches, which highlights a critical strength of our PBP-selective imaging strategy.
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Affiliation(s)
- Shabnam Sharifzadeh
- Departments
of Chemistry, ‡Medicinal Chemistry, and Biochemistry, §Molecular Biology
and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Departments of Biology, ⊥Molecular and Cellular Biochemistry,
and #Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Michael J. Boersma
- Departments
of Chemistry, ‡Medicinal Chemistry, and Biochemistry, §Molecular Biology
and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Departments of Biology, ⊥Molecular and Cellular Biochemistry,
and #Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Ozden Kocaoglu
- Departments
of Chemistry, ‡Medicinal Chemistry, and Biochemistry, §Molecular Biology
and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Departments of Biology, ⊥Molecular and Cellular Biochemistry,
and #Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Alireza Shokri
- Departments
of Chemistry, ‡Medicinal Chemistry, and Biochemistry, §Molecular Biology
and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Departments of Biology, ⊥Molecular and Cellular Biochemistry,
and #Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Clayton L. Brown
- Departments
of Chemistry, ‡Medicinal Chemistry, and Biochemistry, §Molecular Biology
and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Departments of Biology, ⊥Molecular and Cellular Biochemistry,
and #Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Joshua D. Shirley
- Departments
of Chemistry, ‡Medicinal Chemistry, and Biochemistry, §Molecular Biology
and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Departments of Biology, ⊥Molecular and Cellular Biochemistry,
and #Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Malcolm E. Winkler
- Departments
of Chemistry, ‡Medicinal Chemistry, and Biochemistry, §Molecular Biology
and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Departments of Biology, ⊥Molecular and Cellular Biochemistry,
and #Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Erin E. Carlson
- Departments
of Chemistry, ‡Medicinal Chemistry, and Biochemistry, §Molecular Biology
and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Departments of Biology, ⊥Molecular and Cellular Biochemistry,
and #Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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Wang Q, Marchetti R, Prisic S, Ishii K, Arai Y, Ohta I, Inuki S, Uchiyama S, Silipo A, Molinaro A, Husson RN, Fukase K, Fujimoto Y. A Comprehensive Study of the Interaction between Peptidoglycan Fragments and the Extracellular Domain of Mycobacterium tuberculosis Ser/Thr Kinase PknB. Chembiochem 2017; 18:2094-2098. [PMID: 28851116 PMCID: PMC6261334 DOI: 10.1002/cbic.201700385] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Indexed: 11/07/2022]
Abstract
The Mycobacterium tuberculosis Ser/Thr kinase PknB is implicated in the regulation of bacterial cell growth and cell division. The intracellular kinase function of PknB is thought to be triggered by peptidoglycan (PGN) fragments that are recognized by the extracytoplasmic domain of PknB. The PGN in the cell wall of M. tuberculosis has several unusual modifications, including the presence of N-glycolyl groups (in addition to N-acetyl groups) in the muramic acid residues and amidation of d-Glu in the peptide chains. Using synthetic PGN fragments incorporating these diverse PGN structures, we analyzed their binding characters through biolayer interferometry (BLI), NMR spectroscopy, and native mass spectrometry (nMS) techniques. The results of BLI showed that muropeptides containing 1,6-anhydro-MurNAc and longer glycan chains exhibited higher binding potency and that the fourth amino acid of the peptide stem, d-Ala, was crucial for protein recognition. Saturation transfer difference (STD) NMR spectroscopy indicated the major involvement of the stem peptide region in the PASTA-PGN fragment binding. nMS suggested that the binding stoichiometry was 1:1. The data provide the first molecular basis for the specific interaction of PGN with PknB and firmly establish PGNs as the effective ligands of PknB.
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Affiliation(s)
- Qianqian Wang
- Faculty of Science and Technology, Keio University, Hiyoshi 3--14-1, Yokohama, Kanagawa 223--8522 (Japan),
- Graduate School of Science, Osaka University, Machikaneyama 1-1, Toyonaka, Osaka 560--0043 (Japan)
| | - Roberta Marchetti
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cinthia 4, 80126 Napoli (Italy)
| | - Sladjana Prisic
- Division of Infectious Disease, Children’s Hospital Boston, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115 (USA),
| | - Kentaro Ishii
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444--8787 (Japan)
| | - Yohei Arai
- Faculty of Science and Technology, Keio University, Hiyoshi 3--14-1, Yokohama, Kanagawa 223--8522 (Japan),
| | - Ippei Ohta
- Faculty of Science and Technology, Keio University, Hiyoshi 3--14-1, Yokohama, Kanagawa 223--8522 (Japan),
| | - Shinsuke Inuki
- Faculty of Science and Technology, Keio University, Hiyoshi 3--14-1, Yokohama, Kanagawa 223--8522 (Japan),
| | - Susumu Uchiyama
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444--8787 (Japan)
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565--0871 (Japan)
| | - Alba Silipo
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cinthia 4, 80126 Napoli (Italy)
| | - Antonio Molinaro
- Graduate School of Science, Osaka University, Machikaneyama 1-1, Toyonaka, Osaka 560--0043 (Japan)
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cinthia 4, 80126 Napoli (Italy)
| | - Robert N. Husson
- Division of Infectious Disease, Children’s Hospital Boston, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115 (USA),
| | - Koichi Fukase
- Graduate School of Science, Osaka University, Machikaneyama 1-1, Toyonaka, Osaka 560--0043 (Japan)
| | - Yukari Fujimoto
- Faculty of Science and Technology, Keio University, Hiyoshi 3--14-1, Yokohama, Kanagawa 223--8522 (Japan),
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Oodate M, Kimura K, Banno H, Yokoyama S, Jin W, Wachino JI, Hasegawa Y, Arakawa Y. Predominance of Serogroup 19 CC320/271 among Penicillin-Nonsusceptible Streptococcus pneumoniae Isolates after Introduction of the PCV7 Vaccine in Several Regions of Japan. Jpn J Infect Dis 2017; 71:14-20. [PMID: 29093321 DOI: 10.7883/yoken.jjid.2017.236] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Multidrug-resistant Streptococcus pneumoniae serogroup 19, including serotypes 19A and 19F, associated with clonal complex 320/271 (CC320/271), has been previously shown to be predominant in many countries after introduction of a 7-valent pneumococcal conjugate vaccine (PCV7). However, in Japan there has been no epidemiological research focused on penicillin-nonsusceptible isolates after this event. Therefore, we aimed to characterize penicillin-nonsusceptible S. pneumoniae (PNSSP; penicillin minimum inhibitory concentration [MIC] ≥ 4.0 μg/ml) after the introduction of PCV7 in Japan. Throughout Japan, we collected 1,057 pneumococcal isolates from 2010 to 2014. We then evaluated MICs and performed serotyping, multilocus sequence typing, and sequencing of penicillin-binding protein genes in 51 isolates (penicillin MIC ≥ 2.0 μg/ml). Twenty-three isolates (2.2%) showed penicillin nonsusceptibility (penicillin MIC ≥ 4.0 μg/ml). Serotypes 19F (14 isolates, 60.9%) and 23F (4 isolates, 17.4%), which are covered by the vaccine, were predominant among PNSSP strains. Only 3 isolates belonged to nonvaccine serotype 19A. Among the PNSSP isolates, CC320/271 (16/23 strains, 69.6%) was the most prevalent clone. Moreover, CC320/271 clones showed high MIC values of a third-generation cephalosporin. Thus, we demonstrated clonal predominance of serogroup 19 CC320/271 with strong resistance to β-lactams including a third-generation cephalosporin among PNSSP isolates.
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Affiliation(s)
- Mitsuru Oodate
- Department of Bacteriology, Nagoya University Graduate School of Medicine.,Department of Respiratory Medicine, Nagoya University Graduate School of Medicine
| | - Kouji Kimura
- Department of Bacteriology, Nagoya University Graduate School of Medicine
| | - Hirotsugu Banno
- Department of Bacteriology, Nagoya University Graduate School of Medicine
| | - Satoru Yokoyama
- Department of Bacteriology, Nagoya University Graduate School of Medicine
| | - Wanchun Jin
- Department of Bacteriology, Nagoya University Graduate School of Medicine
| | - Jun-Ichi Wachino
- Department of Bacteriology, Nagoya University Graduate School of Medicine
| | - Yoshinori Hasegawa
- Department of Respiratory Medicine, Nagoya University Graduate School of Medicine
| | - Yoshichika Arakawa
- Department of Bacteriology, Nagoya University Graduate School of Medicine
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36
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Pensinger DA, Schaenzer AJ, Sauer JD. Do Shoot the Messenger: PASTA Kinases as Virulence Determinants and Antibiotic Targets. Trends Microbiol 2017; 26:56-69. [PMID: 28734616 DOI: 10.1016/j.tim.2017.06.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 06/15/2017] [Accepted: 06/27/2017] [Indexed: 01/14/2023]
Abstract
All domains of life utilize protein phosphorylation as a mechanism of signal transduction. In bacteria, protein phosphorylation was classically thought to be mediated exclusively by histidine kinases as part of two-component signaling systems. However, it is now well appreciated that eukaryotic-like serine/threonine kinases (eSTKs) control essential processes in bacteria. A subset of eSTKs are single-pass transmembrane proteins that have extracellular penicillin-binding-protein and serine/threonine kinase-associated (PASTA) domains which bind muropeptides. In a variety of important pathogens, PASTA kinases have been implicated in regulating biofilms, antibiotic resistance, and ultimately virulence. Although there are limited examples of direct regulation of virulence factors, PASTA kinases are critical for virulence due to their roles in regulating bacterial physiology in the context of stress. This review focuses on the role of PASTA kinases in virulence for a variety of important Gram-positive pathogens and concludes with a discussion of current efforts to develop kinase inhibitors as novel antimicrobials.
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Affiliation(s)
- Daniel A Pensinger
- Microbiology Doctoral Training Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Adam J Schaenzer
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA; Molecular and Cellular Pharmacology Doctoral Training Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - John-Demian Sauer
- Microbiology Doctoral Training Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA; Molecular and Cellular Pharmacology Doctoral Training Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA.
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37
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Insight into the Diversity of Penicillin-Binding Protein 2x Alleles and Mutations in Viridans Streptococci. Antimicrob Agents Chemother 2017; 61:AAC.02646-16. [PMID: 28193649 PMCID: PMC5404556 DOI: 10.1128/aac.02646-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 01/24/2017] [Indexed: 11/20/2022] Open
Abstract
The identification of commensal streptococci species is an everlasting problem due to their ability to genetically transform. A new challenge in this respect is the recent description of Streptococcus pseudopneumoniae as a new species, which was distinguished from closely related pathogenic S. pneumoniae and commensal S. mitis by a variety of physiological and molecular biological tests. Forty-one atypical S. pneumoniae isolates have been collected at the German National Reference Center for Streptococci (GNRCS). Multilocus sequence typing (MLST) confirmed 35 isolates as the species S. pseudopneumoniae. A comparison with the pbp2x sequences from 120 commensal streptococci isolated from different continents revealed that pbp2x is distinct among penicillin-susceptible S. pseudopneumoniae isolates. Four penicillin-binding protein x (PBPx) alleles of penicillin-sensitive S. mitis account for most of the diverse sequence blocks in resistant S. pseudopneumoniae, S. pneumoniae, and S. mitis, and S. infantis and S. oralis sequences were found in S. pneumoniae from Japan. PBP2x genes of the family of mosaic genes related to pbp2x in the S. pneumoniae clone Spain23F-1 were observed in S. oralis and S. infantis as well, confirming its global distribution. Thirty-eight sites were altered within the PBP2x transpeptidase domains of penicillin-resistant strains, excluding another 37 sites present in the reference genes of sensitive strains. Specific mutational patterns were detected depending on the parental sequence blocks, in agreement with distinct mutational pathways during the development of beta-lactam resistance. The majority of the mutations clustered around the active site, whereas others are likely to affect stability or interactions with the C-terminal domain or partner proteins.
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38
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Calvez P, Breukink E, Roper DI, Dib M, Contreras-Martel C, Zapun A. Substitutions in PBP2b from β-Lactam-resistant Streptococcus pneumoniae Have Different Effects on Enzymatic Activity and Drug Reactivity. J Biol Chem 2017; 292:2854-2865. [PMID: 28062575 DOI: 10.1074/jbc.m116.764696] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 12/22/2016] [Indexed: 12/31/2022] Open
Abstract
Pneumococcus resists β-lactams by expressing variants of its target enzymes, the penicillin-binding proteins (PBPs), with many amino acid substitutions. Up to 10% of the sequence can be modified. These altered PBPs have a much reduced reactivity with the drugs but retain their physiological activity of cross-linking the peptidoglycan, the major constituent of the bacterial cell wall. However, because β-lactams are chemical and structural mimics of the natural substrate, resistance mediated by altered PBPs raises the following paradox: how PBPs that react poorly with the drugs maintain a sufficient level of activity with the physiological substrate. This question is addressed for the first time in this study, which compares the peptidoglycan cross-linking activity of PBP2b from susceptible and resistant strains with their inhibition by different β-lactams. Unexpectedly, the enzymatic activity of the variants did not correlate with their antibiotic reactivity. This finding indicates that some of the numerous amino acid substitutions were selected to restore a viable level of enzymatic activity by a compensatory molecular mechanism.
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Affiliation(s)
- Philippe Calvez
- From the Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Eefjan Breukink
- the Department of Chemical Biology and Organic Chemistry, Institute of Biomembranes, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht 3584 CH, The Netherlands, and
| | - David I Roper
- the School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Mélanie Dib
- From the Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Carlos Contreras-Martel
- From the Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - André Zapun
- From the Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France,
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39
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Hardt P, Engels I, Rausch M, Gajdiss M, Ulm H, Sass P, Ohlsen K, Sahl HG, Bierbaum G, Schneider T, Grein F. The cell wall precursor lipid II acts as a molecular signal for the Ser/Thr kinase PknB of Staphylococcus aureus. Int J Med Microbiol 2016; 307:1-10. [PMID: 27989665 DOI: 10.1016/j.ijmm.2016.12.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 11/22/2016] [Accepted: 12/10/2016] [Indexed: 12/23/2022] Open
Abstract
The assembly of the bacterial cell wall requires synchronization of a multitude of biosynthetic machineries and regulatory networks. The eukaryotic-like serine/threonine kinase PknB has been implicated in coordinating cross-wall formation, autolysis and cell division in Staphylococcus aureus. However, the signal molecule sensed by this kinase remained elusive so far. Here, we provide compelling biochemical evidence that PknB interacts with the ultimate cell wall precursor lipid II, triggering kinase activity. Moreover, we observed crosstalk of PknB with the two component system WalKR and identified the early cell division protein FtsZ as another PknB phosphorylation substrate in S. aureus. In agreement with the implied role in regulation of cell envelope metabolism, we found PknB to preferentially localize to the septum of S. aureus and the PASTA domains to be crucial for recruitment to this site. The data provide a model for the contribution of PknB to control cell wall metabolism and cell division.
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Affiliation(s)
- Patrick Hardt
- Institute for Pharmaceutical Microbiology, University of Bonn, Bonn, Germany
| | - Ina Engels
- Institute for Pharmaceutical Microbiology, University of Bonn, Bonn, Germany; German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Bonn, Germany
| | - Marvin Rausch
- Institute for Pharmaceutical Microbiology, University of Bonn, Bonn, Germany; German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Bonn, Germany
| | - Mike Gajdiss
- Institute of Medical Microbiology, Immunology and Parasitology, University of Bonn, Bonn, Germany
| | - Hannah Ulm
- Institute for Pharmaceutical Microbiology, University of Bonn, Bonn, Germany
| | - Peter Sass
- Interfaculty Institute for Microbiology and Infection Medicine, Department for Microbial Bioactive Compounds, University of Tuebingen, Tuebingen, Germany
| | - Knut Ohlsen
- Institute for Molecular Infection Biology, University of Wuerzburg, Wuerzburg, Germany
| | - Hans-Georg Sahl
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Bonn, Germany; Institute of Medical Microbiology, Immunology and Parasitology, University of Bonn, Bonn, Germany
| | - Gabriele Bierbaum
- Institute of Medical Microbiology, Immunology and Parasitology, University of Bonn, Bonn, Germany
| | - Tanja Schneider
- Institute for Pharmaceutical Microbiology, University of Bonn, Bonn, Germany; German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Bonn, Germany.
| | - Fabian Grein
- Institute for Pharmaceutical Microbiology, University of Bonn, Bonn, Germany; German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Bonn, Germany.
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40
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Gerogiokas G, Southey MWY, Mazanetz MP, Heifetz A, Bodkin M, Law RJ, Henchman RH, Michel J. Assessment of Hydration Thermodynamics at Protein Interfaces with Grid Cell Theory. J Phys Chem B 2016; 120:10442-10452. [PMID: 27645529 DOI: 10.1021/acs.jpcb.6b07993] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Molecular dynamics simulations have been analyzed with the Grid Cell Theory (GCT) method to spatially resolve the binding enthalpies and entropies of water molecules at the interface of 17 structurally diverse proteins. Correlations between computed energetics and structural descriptors have been sought to facilitate the development of simple models of protein hydration. Little correlation was found between GCT-computed binding enthalpies and continuum electrostatics calculations. A simple count of contacts with functional groups in charged amino acids correlates well with enhanced water stabilization, but the stability of water near hydrophobic and polar residues depends markedly on its coordination environment. The positions of X-ray-resolved water molecules correlate with computed high-density hydration sites, but many unresolved waters are significantly stabilized at the protein surfaces. A defining characteristic of ligand-binding pockets compared to nonbinding pockets was a greater solvent-accessible volume, but average water thermodynamic properties were not distinctive from other interfacial regions. Interfacial water molecules are frequently stabilized by enthalpy and destabilized entropy with respect to bulk, but counter-examples occasionally occur. Overall detailed inspection of the local coordinating environment appears necessary to gauge the thermodynamic stability of water in protein structures.
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Affiliation(s)
- Georgios Gerogiokas
- EaStCHEM School of Chemistry , Joseph Black Building, The King's Buildings, Edinburgh EH9 3JJ, United Kingdom
| | - Michelle W Y Southey
- Evotec (U.K.) Limited , 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
| | - Michael P Mazanetz
- Evotec (U.K.) Limited , 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
| | - Alexander Heifetz
- Evotec (U.K.) Limited , 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
| | - Michael Bodkin
- Evotec (U.K.) Limited , 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
| | - Richard J Law
- Evotec (U.K.) Limited , 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4SA, United Kingdom
| | - Richard H Henchman
- Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom.,School of Chemistry, The University of Manchester , Oxford Road, Manchester M13 9PL, United Kingdom
| | - J Michel
- EaStCHEM School of Chemistry , Joseph Black Building, The King's Buildings, Edinburgh EH9 3JJ, United Kingdom
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41
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Irajie C, Mohkam M, Nezafat N, Hosseinzadeh S, Aminlari M, Ghasemi Y. In Silico Analysis of Glutaminase from Different Species of Escherichia and Bacillus. IRANIAN JOURNAL OF MEDICAL SCIENCES 2016; 41:406-14. [PMID: 27582590 PMCID: PMC4967485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
BACKGROUND Glutaminase (EC 3.5.1.2) catalyzes the hydrolytic degradation of L-glutamine to L-glutamic acid and has been introduced for cancer therapy in recent years. The present study was an in silico analysis of glutaminase to further elucidate its structure and physicochemical properties. METHODS Forty glutaminase protein sequences from different species of Escherichia and Bacillus obtained from the UniProt Protein Database were characterized for homology search, physiochemical properties, phylogenetic tree construction, motif, superfamily search, and multiple sequence alignment. RESULTS The sequence level homology was obtained among different groups of glutaminase enzymes, which belonged to superfamily serine-dependent β-lactamases and penicillin-binding proteins. The phylogenetic tree constructed indicated 2 main clusters for the glutaminases. The distribution of common β-lactamase motifs was also observed; however, various non-common motifs were also observed. CONCLUSION Our results showed that the existence of a conserved motif with a signature amino-acid sequence of β-lactamases could be considered for the genetic engineering of glutaminases in view of their potential application in cancer therapy. Nonetheless, further research is needed to improve the stability of glutaminases and decrease their immunogenicity in both medical and food industrial applications.
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Affiliation(s)
- Cambyz Irajie
- Department of Public Health and Food Hygiene, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | - Milad Mohkam
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran,Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Navid Nezafat
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Saeed Hosseinzadeh
- Department of Public Health and Food Hygiene, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | - Mahmood Aminlari
- Department of Biochemistry, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | - Younes Ghasemi
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran,Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran,Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran,Correspondence: Younes Ghasemi, PhD, PharmD; Department of Pharmaceutical Biotechnology, School of Pharmacy, P.O. Box: 71468-64685, Shiraz, Iran Tel/Fax: +98 71 32426729
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42
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Kim L, McGee L, Tomczyk S, Beall B. Biological and Epidemiological Features of Antibiotic-Resistant Streptococcus pneumoniae in Pre- and Post-Conjugate Vaccine Eras: a United States Perspective. Clin Microbiol Rev 2016; 29:525-52. [PMID: 27076637 PMCID: PMC4861989 DOI: 10.1128/cmr.00058-15] [Citation(s) in RCA: 169] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Streptococcus pneumoniae inflicts a huge disease burden as the leading cause of community-acquired pneumonia and meningitis. Soon after mainstream antibiotic usage, multiresistant pneumococcal clones emerged and disseminated worldwide. Resistant clones are generated through adaptation to antibiotic pressures imposed while naturally residing within the human upper respiratory tract. Here, a huge array of related commensal streptococcal strains transfers core genomic and accessory resistance determinants to the highly transformable pneumococcus. β-Lactam resistance is the hallmark of pneumococcal adaptability, requiring multiple independent recombination events that are traceable to nonpneumococcal origins and stably perpetuated in multiresistant clonal complexes. Pneumococcal strains with elevated MICs of β-lactams are most often resistant to additional antibiotics. Basic underlying mechanisms of most pneumococcal resistances have been identified, although new insights that increase our understanding are continually provided. Although all pneumococcal infections can be successfully treated with antibiotics, the available choices are limited for some strains. Invasive pneumococcal disease data compiled during 1998 to 2013 through the population-based Active Bacterial Core surveillance program (U.S. population base of 30,600,000) demonstrate that targeting prevalent capsular serotypes with conjugate vaccines (7-valent and 13-valent vaccines implemented in 2000 and 2010, respectively) is extremely effective in reducing resistant infections. Nonetheless, resistant non-vaccine-serotype clones continue to emerge and expand.
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Affiliation(s)
- Lindsay Kim
- Epidemiology Section, Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lesley McGee
- Streptococcus Laboratory, Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Sara Tomczyk
- Epidemiology Section, Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Bernard Beall
- Streptococcus Laboratory, Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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43
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Li Y, Metcalf BJ, Chochua S, Li Z, Gertz RE, Walker H, Hawkins PA, Tran T, Whitney CG, McGee L, Beall BW. Penicillin-Binding Protein Transpeptidase Signatures for Tracking and Predicting β-Lactam Resistance Levels in Streptococcus pneumoniae. mBio 2016; 7:e00756-16. [PMID: 27302760 PMCID: PMC4916381 DOI: 10.1128/mbio.00756-16] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 05/09/2016] [Indexed: 11/23/2022] Open
Abstract
UNLABELLED β-Lactam antibiotics are the drugs of choice to treat pneumococcal infections. The spread of β-lactam-resistant pneumococci is a major concern in choosing an effective therapy for patients. Systematically tracking β-lactam resistance could benefit disease surveillance. Here we developed a classification system in which a pneumococcal isolate is assigned to a "PBP type" based on sequence signatures in the transpeptidase domains (TPDs) of the three critical penicillin-binding proteins (PBPs), PBP1a, PBP2b, and PBP2x. We identified 307 unique PBP types from 2,528 invasive pneumococcal isolates, which had known MICs to six β-lactams based on broth microdilution. We found that increased β-lactam MICs strongly correlated with PBP types containing divergent TPD sequences. The PBP type explained 94 to 99% of variation in MICs both before and after accounting for genomic backgrounds defined by multilocus sequence typing, indicating that genomic backgrounds made little independent contribution to β-lactam MICs at the population level. We further developed and evaluated predictive models of MICs based on PBP type. Compared to microdilution MICs, MICs predicted by PBP type showed essential agreement (MICs agree within 1 dilution) of >98%, category agreement (interpretive results agree) of >94%, a major discrepancy (sensitive isolate predicted as resistant) rate of <3%, and a very major discrepancy (resistant isolate predicted as sensitive) rate of <2% for all six β-lactams. Thus, the PBP transpeptidase signatures are robust indicators of MICs to different β-lactam antibiotics in clinical pneumococcal isolates and serve as an accurate alternative to phenotypic susceptibility testing. IMPORTANCE The human pathogen Streptococcus pneumoniae is a leading cause of morbidity and mortality worldwide. β-Lactam antibiotics such as penicillin and ceftriaxone are the drugs of choice to treat pneumococcal infections. Some pneumococcal strains have developed β-lactam resistance through altering their penicillin-binding proteins (PBPs) and have become a major concern in choosing effective patient therapy. To systematically track and predict β-lactam resistance, we obtained the sequence signatures of PBPs from a large collection of clinical pneumococcal isolates using whole-genome sequencing data and found that these "PBP types" were predictive of resistance levels. Our findings can benefit the current era of strain surveillance when whole-genome sequencing data often lacks detailed resistance information. Using PBP positions that we found are always substituted within highly resistant strains may lead to further refinements. Sequence-based predictions are accurate and may lead to the ability to extract critical resistance information from nonculturable clinical specimens.
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Affiliation(s)
- Yuan Li
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, Georgia, USA
| | - Benjamin J Metcalf
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, Georgia, USA
| | - Sopio Chochua
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, Georgia, USA
| | - Zhongya Li
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, Georgia, USA
| | - Robert E Gertz
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, Georgia, USA
| | - Hollis Walker
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, Georgia, USA
| | - Paulina A Hawkins
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, Georgia, USA
| | - Theresa Tran
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, Georgia, USA
| | - Cynthia G Whitney
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, Georgia, USA
| | - Lesley McGee
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, Georgia, USA
| | - Bernard W Beall
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, Georgia, USA
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44
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Affiliation(s)
- R. F. Pratt
- Department
of Chemistry, Wesleyan University, Lawn Avenue, Middletown, Connecticut 06459, United States
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45
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Ogawara H. Self-resistance in Streptomyces, with Special Reference to β-Lactam Antibiotics. Molecules 2016; 21:E605. [PMID: 27171072 PMCID: PMC6273383 DOI: 10.3390/molecules21050605] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 04/26/2016] [Accepted: 04/29/2016] [Indexed: 11/30/2022] Open
Abstract
Antibiotic resistance is one of the most serious public health problems. Among bacterial resistance, β-lactam antibiotic resistance is the most prevailing and threatening area. Antibiotic resistance is thought to originate in antibiotic-producing bacteria such as Streptomyces. In this review, β-lactamases and penicillin-binding proteins (PBPs) in Streptomyces are explored mainly by phylogenetic analyses from the viewpoint of self-resistance. Although PBPs are more important than β-lactamases in self-resistance, phylogenetically diverse β-lactamases exist in Streptomyces. While class A β-lactamases are mostly detected in their enzyme activity, over two to five times more classes B and C β-lactamase genes are identified at the whole genomic level. These genes can subsequently be transferred to pathogenic bacteria. As for PBPs, two pairs of low affinity PBPs protect Streptomyces from the attack of self-producing and other environmental β-lactam antibiotics. PBPs with PASTA domains are detectable only in class A PBPs in Actinobacteria with the exception of Streptomyces. None of the Streptomyces has PBPs with PASTA domains. However, one of class B PBPs without PASTA domain and a serine/threonine protein kinase with four PASTA domains are located in adjacent positions in most Streptomyces. These class B type PBPs are involved in the spore wall synthesizing complex and probably in self-resistance. Lastly, this paper emphasizes that the resistance mechanisms in Streptomyces are very hard to deal with, despite great efforts in finding new antibiotics.
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Affiliation(s)
- Hiroshi Ogawara
- HO Bio Institute, 33-9, Yushima-2, Bunkyo-ku, Tokyo 113-0034, Japan.
- Department of Biochemistry, Meiji Pharmaceutical University, 522-1, Noshio-2, Kiyose, Tokyo 204-8588, Japan.
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Fisher JF, Mobashery S. β-Lactam Resistance Mechanisms: Gram-Positive Bacteria and Mycobacterium tuberculosis. Cold Spring Harb Perspect Med 2016; 6:cshperspect.a025221. [PMID: 27091943 DOI: 10.1101/cshperspect.a025221] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The value of the β-lactam antibiotics for the control of bacterial infection has eroded with time. Three Gram-positive human pathogens that were once routinely susceptible to β-lactam chemotherapy-Streptococcus pneumoniae, Enterococcus faecium, and Staphylococcus aureus-now are not. Although a fourth bacterium, the acid-fast (but not Gram-positive-staining) Mycobacterium tuberculosis, has intrinsic resistance to earlier β-lactams, the emergence of strains of this bacterium resistant to virtually all other antibiotics has compelled the evaluation of newer β-lactam combinations as possible contributors to the multidrug chemotherapy required to control tubercular infection. The emerging molecular-level understanding of these resistance mechanisms used by these four bacteria provides the conceptual framework for bringing forward new β-lactams, and new β-lactam strategies, for the future control of their infections.
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Affiliation(s)
- Jed F Fisher
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556-5670
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556-5670
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Murugavel S, Vetri Velan V, Kannan D, Bakthadoss M. Synthesis, crystal structure analysis, spectral investigations, DFT computations, Biological activities and molecular docking of methyl(2E)-2-{[N-(2-formylphenyl)(4-methylbenzene) sulfonamido]methyl}-3-(4-fluorophenyl)prop-2-enoate, a potential bioactive agent. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2015.11.047] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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48
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Distribution of PASTA domains in penicillin-binding proteins and serine/threonine kinases of Actinobacteria. J Antibiot (Tokyo) 2016; 69:660-85. [DOI: 10.1038/ja.2015.138] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Revised: 11/15/2015] [Accepted: 11/25/2015] [Indexed: 01/25/2023]
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Manuse S, Fleurie A, Zucchini L, Lesterlin C, Grangeasse C. Role of eukaryotic-like serine/threonine kinases in bacterial cell division and morphogenesis. FEMS Microbiol Rev 2015; 40:41-56. [DOI: 10.1093/femsre/fuv041] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2015] [Indexed: 11/14/2022] Open
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Metcalf BJ, Gertz RE, Gladstone RA, Walker H, Sherwood LK, Jackson D, Li Z, Law C, Hawkins PA, Chochua S, Sheth M, Rayamajhi N, Bentley SD, Kim L, Whitney CG, McGee L, Beall B. Strain features and distributions in pneumococci from children with invasive disease before and after 13-valent conjugate vaccine implementation in the USA. Clin Microbiol Infect 2015; 22:60.e9-60.e29. [PMID: 26363404 PMCID: PMC4721534 DOI: 10.1016/j.cmi.2015.08.027] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 07/28/2015] [Accepted: 08/29/2015] [Indexed: 11/24/2022]
Abstract
The effect of second-generation pneumococcal conjugate vaccines on invasive pneumococcal disease (IPD) strain distributions have not yet been well described. We analysed IPD isolates recovered from children aged <5 years through Active Bacterial Core surveillance before (2008–2009; n = 828) and after (2011–2013; n = 600) 13-valent pneumococcal conjugate vaccine (PCV13) implementation. We employed conventional testing, PCR/electrospray ionization mass spectrometry and whole genome sequence (WGS) analysis to identify serotypes, resistance features, genotypes, and pilus types. PCV13, licensed in February 2010, effectively targeted all major 19A and 7F genotypes, and decreased antimicrobial resistance, primarily owing to removal of the 19A/ST320 complex. The strain complex contributing most to the remaining β-lactam resistance during 2011–2013 was 35B/ST558. Significant emergence of non-vaccine clonal complexes was not evident. Because of the removal of vaccine serotype strains, positivity for one or both pilus types (PI-1 and PI-2) decreased in the post-PCV13 years 2011–2013 relative to 2008–2009 (decreases of 32–55% for PI-1, and >95% for PI-2 and combined PI-1 + PI-2). β-Lactam susceptibility phenotypes correlated consistently with transpeptidase region sequence combinations of the three major penicillin-binding proteins (PBPs) determined through WGS analysis. Other major resistance features were predictable by DNA signatures from WGS analysis. Multilocus sequence data combined with PBP combinations identified progeny, serotype donors and recipient strains in serotype switch events. PCV13 decreased the frequency of all PCV13 serotype clones and concurrently decreased the frequency of strain subsets with resistance and/or adherence features conducive to successful carriage. Our results serve as a reference describing key features of current paediatric IPD strains in the USA after PCV13 implementation.
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Affiliation(s)
- B J Metcalf
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Atlanta, GA, USA
| | - R E Gertz
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Atlanta, GA, USA
| | - R A Gladstone
- Wellcome Trust Sanger Institute, Hinxton, UK; Department of Medicine, Addenbrookes Hospital, University of Cambridge, UK
| | - H Walker
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Atlanta, GA, USA
| | - L K Sherwood
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Atlanta, GA, USA
| | - D Jackson
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Atlanta, GA, USA
| | - Z Li
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Atlanta, GA, USA
| | - C Law
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Atlanta, GA, USA
| | - P A Hawkins
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Atlanta, GA, USA
| | - S Chochua
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Atlanta, GA, USA
| | - M Sheth
- Centers for Disease Control and Prevention, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, GA, USA
| | - N Rayamajhi
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Atlanta, GA, USA
| | - S D Bentley
- Wellcome Trust Sanger Institute, Hinxton, UK; Department of Medicine, Addenbrookes Hospital, University of Cambridge, UK
| | - L Kim
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Atlanta, GA, USA
| | - C G Whitney
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Atlanta, GA, USA
| | - L McGee
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Atlanta, GA, USA
| | - B Beall
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Atlanta, GA, USA.
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