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Can β-Lactam Antibiotics Be Resurrected to Combat MRSA?
Structural basis for the substrate recognition of peptidoglycan pentapeptides by Enterococcus faecalis VanYB.
Structural basis for the substrate recognition of peptidoglycan pentapeptides by Enterococcus faecalis VanYB.
Int J Biol Macromol. 2018 Jul 14;:
Authors: Kim HS, Hahn H, Kim J, Jang DM, Lee JY, Back JM, Im HN, Kim H, Han BW, Suh SW
Abstract
Vancomycin resistance in Enterococci and its transfer to methicillin-resistant Staphylococcus aureus are challenging problems in health care institutions worldwide. High-level vancomycin resistance is conferred by acquiring either transposable elements of the VanA or VanB type. Enterococcus faecalis VanYB in the VanB-type operon is a d,d-carboxypeptidase that recognizes the peptidyl-d-Ala4-d-Ala5 extremity of peptidoglycan and hydrolyses the terminal d-Ala on the extracellular side of the cell wall, thereby increasing the level of glycopeptide antibiotics resistance. However, at the molecular level, it remains unclear how VanYB manipulates peptidoglycan peptides for vancomycin resistance. In this study, we have determined the crystal structures of E. faecalis VanYB in the d-Ala-d-Ala-bound, d-Ala-bound, and -unbound states. The interactions between VanYB and d-Ala-d-Ala observed in the crystal provide the molecular basis for the recognition of peptidoglycan substrates by VanYB. Moreover, comparisons with the related VanX and VanXY enzymes reveal distinct structural features of E. faecalis VanYB around the active-site cleft, thus shedding light on its unique substrate specificity. Our results could serve as the foundation for unravelling the molecular mechanism of vancomycin resistance and for developing novel antibiotics against the vancomycin-resistant Enterococcus species.
PMID: 30016658 [PubMed - as supplied by publisher]
"One-pot" two-step metabolic labeling of teichoic acids and direct labeling of peptidoglycan reveals the tight coordination of both polymers insertion in pneumococcus cell wall.
"One-pot" two-step metabolic labeling of teichoic acids and direct labeling of peptidoglycan reveals the tight coordination of both polymers insertion in pneumococcus cell wall.
ACS Chem Biol. 2018 Jul 16;:
Authors: Bonnet J, Wong YS, Vernet T, Di Guilmi AM, Zapun A, Durmort C
Abstract
A method for labeling teichoic acids in the human pathogen Streptococcus pneumoniae has been developed using a "one-pot" two steps metabolic labeling approach. The essential nutriment choline modified with an azido-group was incorporated and exposed at the cell surface more rapidly than it reacted with the strain promoted azide alkyne cycloaddition SPAAC partner also present in the medium. Once at the cell surface on teichoic acids, coupling of the azido-group could then occur within 5 min by the bio-orthogonal click reaction with a DIBO-linked fluorophore. This fast and easy method allowed pulse-chase experiments and was combined with another fluorescent labeling approach to compare the insertion of teichoic acids with peptidoglycan synthesis with unprecedented temporal resolution. It has revealed that teichoic acid and peptidoglycan processes are largely concomitant, but teichoic acid insertion persists later at the division site.
PMID: 30010316 [PubMed - as supplied by publisher]
[ASAP] A Library Approach to Cationic Amphiphilic Polyproline Helices that Target Intracellular Pathogenic Bacteria
Structural insights into the signalling mechanisms of two-component systems
Structural insights into the signalling mechanisms of two-component systems
Structural insights into the signalling mechanisms of two-component systems, Published online: 15 July 2018; doi:10.1038/s41579-018-0055-7
Canonical two-component systems catalyse autophosphorylation of the histidine kinase, transfer of the phosphoryl group to the regulator and dephosphorylation of the phosphoregulator. In this Progress article, Jacob-Dubuisson and colleagues highlight recent structural insights into the signalling and catalytic mechanisms of sensor histidine kinases.A cluster of residues in the lipopolysaccharide exporter that selects substrate variants for transport to the outer membrane.
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A cluster of residues in the lipopolysaccharide exporter that selects substrate variants for transport to the outer membrane.
Mol Microbiol. 2018 08;109(4):541-554
Authors: Bertani BR, Taylor RJ, Nagy E, Kahne D, Ruiz N
Abstract
Most Gram-negative bacteria assemble lipopolysaccharides (LPS) on their surface to form a permeability barrier against many antimicrobials. LPS is synthesized at the inner membrane and then transported to the outer leaflet of the outer membrane. Although the overall LPS structure is conserved, LPS molecules can differ in composition at the species and strain level. Some bacteria also regulate when to modify phosphates on LPS at the inner membrane in order to become resistant to cationic antimicrobial peptides. The multi-protein Lpt trans-envelope machine, which transports LPS from the inner to the outer membrane, must therefore handle a variety of substrates. The most poorly understood step in LPS transport is how the ATP-binding cassette LptB2 FG transporter extracts LPS from the inner membrane. Here, we define residue K34 in LptG as a site within the structural cavity of the Escherichia coli LptB2 FG transporter that interacts electrostatically with phosphates on unmodified LPS. Alterations to this residue cause transport defects that are suppressed by the activation of the BasSR two-component signaling system, which results in modifications to the LPS phosphates. We also show this residue is part of a larger site in LptG that differentially contributes to the transport of unmodified and modified LPS.
PMID: 29995974 [PubMed - indexed for MEDLINE]
Tetrazine-mediated bioorthogonal prodrug–prodrug activation
DOI: 10.1039/C8SC02610F, Edge Article
Open Access
  This article is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported Licence.
Prodrug–prodrug activation describes the simultaneous, traceless and bioorthogonal activation of two drugs.
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Aspartate deficiency limits peptidoglycan synthesis and sensitizes cells to antibiotics targeting cell wall synthesis in Bacillus subtilis.
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Aspartate deficiency limits peptidoglycan synthesis and sensitizes cells to antibiotics targeting cell wall synthesis in Bacillus subtilis.
Mol Microbiol. 2018 Jul 11;:
Authors: Zhao H, Roistacher DM, Helmann JD
Abstract
Peptidoglycan synthesis is an important target for antibiotics and relies on intermediates derived from central metabolism. As a result, alterations of metabolism may affect antibiotic sensitivity. An aspB mutant is auxotrophic for aspartate (Asp) and asparagine (Asn) and lyses when grown in Difco sporulation medium (DSM), but not in LB medium. Genetic and physiological studies, supported by amino acid analysis, reveal that cell lysis in DSM results from Asp limitation due to a relatively low Asp and high glutamate (Glu) concentrations, with Glu functioning as a competitive inhibitor of Asp uptake by the major Glu/Asp transporter GltT. Lysis can be specifically suppressed by supplementation with 2,6-diaminopimelate (DAP), which is imported by two different cystine uptake systems. These studies suggest that aspartate limitation depletes the peptidoglycan precursor meso-2,6-diaminopimelate (mDAP), inhibits peptidoglycan synthesis, upregulates the cell envelope stress response mediated by σM and eventually leads to cell lysis. Aspartate limitation sensitizes cells to antibiotics targeting late steps of PG synthesis, but not steps prior to the addition of mDAP into the pentapeptide sidechain. This work highlights the ability of perturbations of central metabolism to sensitize cells to peptidoglycan synthesis inhibitors. This article is protected by copyright. All rights reserved.
PMID: 29995990 [PubMed - as supplied by publisher]
Enzyme discovery could help in fight against tuberculosis
Antiprotozoal and cysteine proteases inhibitory activity of dipeptidyl enoates
Publication date: 1 September 2018
Source: Bioorganic & Medicinal Chemistry, Volume 26, Issue 16
Author(s): Santiago Royo, Tanja Schirmeister, Marcel Kaiser, Sascha Jung, Santiago Rodríguez, José Manuel Bautista, Florenci V. González
Abstract
A family of dipeptidyl enoates has been prepared and tested against the parasitic cysteine proteases rhodesain, cruzain and falcipain-2 related to sleeping sickness, Chagas disease and malaria, respectively. They have also been tested against human cathepsins B and L1 for selectivity. Dipeptidyl enoates resulted to be irreversible inhibitors of these enzymes. Some of the members of the family are very potent inhibitors of parasitic cysteine proteases displaying k2nd (M−1s−1) values of seven orders of magnitude. In vivo antiprotozoal testing was also performed. Inhibitors exhibited IC50 values in the micromolar range against Plasmodium falciparum, Trypanosoma brucei, Trypanosoma cruzi and even more promising lower values against Leishmania donovanii.
Graphical abstract
Structural Polymorphism of Alzheimer's β-Amyloid Fibrils as Controlled by an E22 Switch: A Solid-State NMR Study.
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Structural Polymorphism of Alzheimer's β-Amyloid Fibrils as Controlled by an E22 Switch: A Solid-State NMR Study.
J Am Chem Soc. 2016 08 10;138(31):9840-52
Authors: Elkins MR, Wang T, Nick M, Jo H, Lemmin T, Prusiner SB, DeGrado WF, Stöhr J, Hong M
Abstract
The amyloid-β (Aβ) peptide of Alzheimer's disease (AD) forms polymorphic fibrils on the micrometer and molecular scales. Various fibril growth conditions have been identified to cause polymorphism, but the intrinsic amino acid sequence basis for this polymorphism has been unclear. Several single-site mutations in the center of the Aβ sequence cause different disease phenotypes and fibrillization properties. The E22G (Arctic) mutant is found in familial AD and forms protofibrils more rapidly than wild-type Aβ. Here, we use solid-state NMR spectroscopy to investigate the structure, dynamics, hydration and morphology of Arctic E22G Aβ40 fibrils. (13)C, (15)N-labeled synthetic E22G Aβ40 peptides are studied and compared with wild-type and Osaka E22Δ Aβ40 fibrils. Under the same fibrillization conditions, Arctic Aβ40 exhibits a high degree of polymorphism, showing at least four sets of NMR chemical shifts for various residues, while the Osaka and wild-type Aβ40 fibrils show a single or a predominant set of chemical shifts. Thus, structural polymorphism is intrinsic to the Arctic E22G Aβ40 sequence. Chemical shifts and inter-residue contacts obtained from 2D correlation spectra indicate that one of the major Arctic conformers has surprisingly high structural similarity with wild-type Aβ42. (13)C-(1)H dipolar order parameters, (1)H rotating-frame spin-lattice relaxation times and water-to-protein spin diffusion experiments reveal substantial differences in the dynamics and hydration of Arctic, Osaka and wild-type Aβ40 fibrils. Together, these results strongly suggest that electrostatic interactions in the center of the Aβ peptide sequence play a crucial role in the three-dimensional fold of the fibrils, and by inference, fibril-induced neuronal toxicity and AD pathogenesis.
PMID: 27414264 [PubMed - indexed for MEDLINE]
Synthesis of functionalized N-acetyl muramic acids to probe bacterial cell wall recycling and biosynthesis.
Synthesis of functionalized N-acetyl muramic acids to probe bacterial cell wall recycling and biosynthesis.
J Am Chem Soc. 2018 Jul 09;:
Authors: DeMeester KE, Liang H, Jensen MR, Jones ZS, D'Ambrosio EA, Scinto SL, Zhou J, Grimes CL
Abstract
Uridine diphosphate N-acetyl muramic acid (UDP NAM) is a critical intermediate in bacterial peptidoglycan (PG) biosynthesis. As the primary source of muramic acid that shapes the PG backbone, modifications installed at the UDP NAM intermediate can be used to selectively tag and manipulate this polymer via metabolic incorporation. However, synthetic and purification strategies to access large quantities of these PG building blocks, as well as their derivatives, are challenging. A robust chemoenzymatic synthesis was developed using an expanded NAM library to produce a variety of 2-N functionalized UDP-NAMs. In addition, a synthetic strategy to access biorthogonal 3-lactic acid NAM derivatives was developed. The chemoenzymatic UDP synthesis revealed that the bacterial cell wall recycling enzymes MurNAc/GlcNAc anomeric kinase (AmgK) and NAM α-1 phosphate uridylyl transferase (MurU) were permissive to permutations at the two and three positions of the sugar donor. We further explored the utility of these derivatives in the fluorescent labeling of both Gram (-) and Gram (+) PG in whole cells using a variety of bioorthogonal chemistries including the tetrazine ligation. This report allows for rapid and scalable access to a variety of function-alized NAMs and UDP NAMs, which now can be used in tandem with other complementary bioorthogonal labeling strategies to address fundamental questions surrounding PG's role in immunology and microbiology.
PMID: 29986130 [PubMed - as supplied by publisher]
[ASAP] In Vivo Photopharmacology
[ASAP] Pseudaminic Acid on Exopolysaccharide of Acinetobacter baumannii Plays a Critical Role in Phage-Assisted Preparation of Glycoconjugate Vaccine with High Antigenicity
New "Immunobiotic" Could Treat Antibiotic-Resistant Superbugs
Antibody–Bactericidal Macrocyclic Peptide Conjugates To Target Gram‐Negative Bacteria
Synthetic Immunotherapeutics against Gram-negative Pathogens
Immunotherapy for deadly bacteria shows early promise
What should you eat while taking antibiotics?
Mycobacterium tuberculosis
Publication date: June 2018
Source: Trends in Microbiology, Volume 26, Issue 6
Author(s): Anastasia Koch, Valerie Mizrahi
In this infographic, the genetics, phylogeny, physiology, and pathogenesis mechanisms of Mycobacterium tuberculosis are shown.
Mycobacterium tuberculosis is the etiological agent of tuberculosis (TB), the leading cause of death due to a single infectious agent, claiming 1.7 million lives in 2016. Of the deaths attributable to TB in 2016, 22% occurred in people coinfected with HIV, and close to 5% of the 10.4 million incident cases of this disease were resistant to at least two of the first-line TB drugs. In this infographic, we describe the fundamental features of the genetics, phylogeny, and physiology of this member of the phylum Actinobacteria, which is associated increasingly with drug resistance mediated by mutations and rearrangements in its single, circular chromosome. We also highlight the key pathogenesis mechanisms employed by this slow-growing, facultative intracellular bacterium, which include avoidance of host cell clearance by arrest of the normal macrophage maturation process.
Structure activity relationship studies on rhodanines and derived enethiol inhibitors of metallo-β-lactamases
Publication date: 15 July 2018
Source: Bioorganic & Medicinal Chemistry, Volume 26, Issue 11
Author(s): Dong Zhang, Marios S. Markoulides, Dmitrijs Stepanovs, Anna M. Rydzik, Ahmed El-Hussein, Corentin Bon, Jos J.A.G. Kamps, Klaus-Daniel Umland, Patrick M. Collins, Samuel T. Cahill, David Y. Wang, Frank von Delft, Jürgen Brem, Michael A. McDonough, Christopher J. Schofield
Abstract
Metallo-β-lactamases (MBLs) enable bacterial resistance to almost all classes of β-lactam antibiotics. We report studies on enethiol containing MBL inhibitors, which were prepared by rhodanine hydrolysis. The enethiols inhibit MBLs from different subclasses. Crystallographic analyses reveal that the enethiol sulphur displaces the di-Zn(II) ion bridging ‘hydrolytic’ water. In some, but not all, cases biophysical analyses provide evidence that rhodanine/enethiol inhibition involves formation of a ternary MBL enethiol rhodanine complex. The results demonstrate how low molecular weight active site Zn(II) chelating compounds can inhibit a range of clinically relevant MBLs and provide additional evidence for the potential of rhodanines to be hydrolysed to potent inhibitors of MBL protein fold and, maybe, other metallo-enzymes, perhaps contributing to the complex biological effects of rhodanines. The results imply that any medicinal chemistry studies employing rhodanines (and related scaffolds) as inhibitors should as a matter of course include testing of their hydrolysis products.
Graphical abstract
Structure-activity relationships in a new class of non-substrate-like covalent inhibitors of the bacterial glycosyltransferase LgtC
Publication date: 15 July 2018
Source: Bioorganic & Medicinal Chemistry, Volume 26, Issue 11
Author(s): Yong Xu, Jon Cuccui, Carmen Denman, Tripty Maharjan, Brendan W. Wren, Gerd K. Wagner
Abstract
Lipooligosaccharide (LOS) structures in the outer core of Gram-negative mucosal pathogens such as Neisseria meningitidis and Haemophilus influenzae contain characteristic glycoepitopes that contribute significantly to bacterial virulence. An important example is the digalactoside epitope generated by the retaining α-1,4-galactosyltransferase LgtC. These digalactosides camouflage the pathogen from the host immune system and increase its serum resistance. Small molecular inhibitors of LgtC are therefore sought after as chemical tools to study bacterial virulence, and as potential candidates for anti-virulence drug discovery. We have recently discovered a new class of non-substrate-like inhibitors of LgtC. The new inhibitors act via a covalent mode of action, targeting a non-catalytic cysteine residue in the LgtC active site. Here, we describe, for the first time, structure-activity relationships for this new class of glycosyltransferase inhibitors. We have carried out a detailed analysis of the inhibition kinetics to establish the relative contribution of the non-covalent binding and the covalent inactivation steps for overall inhibitory activity. Selected inhibitors were also evaluated against a serum-resistant strain of Haemophilus influenzae, but did not enhance the killing effect of human serum.
Graphical abstract
[ASAP] Protein Labeling via a Specific Lysine-Isopeptide Bond Using the Pilin Polymerizing Sortase from Corynebacterium diphtheriae
[ASAP] Augmenting Vaccine Immunogenicity through the Use of Natural Human Anti-rhamnose Antibodies
[ASAP] Cancer Metabolism: Current Understanding and Therapies
[ASAP] A Bifunctional Noncanonical Amino Acid: Synthesis, Expression, and Residue-Specific Proteome-wide Incorporation
Caenorhabditis elegans in high-throughput screens for anti-infective compounds.
Caenorhabditis elegans in high-throughput screens for anti-infective compounds.
Curr Opin Immunol. 2018 Jun 20;54:59-65
Authors: Peterson ND, Pukkila-Worley R
Abstract
New classes of antimicrobials that are effective therapies for infections with multi-drug resistant pathogens are urgently needed. The nematode Caenorhabditis elegans has been incorporated into small molecule screening platforms to identify anti-infective compounds that provide protection of a host during infection. The use of a live animal in these screening systems offers several advantages, including the ability to identify molecules that boost innate immune responses in a manner advantageous to host survival and compounds that disrupt bacterial virulence mechanisms. In addition, new classes of antimicrobials that target the pathogen have been uncovered, as well as interesting chemical probes that can be used to dissect new mechanisms of host-pathogen interactions.
PMID: 29935375 [PubMed - as supplied by publisher]
PBP4: A New Perspective on Staphylococcus aureus β-Lactam Resistance.
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PBP4: A New Perspective on Staphylococcus aureus β-Lactam Resistance.
Microorganisms. 2018 Jun 22;6(3):
Authors: da Costa TM, de Oliveira CR, Chambers HF, Chatterjee SS
Abstract
β-lactam antibiotics are excellent drugs for treatment of staphylococcal infections, due to their superior efficacy and safety compared to other drugs. Effectiveness of β-lactams is severely compromised due to resistance, which is widespread among clinical strains of Staphylococcus aureus. β-lactams inhibit bacterial cells by binding to penicillin binding proteins (PBPs), which perform the penultimate steps of bacterial cell wall synthesis. Among PBPs of S. aureus, PBP2a has received the most attention for the past several decades due to its preeminent role in conferring both high-level and broad-spectrum resistance to the entire class of β-lactam drugs. Studies on PBP2a have thus unraveled incredible details of its mechanism of action. We have recently identified that an uncanonical, low molecular weight PBP of S. aureus, PBP4, can also provide high-level and broad-spectrum resistance to the entire class of β-lactam drugs at a level similar to that of PBP2a. The role of PBP4 has typically been considered not so important for β-lactam resistance of S. aureus, and as a result its mode of action remains largely unknown. In this article, we review our current knowledge of PBP4 mediating β-lactam resistance in S. aureus.
PMID: 29932109 [PubMed]
[ASAP] Mechanobiology of Tumor Growth
An Assembly-Activating Site in the Hepatitis B Virus Capsid Protein Can Also Trigger Disassembly.
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An Assembly-Activating Site in the Hepatitis B Virus Capsid Protein Can Also Trigger Disassembly.
ACS Chem Biol. 2018 08 17;13(8):2114-2120
Authors: Qazi S, Schlicksup CJ, Rittichier J, VanNieuwenhze MS, Zlotnick A
Abstract
The Hepatitis B Virus (HBV) core protein homodimers self-assemble to form an icosahedral capsid that packages the viral genome. Disassembly occurs in the nuclear basket to release the mature genome to the nucleus. Small molecules have been developed that bind to a pocket at the interdimer interface to accelerate assembly and strengthen interactions between subunits; these are under development as antiviral agents. Here, we explore the role of the dimer-dimer interface by mutating sites in the drug-binding pocket to cysteine and examining the effect of covalently linking small molecules to them. We find that ligands bound to the pocket may trigger capsid disassembly in a dose-dependent manner. This result indicates that, at least transiently, the pocket adopts a destabilizing conformation. We speculate that this pocket also plays a role in virus disassembly and genome release by binding ligands that are incompatible with virus stability, "unwanted guests." Investigating protein-protein interactions, especially large protein polymers, offers new and unique challenges. By using an engineered addressable thiol, we provide a means to examine the effects of modifying an interface without requiring drug-like properties for the ligand.
PMID: 29920071 [PubMed - indexed for MEDLINE]