1
|
Huang W, Baliga C, Vázquez-Laslop N, Mankin A. Sequence diversity of apidaecin-like peptides arresting the terminating ribosome. Nucleic Acids Res 2024; 52:8967-8978. [PMID: 38953159 PMCID: PMC11347161 DOI: 10.1093/nar/gkae567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/31/2024] [Accepted: 06/22/2024] [Indexed: 07/03/2024] Open
Abstract
The Proline-rich Antimicrobial Peptide (PrAMP) apidaecin (Api) inhibits translation by binding in the ribosomal nascent peptide exit tunnel, trapping release factors RF1 or RF2, and arresting ribosomes at stop codons. To explore the extent of sequence variations of the native 18-amino acid Api that allows it to preserve its activity, we screened a library of synthetic mutant Api genes expressed in bacterial cells, resulting in nearly 350000 peptide variants with multiple substitutions. By applying orthogonal negative and positive selection strategies, we identified a number of multi-substituted Api variants capable of arresting ribosomes at stop codons. Our findings underscore the critical contribution of specific amino acid residues of the peptide for its on-target function while significantly expanding the variety of PrAMPs acting on the terminating ribosome. Additionally, some of the tested synthesized multi-substituted Api variants exhibit improved antibacterial activity compared to that of the wild type PrAMP and may constitute the starting point to develop clinically useful antimicrobials.
Collapse
Affiliation(s)
- Weiping Huang
- Department of Pharmaceutical Sciences and Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Chetana Baliga
- Department of Pharmaceutical Sciences and Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Nora Vázquez-Laslop
- Department of Pharmaceutical Sciences and Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Alexander S Mankin
- Department of Pharmaceutical Sciences and Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| |
Collapse
|
2
|
Koller TO, Berger MJ, Morici M, Paternoga H, Bulatov T, Di Stasi A, Dang T, Mainz A, Raulf K, Crowe-McAuliffe C, Scocchi M, Mardirossian M, Beckert B, Vázquez-Laslop N, Mankin A, Süssmuth RD, Wilson DN. Paenilamicins from the honey bee pathogen Paenibacillus larvae are context-specific translocation inhibitors of protein synthesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.21.595107. [PMID: 38826346 PMCID: PMC11142091 DOI: 10.1101/2024.05.21.595107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
The paenilamicins are a group of hybrid non-ribosomal peptide-polyketide compounds produced by the honey bee pathogen Paenibacillus larvae that display activity against Gram-positive pathogens, such as Staphylococcus aureus. While paenilamicins have been shown to inhibit protein synthesis, their mechanism of action has remained unclear. Here, we have determined structures of the paenilamicin PamB2 stalled ribosomes, revealing a unique binding site on the small 30S subunit located between the A- and P-site tRNAs. In addition to providing a precise description of interactions of PamB2 with the ribosome, the structures also rationalize the resistance mechanisms utilized by P. larvae. We could further demonstrate that PamB2 interferes with the translocation of mRNA and tRNAs through the ribosome during translation elongation, and that this inhibitory activity is influenced by the presence of modifications at position 37 of the A-site tRNA. Collectively, our study defines the paenilamicins as a new class of context-specific translocation inhibitors.
Collapse
Affiliation(s)
- Timm O. Koller
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Max J. Berger
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Martino Morici
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Helge Paternoga
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Timur Bulatov
- Institut für Chemie, Technische Universität Berlin, 10623 Berlin, Germany
| | - Adriana Di Stasi
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Tam Dang
- Institut für Chemie, Technische Universität Berlin, 10623 Berlin, Germany
| | - Andi Mainz
- Institut für Chemie, Technische Universität Berlin, 10623 Berlin, Germany
| | - Karoline Raulf
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Caillan Crowe-McAuliffe
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Marco Scocchi
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Mario Mardirossian
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Bertrand Beckert
- Dubochet Center for Imaging (DCI) at EPFL, EPFL SB IPHYS DCI, Lausanne, Switzerland
| | - Nora Vázquez-Laslop
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607
| | - Alexander Mankin
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607
| | | | - Daniel N. Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| |
Collapse
|
3
|
Perlmutter JI, Chapman JR, Wilkinson MC, Nevarez-Saenz I, Unckless RL. A single amino acid polymorphism in natural Metchnikowin alleles of Drosophila results in systemic immunity and life history tradeoffs. PLoS Genet 2024; 20:e1011155. [PMID: 38466751 PMCID: PMC10957085 DOI: 10.1371/journal.pgen.1011155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 03/21/2024] [Accepted: 01/26/2024] [Indexed: 03/13/2024] Open
Abstract
Antimicrobial peptides (AMPs) are at the interface of interactions between hosts and microbes and are therefore expected to be rapidly evolving in a coevolutionary arms race with pathogens. In contrast, previous work demonstrated that insect AMPs tend to evolve more slowly than the genome average. Metchikowin (Mtk) is a Drosophila AMP that has a single amino acid residue that segregates as either proline (P) or arginine (R) in populations of four different species, some of which diverged more than 10 million years ago. These results suggest that there is a distinct functional importance to each allele. The most likely hypotheses are driven by two main questions: does each allele have a different efficacy against different specific pathogens (specificity hypothesis)? Or, is one allele a more potent antimicrobial, but with a host fitness cost (autoimmune hypothesis)? To assess their functional differences, we created D. melanogaster lines with the P allele, R allele, or Mtk null mutation using CRISPR/Cas9 genome editing and performed a series of life history and infection assays to assess them. In males, testing of systemic immune responses to a repertoire of bacteria and fungi demonstrated that the R allele performs as well or better than the P and null alleles with most infections. Females show some results that contrast with males, with Mtk alleles either not contributing to survival or with the P allele outperforming the R allele. In addition, measurements of life history traits demonstrate that the R allele is more costly in the absence of infection for both sexes. These results are consistent with both the specificity hypothesis (either allele can perform better against certain pathogens depending on context), and the autoimmune hypothesis (the R allele is generally the more potent antimicrobial in males, and carries a fitness cost). These results provide strong in vivo evidence that differential fitness with or without infection and sex-based functional differences in alleles may be adaptive mechanisms of maintaining immune gene polymorphisms in contrast with expectations of rapid evolution. Therefore, a complex interplay of forces including pathogen species and host sex may lead to balancing selection for immune genotypes. Strikingly, this selection may act on even a single amino acid polymorphism in an AMP.
Collapse
Affiliation(s)
- Jessamyn I. Perlmutter
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
| | - Joanne R. Chapman
- Institute of Environmental and Scientific Research (ESR), Christchurch, New Zealand
| | - Mason C. Wilkinson
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Isaac Nevarez-Saenz
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
| | - Robert L. Unckless
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
| |
Collapse
|
4
|
Collins J, McConnell A, Schmitz ZD, Hackel BJ. Sequence-function mapping of proline-rich antimicrobial peptides. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.28.577586. [PMID: 38352424 PMCID: PMC10862732 DOI: 10.1101/2024.01.28.577586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
Antimicrobial peptides (AMPs) are essential elements of natural cellular combat and candidates as antibiotic therapy. Elevated function may be needed for robust physiological performance. Yet, both pure protein design and combinatorial library discovery are hindered by the complexity of antimicrobial activity. We applied a recently developed high-throughput technique, sequence-activity mapping of AMPs via depletion (SAMP-Dep), to proline-rich AMPs. Robust self-inhibition was achieved for metalnikowin 1 (Met) and apidaecin 1b (Api). SAMP-Dep exhibited high reproducibility with correlation coefficients 0.90 and 0.92, for Met and Api, respectively, between replicates and 0.99 and 0.96 for synonymous genetic variants. Sequence-activity maps were obtained via characterization of 26,000 and 34,000 mutants of Met and Api, respectively. Both AMPs exhibit similar mutational profiles including beneficial mutations at one terminus, the C-terminus for Met and N-terminus for Api, which is consistent with their opposite binding orientations in the ribosome. While Met and Api reside with the family of proline-rich AMPs, different proline sites exhibit substantially different mutational tolerance. Within the PRP motif, proline mutation eliminates activity, whereas non-PRP prolines readily tolerate mutation. Homologous mutations are more tolerated, particularly at alternating sites on one 'face' of the peptide. Important and consistent epistasis was observed following the PRP domain within the segment that extends into the ribosomal exit tunnel for both peptides. Variants identified from the SAMP-Dep platform were produced and exposed toward Gram-negative species exogenously, showing either increased potency or specificity for strains tested. In addition to mapping sequence-activity space for fundamental insight and therapeutic engineering, the results advance the robustness of the SAMP-Dep platform for activity characterization.
Collapse
Affiliation(s)
| | | | - Zachary D Schmitz
- Chemical Engineering and Materials Science University of Minnesota, Minneapolis, MN 55455
| | - Benjamin J Hackel
- Biomedical Engineering, Minneapolis, MN 55455
- Chemical Engineering and Materials Science University of Minnesota, Minneapolis, MN 55455
| |
Collapse
|
5
|
Collins J, Hackel BJ. Sequence-activity mapping via depletion reveals striking mutational tolerance and elucidates functional motifs in Tur1a antimicrobial peptide. Protein Eng Des Sel 2024; 37:gzae006. [PMID: 38484121 DOI: 10.1093/protein/gzae006] [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: 01/28/2024] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 03/27/2024] Open
Abstract
Proline-rich antimicrobial peptides (PrAMPs) are attractive antibiotic candidates that target gram-negative bacteria ribosomes. We elucidated the sequence-function landscape of 43 000 variants of a recently discovered family member, Tur1a, using the validated SAMP-Dep platform that measures intracellular AMP potency in a high-throughput manner via self-depletion of the cellular host. The platform exhibited high replicate reproducibility (ρ = 0.81) and correlation between synonymous genetic variants (R2 = 0.93). Only two segments within Tur1a exhibited stringent mutational requirements to sustain potency: residues 9YLP11 and 19FP20. This includes the aromatic residue in the hypothesized binding domain but not the PRP domain. Along with unexpected mutational tolerance of PRP, the data contrast hypothesized importance of the 1RRIR4 motif and arginines in general. In addition to mutational tolerance of residue segments with presumed significance, 77% of mutations are functionally neutral. Multimutant performance mainly shows compounding effects from removed combinations of prolines and arginines in addition to the two segments of residues showing individual importance. Several variants identified as active from SAMP-Dep were externally produced and maintained activity when applied to susceptible species exogenously.
Collapse
Affiliation(s)
- Jonathan Collins
- Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, United States
| | - Benjamin J Hackel
- Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, United States
- Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, United States
| |
Collapse
|
6
|
Tereshchenkov AG, Khairullina ZZ, Volynkina IA, Lukianov DA, Nazarov PA, Pavlova JA, Tashlitsky VN, Razumova EA, Ipatova DA, Timchenko YV, Senko DA, Efremenkova OV, Paleskava A, Konevega AL, Osterman IA, Rodin IA, Sergiev PV, Dontsova OA, Bogdanov AA, Sumbatyan NV. Triphenylphosphonium Analogs of Short Peptide Related to Bactenecin 7 and Oncocin 112 as Antimicrobial Agents. Pharmaceutics 2024; 16:148. [PMID: 38276518 PMCID: PMC10818380 DOI: 10.3390/pharmaceutics16010148] [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: 11/22/2023] [Revised: 01/01/2024] [Accepted: 01/15/2024] [Indexed: 01/27/2024] Open
Abstract
Antimicrobial peptides (AMPs) have recently attracted attention as promising antibacterial agents capable of acting against resistant bacterial strains. In this work, an approach was applied, consisting of the conjugation of a peptide related to the sequences of bactenecin 7 (Bac7) and oncocin (Onc112) with the alkyl(triphenyl)phosphonium (alkyl-TPP) fragment in order to improve the properties of the AMP and introduce new ones, expand the spectrum of antimicrobial activity, and reduce the inhibitory effect on the eukaryotic translation process. Triphenylphosphonium (TPP) derivatives of a decapeptide RRIRPRPPYL were synthesized. It was comprehensively studied how the modification of the AMP affected the properties of the new compounds. It was shown that while the reduction in the Bac7 length to 10 a.a. residues dramatically decreased the affinity to bacterial ribosomes, the modification of the peptide with alkyl-TPP moieties led to an increase in the affinity. New analogs with structures that combined a decapeptide related to Bac7 and Onc112-Bac(1-10, R/Y)-and TPP attached to the C-terminal amino acid residue via alkylamide linkers, inhibited translation in vitro and were found to be more selective inhibitors of bacterial translation compared with eukaryotic translation than Onc112 and Bac7. The TPP analogs of the decapeptide related to Bac7 and Onc112 suppressed the growth of both Gram-negative bacteria, similar to Onc112 and Bac7, and Gram-positive ones, similar to alkyl-TPP derivatives, and also acted against some resistant laboratory strains. Bac(1-10, R/Y)-C2-TPP, containing a short alkylamide linker between the decapeptide and TPP, was transferred into the E. coli cells via the SbmA transporter protein. TPP derivatives of the decapeptide Bac(1-10, R/Y) containing either a decylamide or ethylamide linker caused B. subtilis membrane depolarization, similar to alkyl-TPP. The Bac(1-10, R/Y)-C2-TPP analog was proven to be non-toxic for mammalian cells using the MTT test.
Collapse
Affiliation(s)
- Andrey G. Tereshchenkov
- Department of Chemistry, Lomonosov Moscow State University, 1/3 Leninskie Gory, 119991 Moscow, Russia (Z.Z.K.); (I.A.V.); (D.A.L.); (E.A.R.); (I.A.O.); (P.V.S.); (O.A.D.)
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 1/40 Leninskie Gory, 119991 Moscow, Russia
| | - Zimfira Z. Khairullina
- Department of Chemistry, Lomonosov Moscow State University, 1/3 Leninskie Gory, 119991 Moscow, Russia (Z.Z.K.); (I.A.V.); (D.A.L.); (E.A.R.); (I.A.O.); (P.V.S.); (O.A.D.)
| | - Inna A. Volynkina
- Department of Chemistry, Lomonosov Moscow State University, 1/3 Leninskie Gory, 119991 Moscow, Russia (Z.Z.K.); (I.A.V.); (D.A.L.); (E.A.R.); (I.A.O.); (P.V.S.); (O.A.D.)
| | - Dmitrii A. Lukianov
- Department of Chemistry, Lomonosov Moscow State University, 1/3 Leninskie Gory, 119991 Moscow, Russia (Z.Z.K.); (I.A.V.); (D.A.L.); (E.A.R.); (I.A.O.); (P.V.S.); (O.A.D.)
| | - Pavel A. Nazarov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 1/40 Leninskie Gory, 119991 Moscow, Russia
| | - Julia A. Pavlova
- Department of Chemistry, Lomonosov Moscow State University, 1/3 Leninskie Gory, 119991 Moscow, Russia (Z.Z.K.); (I.A.V.); (D.A.L.); (E.A.R.); (I.A.O.); (P.V.S.); (O.A.D.)
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 1/40 Leninskie Gory, 119991 Moscow, Russia
| | - Vadim N. Tashlitsky
- Department of Chemistry, Lomonosov Moscow State University, 1/3 Leninskie Gory, 119991 Moscow, Russia (Z.Z.K.); (I.A.V.); (D.A.L.); (E.A.R.); (I.A.O.); (P.V.S.); (O.A.D.)
| | - Elizaveta A. Razumova
- Department of Chemistry, Lomonosov Moscow State University, 1/3 Leninskie Gory, 119991 Moscow, Russia (Z.Z.K.); (I.A.V.); (D.A.L.); (E.A.R.); (I.A.O.); (P.V.S.); (O.A.D.)
| | - Daria A. Ipatova
- Department of Chemistry, Lomonosov Moscow State University, 1/3 Leninskie Gory, 119991 Moscow, Russia (Z.Z.K.); (I.A.V.); (D.A.L.); (E.A.R.); (I.A.O.); (P.V.S.); (O.A.D.)
| | - Yury V. Timchenko
- Department of Chemistry, Lomonosov Moscow State University, 1/3 Leninskie Gory, 119991 Moscow, Russia (Z.Z.K.); (I.A.V.); (D.A.L.); (E.A.R.); (I.A.O.); (P.V.S.); (O.A.D.)
| | - Dmitry A. Senko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Olga V. Efremenkova
- Gause Institute of New Antibiotics, 11 B. Pirogovskaya Street, 119021 Moscow, Russia;
| | - Alena Paleskava
- Molecular and Radiation Biophysics Division, Petersburg Nuclear Physics Institute, NRC “Kurchatov Institute”, 188300 Gatchina, Russia (A.L.K.)
- Institute of Biomedical Systems and Biotechnology, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia
| | - Andrey L. Konevega
- Molecular and Radiation Biophysics Division, Petersburg Nuclear Physics Institute, NRC “Kurchatov Institute”, 188300 Gatchina, Russia (A.L.K.)
- Institute of Biomedical Systems and Biotechnology, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia
- NBICS Center, NRC “Kurchatov Institute”, 123182 Moscow, Russia
| | - Ilya A. Osterman
- Department of Chemistry, Lomonosov Moscow State University, 1/3 Leninskie Gory, 119991 Moscow, Russia (Z.Z.K.); (I.A.V.); (D.A.L.); (E.A.R.); (I.A.O.); (P.V.S.); (O.A.D.)
| | - Igor A. Rodin
- Department of Chemistry, Lomonosov Moscow State University, 1/3 Leninskie Gory, 119991 Moscow, Russia (Z.Z.K.); (I.A.V.); (D.A.L.); (E.A.R.); (I.A.O.); (P.V.S.); (O.A.D.)
| | - Petr V. Sergiev
- Department of Chemistry, Lomonosov Moscow State University, 1/3 Leninskie Gory, 119991 Moscow, Russia (Z.Z.K.); (I.A.V.); (D.A.L.); (E.A.R.); (I.A.O.); (P.V.S.); (O.A.D.)
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 1/40 Leninskie Gory, 119991 Moscow, Russia
- Institute of Functional Genomics, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Olga A. Dontsova
- Department of Chemistry, Lomonosov Moscow State University, 1/3 Leninskie Gory, 119991 Moscow, Russia (Z.Z.K.); (I.A.V.); (D.A.L.); (E.A.R.); (I.A.O.); (P.V.S.); (O.A.D.)
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 1/40 Leninskie Gory, 119991 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Alexey A. Bogdanov
- Department of Chemistry, Lomonosov Moscow State University, 1/3 Leninskie Gory, 119991 Moscow, Russia (Z.Z.K.); (I.A.V.); (D.A.L.); (E.A.R.); (I.A.O.); (P.V.S.); (O.A.D.)
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 1/40 Leninskie Gory, 119991 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Natalia V. Sumbatyan
- Department of Chemistry, Lomonosov Moscow State University, 1/3 Leninskie Gory, 119991 Moscow, Russia (Z.Z.K.); (I.A.V.); (D.A.L.); (E.A.R.); (I.A.O.); (P.V.S.); (O.A.D.)
| |
Collapse
|
7
|
Brakel A, Grochow T, Fritsche S, Knappe D, Krizsan A, Fietz SA, Alber G, Hoffmann R, Müller U. Evaluation of proline-rich antimicrobial peptides as potential lead structures for novel antimycotics against Cryptococcus neoformans. Front Microbiol 2024; 14:1328890. [PMID: 38260890 PMCID: PMC10800876 DOI: 10.3389/fmicb.2023.1328890] [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: 10/27/2023] [Accepted: 12/18/2023] [Indexed: 01/24/2024] Open
Abstract
Background Cryptococcosis and cryptococcal meningitis, caused by Cryptococcus neoformans infections, lead to approximately 180,000 deaths per year, primarily in developing countries. Individuals with compromised immune systems, e.g., due to HIV infection (AIDS) or chemotherapy, are particularly vulnerable. Conventional treatment options are often limited and can cause severe side effects. Therefore, this study aimed to investigate the antifungal effect of insect-derived proline-rich antimicrobial peptides (PrAMPs) against C. neoformans. These peptides are known for their low toxicity and their high efficacy in murine infection models, making them a promising alternative for treatment. Results A preliminary screening of the minimal inhibitory concentrations (MICs) of 20 AMPs, including the well-known PrAMPs Onc112, Api137, and Chex1Arg20 as well as the cathelicidin CRAMP against the C. neoformans strains 1841, H99, and KN99α revealed promising results, with MICs as low as 1.6 μmol/L. Subsequent investigations of selected peptides, determining their influence on fungal colony-forming units, confirmed their strong activity. The antifungal activity was affected by factors such as peptide net charge and sequence, with stronger effects at higher net charges probably due to better intracellular uptake confirmed by confocal laser scanning microscopy. Inactive scrambled peptides suggest a specific intracellular target, although scanning electron microscopy showed that PrAMPs also damaged the cell exterior for a low proportion of the cells. Possible pore formation could facilitate entry into the cytosol.
Collapse
Affiliation(s)
- Alexandra Brakel
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Bioanalytical Chemistry, Leipzig University, Leipzig, Germany
- Center for Biotechnology and Biomedicine, Leipzig University, Leipzig, Germany
| | - Thomas Grochow
- Institute of Veterinary Anatomy, Histology and Embryology, Faculty of Veterinary Medicine, Leipzig University, Leipzig, Germany
| | - Stefanie Fritsche
- Center for Biotechnology and Biomedicine, Leipzig University, Leipzig, Germany
- Institute of Immunology/Molecular Pathogenesis, Faculty of Veterinary Medicine, Leipzig University, Leipzig, Germany
| | - Daniel Knappe
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Bioanalytical Chemistry, Leipzig University, Leipzig, Germany
- Center for Biotechnology and Biomedicine, Leipzig University, Leipzig, Germany
| | - Andor Krizsan
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Bioanalytical Chemistry, Leipzig University, Leipzig, Germany
- Center for Biotechnology and Biomedicine, Leipzig University, Leipzig, Germany
| | - Simone A. Fietz
- Institute of Veterinary Anatomy, Histology and Embryology, Faculty of Veterinary Medicine, Leipzig University, Leipzig, Germany
| | - Gottfried Alber
- Center for Biotechnology and Biomedicine, Leipzig University, Leipzig, Germany
- Institute of Immunology/Molecular Pathogenesis, Faculty of Veterinary Medicine, Leipzig University, Leipzig, Germany
| | - Ralf Hoffmann
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Bioanalytical Chemistry, Leipzig University, Leipzig, Germany
- Center for Biotechnology and Biomedicine, Leipzig University, Leipzig, Germany
| | - Uwe Müller
- Center for Biotechnology and Biomedicine, Leipzig University, Leipzig, Germany
- Institute of Immunology/Molecular Pathogenesis, Faculty of Veterinary Medicine, Leipzig University, Leipzig, Germany
| |
Collapse
|
8
|
Bonvin E, Personne H, Paschoud T, Reusser J, Gan BH, Luscher A, Köhler T, van Delden C, Reymond JL. Antimicrobial Peptide-Peptoid Hybrids with and without Membrane Disruption. ACS Infect Dis 2023; 9:2593-2606. [PMID: 38062792 PMCID: PMC10714400 DOI: 10.1021/acsinfecdis.3c00421] [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: 08/18/2023] [Revised: 11/06/2023] [Accepted: 11/06/2023] [Indexed: 12/18/2023]
Abstract
Among synthetic analogues of antimicrobial peptides (AMPs) under investigation to address antimicrobial resistance, peptoids (N-alkylated oligoglycines) have been reported to act both by membrane disruption and on intracellular targets. Here we gradually introduced peptoid units into the membrane-disruptive undecapeptide KKLLKLLKLLL to test a possible transition toward intracellular targeting. We found that selected hybrids containing up to five peptoid units retained the parent AMP's α-helical folding, membrane disruption, and antimicrobial effects against Gram-negative bacteria including multidrug-resistant (MDR) strains of Pseudomonas aeruginosa and Klebsiella pneumoniae while showing reduced hemolysis and cell toxicities. Furthermore, some hybrids containing as few as three peptoid units as well as the full peptoid lost folding, membrane disruption, hemolysis, and cytotoxicity but displayed strong antibacterial activity under dilute medium conditions typical for proline-rich antimicrobial peptides (PrAMPs), pointing to intracellular targeting. These findings parallel previous reports that partially helical amphiphilic peptoids are privileged oligomers for antibiotic development.
Collapse
Affiliation(s)
- Etienne Bonvin
- Department
of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Hippolyte Personne
- Department
of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Thierry Paschoud
- Department
of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Jérémie Reusser
- Department
of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Bee-Ha Gan
- Department
of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Alexandre Luscher
- Department
of Microbiology and Molecular Medicine, University of Geneva, CH-1211 Geneva, Switzerland
- Service of
Infectious Diseases, University Hospital
of Geneva, CH-1211 Geneva, Switzerland
| | - Thilo Köhler
- Department
of Microbiology and Molecular Medicine, University of Geneva, CH-1211 Geneva, Switzerland
- Service of
Infectious Diseases, University Hospital
of Geneva, CH-1211 Geneva, Switzerland
| | - Christian van Delden
- Department
of Microbiology and Molecular Medicine, University of Geneva, CH-1211 Geneva, Switzerland
- Service of
Infectious Diseases, University Hospital
of Geneva, CH-1211 Geneva, Switzerland
| | - Jean-Louis Reymond
- Department
of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| |
Collapse
|
9
|
Shaikh AY, Björkling F, Zabicka D, Tomczak M, Urbas M, Domraceva I, Kreicberga A, Franzyk H. Structure-activity study of oncocin: On-resin guanidinylation and incorporation of homoarginine, 4-hydroxyproline or 4,4-difluoroproline residues. Bioorg Chem 2023; 141:106876. [PMID: 37797458 DOI: 10.1016/j.bioorg.2023.106876] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/14/2023] [Accepted: 09/18/2023] [Indexed: 10/07/2023]
Abstract
Antimicrobial peptides (AMPs) often display guanidinium functionalities, and hence robust synthetic procedures are needed to facilitate access to analogues with unnatural homologues of arginine (Arg = R). Initially, a resin-bound Arg/Pro-rich fluoren-9-yl-methyloxycarbonyl-protected fragment (Fmoc-RPRPPR) of the AMP oncocin (i.e., VDKPPYLPRPRPPRRIYNR-NH2) was employed in a comparative on-resin assessment of commercial guanidinylation reagents head-to-head with the recently studied bis-Boc-protected triazole-based reagent, 1H-triazole-1-[N,N'-bis(tert-butoxycarbonyl)]-carboxamidine, which was synthesized by a chromatography-free procedure. This reagent was found to enable quantitative conversion in solid-phase peptide synthesis (SPPS) of peptides displaying homoarginine (Har) residues and/or an N-terminal guanidinium group. SPPS was used to obtain analogues of the 18-mer oncocin with single as well as multiple Arg → Har modifications. In addition, the effect of replacement of proline (Pro) residues in oncocin was explored by incorporating single or multiple trans-4-hydroxy-l-proline (Hyp) or 4,4-difluoro-l-proline (Dfp) residues, which both affected hydrophobicity. The resulting peptide library was tested against both Gram-negative and Gram-positive bacteria. Analysis of the minimal inhibitory concentrations (MICs) showed that analogues, displaying modifications at positions 4, 5 and 12 (originally Pro residues), had retained or slightly improved antimicrobial activity. Next, an oncocin analogue with two stabilizing l-Arg → d-Arg replacements in the C-terminal part was further modified by triple-replacement of Pro by either Dfp or Hyp in positions 4, 5, and 12. The resulting analogue displaying three Pro → Dfp modifications proved to possess the best activity profile: MICs of 1-2 µg/mL against E. coli and Klebsiella pneumoniae, less than 1% hemolysis at 800 µg/mL, and an IC50 above 1280 µg/mL in HepG2 cells. Thus, incorporation of bis-fluorinated Pro residues appears to constitute a novel tool in structure-activity studies aimed at optimization of Pro-rich AMPs.
Collapse
Affiliation(s)
- Ashif Y Shaikh
- Center for Peptide-Based Antibiotics, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, DK-2100, Denmark; Department of Chemistry, Khalifa University, Abu Dhabi 127788, United Arab Emirates
| | - Fredrik Björkling
- Center for Peptide-Based Antibiotics, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, DK-2100, Denmark
| | - Dorota Zabicka
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, ul. Chełmska 30/34, 00-725 Warsaw, Poland
| | - Magdalena Tomczak
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, ul. Chełmska 30/34, 00-725 Warsaw, Poland
| | - Malgorzata Urbas
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, ul. Chełmska 30/34, 00-725 Warsaw, Poland
| | - Ilona Domraceva
- Latvian Institute of Organic Synthesis, Aizkraukles 21, 1006 Riga, Latvia
| | - Agrita Kreicberga
- Latvian Institute of Organic Synthesis, Aizkraukles 21, 1006 Riga, Latvia
| | - Henrik Franzyk
- Center for Peptide-Based Antibiotics, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, DK-2100, Denmark.
| |
Collapse
|
10
|
Gasu EN, Mensah JK, Borquaye LS. Computer-aided design of proline-rich antimicrobial peptides based on the chemophysical properties of a peptide isolated from Olivancillaria hiatula. J Biomol Struct Dyn 2023; 41:8254-8275. [PMID: 36218088 DOI: 10.1080/07391102.2022.2131626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 09/27/2022] [Indexed: 10/17/2022]
Abstract
The chemophysical properties of a peptide isolated from Olivancillaria hiatula were combined with computational tools to design new antimicrobial peptides (AMPs). The in silico peptide design utilized arbitrary sequence shuffling, AMP sequence prediction and alignments such that putative sequences mimicked those of proline-rich AMPs (PrAMPs) and were potentially active against bacteria. Molecular modelling and docking experiments were used to monitor peptide binding to some intracellular targets like bacteria ribosome, DnaK and LasR. Peptide candidates were tested in vitro for antibacterial and antivirulence activities. Chemophysical studies of peptide extract suggested hydrophobic, acidic and proline-rich peptide properties. The amino acid signature of the extract matched that of AMPs that inhibit intracellular targets. Two of the designed PrAMP peptides (OhPrP-3 and OhPrP-5) had high affinity for the ribosome and DnaK. OhPrP-1, 2 and 4 also had favorable interactions with the biomolecular targets investigated. Peptides had bactericidal activity at the minimum inhibitory concentration against Pseudomonas aeruginosa. The designed peptides docked strongly to LasR suggesting possible interference with quorum sensing, and this was corroborated by in vitro data where sub-inhibitory doses of all peptides reduced pyocyanin and pyoverdine expression. The designed peptides can be further studied for the development of new anti-infective agents.
Collapse
Affiliation(s)
- Edward Ntim Gasu
- Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Central Laboratory, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - John Kenneth Mensah
- Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Lawrence Sheringham Borquaye
- Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Central Laboratory, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| |
Collapse
|
11
|
Mangano K, Klepacki D, Ohanmu I, Baliga C, Huang W, Brakel A, Krizsan A, Polikanov YS, Hoffmann R, Vázquez-Laslop N, Mankin AS. Inhibition of translation termination by the antimicrobial peptide Drosocin. Nat Chem Biol 2023; 19:1082-1090. [PMID: 36997647 PMCID: PMC10757563 DOI: 10.1038/s41589-023-01300-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 02/24/2023] [Indexed: 04/01/2023]
Abstract
The proline-rich antimicrobial peptide (PrAMP) Drosocin (Dro) from fruit flies shows sequence similarity to other PrAMPs that bind to the ribosome and inhibit protein synthesis by varying mechanisms. The target and mechanism of action of Dro, however, remain unknown. Here we show that Dro arrests ribosomes at stop codons, probably sequestering class 1 release factors associated with the ribosome. This mode of action is comparable to that of apidaecin (Api) from honeybees, making Dro the second member of the type II PrAMP class. Nonetheless, analysis of a comprehensive library of endogenously expressed Dro mutants shows that the interactions of Dro and Api with the target are markedly distinct. While only a few C-terminal amino acids of Api are critical for binding, the interaction of Dro with the ribosome relies on multiple amino acid residues distributed throughout the PrAMP. Single-residue substitutions can substantially enhance the on-target activity of Dro.
Collapse
Affiliation(s)
- Kyle Mangano
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Dorota Klepacki
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Irueosa Ohanmu
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Chetana Baliga
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Weiping Huang
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Alexandra Brakel
- Faculty of Chemistry and Mineralogy, Institute of Bioanalytical Chemistry, Leipzig University, Leipzig, Germany
- Center for Biotechnology and Biomedicine (BBZ), Leipzig University, Leipzig, Germany
| | - Andor Krizsan
- Faculty of Chemistry and Mineralogy, Institute of Bioanalytical Chemistry, Leipzig University, Leipzig, Germany
- Center for Biotechnology and Biomedicine (BBZ), Leipzig University, Leipzig, Germany
| | - Yury S Polikanov
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Ralf Hoffmann
- Faculty of Chemistry and Mineralogy, Institute of Bioanalytical Chemistry, Leipzig University, Leipzig, Germany.
- Center for Biotechnology and Biomedicine (BBZ), Leipzig University, Leipzig, Germany.
| | - Nora Vázquez-Laslop
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA.
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA.
| | - Alexander S Mankin
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA.
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA.
| |
Collapse
|
12
|
Koller TO, Morici M, Berger M, Safdari HA, Lele DS, Beckert B, Kaur KJ, Wilson DN. Structural basis for translation inhibition by the glycosylated drosocin peptide. Nat Chem Biol 2023; 19:1072-1081. [PMID: 36997646 PMCID: PMC10449632 DOI: 10.1038/s41589-023-01293-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 02/14/2023] [Indexed: 04/07/2023]
Abstract
The proline-rich antimicrobial peptide (PrAMP) drosocin is produced by Drosophila species to combat bacterial infection. Unlike many PrAMPs, drosocin is O-glycosylated at threonine 11, a post-translation modification that enhances its antimicrobial activity. Here we demonstrate that the O-glycosylation not only influences cellular uptake of the peptide but also interacts with its intracellular target, the ribosome. Cryogenic electron microscopy structures of glycosylated drosocin on the ribosome at 2.0-2.8-Å resolution reveal that the peptide interferes with translation termination by binding within the polypeptide exit tunnel and trapping RF1 on the ribosome, reminiscent of that reported for the PrAMP apidaecin. The glycosylation of drosocin enables multiple interactions with U2609 of the 23S rRNA, leading to conformational changes that break the canonical base pair with A752. Collectively, our study reveals novel molecular insights into the interaction of O-glycosylated drosocin with the ribosome, which provide a structural basis for future development of this class of antimicrobials.
Collapse
Affiliation(s)
- Timm O Koller
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Martino Morici
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Max Berger
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Haaris A Safdari
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Deepti S Lele
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India
| | - Bertrand Beckert
- Dubochet Center for Imaging (DCI) at EPFL, EPFL SB IPHYS DCI, Lausanne, Switzerland
| | - Kanwal J Kaur
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India
| | - Daniel N Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany.
| |
Collapse
|
13
|
Chen N, Jiang C. Antimicrobial peptides: Structure, mechanism, and modification. Eur J Med Chem 2023; 255:115377. [PMID: 37099837 DOI: 10.1016/j.ejmech.2023.115377] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/03/2023] [Accepted: 04/11/2023] [Indexed: 04/28/2023]
Affiliation(s)
- Na Chen
- School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China
| | - Cheng Jiang
- School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China.
| |
Collapse
|
14
|
Fostier CR, Ousalem F, Leroy EC, Ngo S, Soufari H, Innis CA, Hashem Y, Boël G. Regulation of the macrolide resistance ABC-F translation factor MsrD. Nat Commun 2023; 14:3891. [PMID: 37393329 PMCID: PMC10314930 DOI: 10.1038/s41467-023-39553-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 06/19/2023] [Indexed: 07/03/2023] Open
Abstract
Antibiotic resistance ABC-Fs (ARE ABC-Fs) are translation factors that provide resistance against clinically important ribosome-targeting antibiotics which are proliferating among pathogens. Here, we combine genetic and structural approaches to determine the regulation of streptococcal ARE ABC-F gene msrD in response to macrolide exposure. We show that binding of cladinose-containing macrolides to the ribosome prompts insertion of the leader peptide MsrDL into a crevice of the ribosomal exit tunnel, which is conserved throughout bacteria and eukaryotes. This leads to a local rearrangement of the 23 S rRNA that prevents peptide bond formation and accommodation of release factors. The stalled ribosome obstructs the formation of a Rho-independent terminator structure that prevents msrD transcriptional attenuation. Erythromycin induction of msrD expression via MsrDL, is suppressed by ectopic expression of mrsD, but not by mutants which do not provide antibiotic resistance, showing correlation between MsrD function in antibiotic resistance and its action on this stalled complex.
Collapse
Affiliation(s)
- Corentin R Fostier
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, 75005, Paris, France
| | - Farès Ousalem
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, 75005, Paris, France
| | - Elodie C Leroy
- ARNA Laboratory, UMR 5320, U1212, Institut Européen de Chimie et Biologie, Univ. Bordeaux, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, 33607, Pessac, France
| | - Saravuth Ngo
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, 75005, Paris, France
| | - Heddy Soufari
- ARNA Laboratory, UMR 5320, U1212, Institut Européen de Chimie et Biologie, Univ. Bordeaux, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, 33607, Pessac, France
- SPT Labtech Ltd., SG8 6HB, Melbourn, United Kingdom
| | - C Axel Innis
- ARNA Laboratory, UMR 5320, U1212, Institut Européen de Chimie et Biologie, Univ. Bordeaux, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, 33607, Pessac, France
| | - Yaser Hashem
- ARNA Laboratory, UMR 5320, U1212, Institut Européen de Chimie et Biologie, Univ. Bordeaux, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, 33607, Pessac, France.
| | - Grégory Boël
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, 75005, Paris, France.
| |
Collapse
|
15
|
Gambato S, Bellotto O, Mardirossian M, Di Stasi A, Gennaro R, Pacor S, Caporale A, Berti F, Scocchi M, Tossi A. Designing New Hybrid Antibiotics: Proline-Rich Antimicrobial Peptides Conjugated to the Aminoglycoside Tobramycin. Bioconjug Chem 2023. [PMID: 37379329 PMCID: PMC10360068 DOI: 10.1021/acs.bioconjchem.2c00467] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
Abstract
Resistance to aminoglycoside antibiotics is a serious problem, typically arising from inactivating enzymes, reduced uptake, or increased efflux in the important pathogens for which they are used as treatment. Conjugating aminoglycosides to proline-rich antimicrobial peptides (PrAMPs), which also target ribosomes and have a distinct bacterial uptake mechanism, might mutually benefit their individual activities. To this aim we have developed a strategy for noninvasively modifying tobramycin to link it to a Cys residue and through this covalently link it to a Cys-modified PrAMP by formation of a disulfide bond. Reduction of this bridge in the bacterial cytosol should release the individual antimicrobial moieties. We found that the conjugation of tobramycin to the well-characterized N-terminal PrAMP fragment Bac7(1-35) resulted in a potent antimicrobial capable of inactivating not only tobramycin-resistant bacterial strains but also those less susceptible to the PrAMP. To a certain extent, this activity also extends to the shorter and otherwise poorly active fragment Bac7(1-15). Although the mechanism that allows the conjugate to act when its individual components do not is as yet unclear, results are very promising and suggest this may be a way of resensitizing pathogens that have developed resistance to the antibiotic.
Collapse
Affiliation(s)
- Stefano Gambato
- Department of Life Sciences, University of Trieste, Via L. Giorgeri, 5, 34127 Trieste, Italy
| | - Ottavia Bellotto
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgeri, 1, 34127 Trieste, Italy
| | - Mario Mardirossian
- Department of Life Sciences, University of Trieste, Via L. Giorgeri, 5, 34127 Trieste, Italy
| | - Adriana Di Stasi
- Department of Life Sciences, University of Trieste, Via L. Giorgeri, 5, 34127 Trieste, Italy
| | - Renato Gennaro
- Department of Life Sciences, University of Trieste, Via L. Giorgeri, 5, 34127 Trieste, Italy
| | - Sabrina Pacor
- Department of Life Sciences, University of Trieste, Via L. Giorgeri, 5, 34127 Trieste, Italy
| | - Andrea Caporale
- CNR, Institute of Crystallography, SS 14 Km 163.5 c/o Area Science Park, Basovizza, 34149 Trieste, Italy
- CIRPeB, Research Centre on Bioactive Peptides "Carlo Pedone", University of Naples "Federico II", 80134 Napoli, Italy
| | - Federico Berti
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgeri, 1, 34127 Trieste, Italy
| | - Marco Scocchi
- Department of Life Sciences, University of Trieste, Via L. Giorgeri, 5, 34127 Trieste, Italy
| | - Alessandro Tossi
- Department of Life Sciences, University of Trieste, Via L. Giorgeri, 5, 34127 Trieste, Italy
| |
Collapse
|
16
|
Dho M, Candian V, Tedeschi R. Insect Antimicrobial Peptides: Advancements, Enhancements and New Challenges. Antibiotics (Basel) 2023; 12:952. [PMID: 37370271 DOI: 10.3390/antibiotics12060952] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/21/2023] [Accepted: 05/21/2023] [Indexed: 06/29/2023] Open
Abstract
Several insects are known as vectors of a wide range of animal and human pathogens causing various diseases. However, they are also a source of different substances, such as the Antimicrobial Peptides (AMPs), which can be employed in the development of natural bioactive compounds for medical, veterinary and agricultural applications. It is well known that AMP activity, in contrast to most classical antibiotics, does not lead to the development of natural bacterial resistance, or at least the frequency of resistance is considered to be low. Therefore, there is a strong interest in assessing the efficacy of the various peptides known to date, identifying new compounds and evaluating possible solutions in order to increase their production. Moreover, implementing AMP modulation in insect rearing could preserve insect health in large-scale production. This review describes the current knowledge on insect AMPs, presenting the validated ones for the different insect orders. A brief description of their mechanism of action is reported with focus on proposed applications. The possible effects of insect diet on AMP translation and synthesis have been discussed.
Collapse
Affiliation(s)
- Matteo Dho
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), University of Torino, Largo P. Braccini 2, 10095 Grugliasco, Italy
| | - Valentina Candian
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), University of Torino, Largo P. Braccini 2, 10095 Grugliasco, Italy
| | - Rosemarie Tedeschi
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), University of Torino, Largo P. Braccini 2, 10095 Grugliasco, Italy
| |
Collapse
|
17
|
Makvandi P, Song H, Yiu CKY, Sartorius R, Zare EN, Rabiee N, Wu WX, Paiva-Santos AC, Wang XD, Yu CZ, Tay FR. Bioengineered materials with selective antimicrobial toxicity in biomedicine. Mil Med Res 2023; 10:8. [PMID: 36829246 PMCID: PMC9951506 DOI: 10.1186/s40779-023-00443-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 01/31/2023] [Indexed: 02/26/2023] Open
Abstract
Fungi and bacteria afflict humans with innumerous pathogen-related infections and ailments. Most of the commonly employed microbicidal agents target commensal and pathogenic microorganisms without discrimination. To distinguish and fight the pathogenic species out of the microflora, novel antimicrobials have been developed that selectively target specific bacteria and fungi. The cell wall features and antimicrobial mechanisms that these microorganisms involved in are highlighted in the present review. This is followed by reviewing the design of antimicrobials that selectively combat a specific community of microbes including Gram-positive and Gram-negative bacterial strains as well as fungi. Finally, recent advances in the antimicrobial immunomodulation strategy that enables treating microorganism infections with high specificity are reviewed. These basic tenets will enable the avid reader to design novel approaches and compounds for antibacterial and antifungal applications.
Collapse
Affiliation(s)
- Pooyan Makvandi
- Istituto Italiano di Tecnologia, Centre for Materials Interfaces, Pontedera, 56025, Italy. .,The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, 324000, Zhejiang, China.
| | - Hao Song
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Cynthia K Y Yiu
- Paediatric Dentistry and Orthodontics, Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, Hong Kong SAR, China
| | - Rossella Sartorius
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council (CNR), 80131, Naples, Italy
| | | | - Navid Rabiee
- School of Engineering, Macquarie University, Sydney, NSW, 2109, Australia.,Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, 6150, Australia
| | - Wei-Xi Wu
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ana Cláudia Paiva-Santos
- Department of Pharmaceutical Technology, Faculty of Pharmacy of the University of Coimbra, University of Coimbra, 3000-548, Coimbra, Portugal.,REQUIMTE/LAQV, Group of Pharmaceutical Technology, Faculty of Pharmacy of the University of Coimbra, University of Coimbra, 3000-548, Coimbra, Portugal
| | - Xiang-Dong Wang
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University Shanghai Medical College, Shanghai, 200032, China
| | - Cheng-Zhong Yu
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, 4072, Australia.,School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, China
| | - Franklin R Tay
- The Graduate School, Augusta University, Augusta, GA, 30912, USA.
| |
Collapse
|
18
|
In Vitro Pharmacokinetics of LL-37 and Oncorhyncin II Combination Against Acinetobacter baumannii. Jundishapur J Microbiol 2023. [DOI: 10.5812/jjm-131299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Background: Multidrug-resistant (MDR) Acinetobacter baumannii is one of the most common nosocomial pathogens. Antimicrobial peptides (AMPs) have been introduced as a viable alternative to antibiotics in the treatment of MDR pathogens. Objectives: This study was designed to assess the in vitro pharmacokinetics of the combination of two potent AMPs, LL-37 and oncorhyncin II, against A. baumannii (ATCC19606). Methods: The synthesized genes of oncorhyncin II and LL-37 were introduced into Escherichia coli BL21 as the expression host. The minimum inhibitory concentration (MIC), time-kills, and growth kinetics of these peptides were used to evaluate their antimicrobial efficiencies against A. baumannii (ATCC19606). Results: LL-37 and oncorhyncin II recombinant peptides showed MIC of 30.6 and 95.87 µg/mL against A. baumannii, respectively. Additive action was confirmed by combining the generated AMPs at the checkerboard approach. The combination of LL-37 and oncorhyncin II at 2 × MIC resulted in a rapid drop in log10 CFU/mL of A. baumannii in the time-kill and growth kinetic findings studies. Conclusions: The combination of the produced LL-37 and oncorhyncin II synergizes the bioactivity of the individual peptides. Therefore, these peptides or their combinations might function as novel antibiotics and be used to develop and produce new antimicrobial drugs for the treatment of infections caused by A. baumannii.
Collapse
|
19
|
Perlmutter JI, Chapman JR, Wilkinson MC, Nevarez-Saenz I, Unckless RL. A single amino acid polymorphism in natural Metchnikowin alleles of Drosophila results in systemic immunity and life history tradeoffs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.16.524277. [PMID: 36712113 PMCID: PMC9882182 DOI: 10.1101/2023.01.16.524277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Antimicrobial peptides (AMPs) are at the interface of interactions between hosts and microbes and are therefore expected to be fast evolving in a coevolutionary arms race with pathogens. In contrast, previous work demonstrated that one AMP, Metchikowin (Mtk), has a single residue that segregates as either proline (P) or arginine (R) in populations of four different Drosophila species, some of which diverged more than 10 million years ago. The recurrent finding of this polymorphism regardless of geography or host species, coupled with evidence of balancing selection in Drosophila AMPs, suggest there is a distinct functional importance to each allele. The most likely hypotheses involve alleles having specificity to different pathogens or the more potent allele conferring a cost on the host. To assess their functional differences, we created D. melanogaster lines with the P allele, R allele, or Mtk null mutation using CRISPR/Cas9 genome editing. Here, we report results from experiments assessing the two hypotheses using these lines. In males, testing of systemic immune responses to a repertoire of bacteria and fungi demonstrated that the R allele performs as well or better than the P and null alleles with most infections. With some pathogens, however, females show results in contrast with males where Mtk alleles either do not contribute to survival or where the P allele outperforms the R allele. In addition, measurements of life history traits demonstrate that the R allele is more costly in the absence of infection for both sexes. These results provide strong in vivo evidence that differential fitness with or without infection and sex-based functional differences in alleles may be adaptive mechanisms of maintaining immune gene polymorphisms in contrast with expectations of rapid evolution. Therefore, a complex interplay of forces including pathogen species and host sex may lead to balancing selection for immune genotypes. Strikingly, this selection may act on even a single amino acid polymorphism in an AMP.
Collapse
Affiliation(s)
| | - Joanne R. Chapman
- Institute of Environmental and Scientific Research (ESR), Christchurch, New Zealand
| | - Mason C. Wilkinson
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Isaac Nevarez-Saenz
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | - Robert L. Unckless
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| |
Collapse
|
20
|
Borovsky D, Rougé P, Shatters RG. Bactericidal Properties of Proline-Rich Aedes aegypti Trypsin Modulating Oostatic Factor ( AeaTMOF). LIFE (BASEL, SWITZERLAND) 2022; 13:life13010019. [PMID: 36675967 PMCID: PMC9862690 DOI: 10.3390/life13010019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/16/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
The antimicrobial properties of proline-rich Aedes aegypti decapeptide TMOF (AeaTMOF) and oncocin112 (1-13) were compared. Incubations with multidrug-resistant Escherichia coli cells showed that AeaTMOF (5 mM) was able to completely inhibit bacterial cell growth, whereas oncocin112 (1-13) (20 mM) partially inhibited bacterial growth as compared with bacterial cells that were not multidrug-resistant cells. AeaTMOF (5 mM) was very effective against Acinetobacter baumannii and Pseudomonas aeruginosa, completely inhibiting cell growth during 15 h incubations. AeaTMOF (5 mM) completely inhibited the Gram-positive bacteria Staphylococcus aureus and Bacillus thurengiensis sups. Israelensis cell growth, whereas oncocin112 (1-13) (10 and 20 mM) failed to affect bacterial cell growth. E. coli cells that lack the SbmA transporter were inhibited by AeaTMOF (5 mM) and not by oncocin112 (1-13) (10 to 20 mM), indicating that AeaTMOF can use other bacterial transporters than SbmA that is mainly used by proline-rich antimicrobial peptides. Incubation of E. coli cells with NaAzide showed that AeaTMOF does not use ABC-like transporters that use ATP hydrolysis to import molecules into bacterial cells. Three-dimensional modeling and docking of AeaTMOF to SbmA and MdtM transporters showed that AeaTMOF can bind these proteins, and the binding location of AeaTMOF inside these protein transporters allows AeaTMOF to be transported into the bacterial cytosol. These results show that AeaTMOF can be used as a future antibacterial agent against both multidrug-resistant Gram-positive and -negative bacteria.
Collapse
Affiliation(s)
- Dov Borovsky
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Correspondence:
| | - Pierre Rougé
- Faculte des Sciences Pharmaceutiques, 3106 Toulouse, France
| | | |
Collapse
|
21
|
Structure of Lacticaseicin 30 and Its Engineered Variants Revealed an Interplay between the N-Terminal and C-Terminal Regions in the Activity against Gram-Negative Bacteria. Pharmaceutics 2022; 14:pharmaceutics14091921. [PMID: 36145669 PMCID: PMC9505257 DOI: 10.3390/pharmaceutics14091921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 09/04/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022] Open
Abstract
Lacticaseicin 30 is one of the five bacteriocins produced by the Gram-positive Lacticaseibacillus paracasei CNCM I-5369. This 111 amino acid bacteriocin is noteworthy for being active against Gram-negative bacilli including Escherichia coli strains resistant to colistin. Prediction of the lacticaseicin 30 structure using the Alphafold2 pipeline revealed a largely helical structure including five helix segments, which was confirmed by circular dichroism. To identify the structural requirements of the lacticaseicin 30 activity directed against Gram-negative bacilli, a series of variants, either shortened or containing point mutations, was heterologously produced in Escherichia coli and assayed for their antibacterial activity against a panel of target strains including Gram-negative bacteria and the Gram-positive Listeria innocua. Lacticaseicin 30 variants comprising either the N-terminal region (amino acids 1 to 39) or the central and C-terminal regions (amino acids 40 to 111) were prepared. Furthermore, mutations were introduced by site-directed mutagenesis to obtain ten bacteriocin variants E6G, T7P, E32G, T33P, T52P, D57G, A74P, Y78S, Y93S and A97P. Compared to lacticaseicin 30, the anti-Gram-negative activity of the N-terminal peptide and variants E32G, T33P and D57G remained almost unchanged, while that of the C-terminal peptide and variants E6G, T7P, T52P, A74P, Y78S, Y93S and A97P was significantly altered. Finally, the N-terminal region was further shortened to keep only the first 20 amino acid part that was predicted to include the first helix. The anti-Gram-negative activity of this truncated peptide was completely abolished. Overall, this study shows that activity of lacticaseicin 30, one of the rare Gram-positive bacteriocins inhibiting Gram-negative bacteria, requires at least two helices in the N-terminal region and that the C-terminal region carries amino acids playing a role in modulation of the activity. Taken together, these data will help to design forthcoming variants of lacticaseicin 30 as promising therapeutic agents to treat infections caused by Gram-negative bacilli.
Collapse
|
22
|
Khairullina ZZ, Makarov GI, Tereshchenkov AG, Buev VS, Lukianov DA, Polshakov VI, Tashlitsky VN, Osterman IA, Sumbatyan NV. Conjugates of Desmycosin with Fragments of Antimicrobial Peptide Oncocin: Synthesis, Antibacterial Activity, Interaction with Ribosome. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:871-889. [PMID: 36180983 DOI: 10.1134/s0006297922090024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/17/2022] [Accepted: 06/18/2022] [Indexed: 06/16/2023]
Abstract
Design and synthesis of conjugates consisting of the macrolide antibiotic desmycosin and fragments of the antibacterial peptide oncocin were performed in attempt to develop new antimicrobial compounds. New compounds were shown to bind to the E. coli 70S ribosomes, to inhibit bacterial protein synthesis in vitro, as well as to suppress bacterial growth. The conjugates of N-terminal hexa- and tripeptide fragments of oncocin and 3,2',4''-triacetyldesmycosin were found to be active against some strains of macrolide-resistant bacteria. By simulating molecular dynamics of the complexes of these compounds with the wild-type bacterial ribosomes and with ribosomes, containing A2059G 23S RNA mutation, the specific structural features of their interactions were revealed.
Collapse
Affiliation(s)
| | | | - Andrey G Tereshchenkov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Vitaly S Buev
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Dmitrii A Lukianov
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, 143025, Russia
| | - Vladimir I Polshakov
- Faculty of Fundamental Medicine, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Vadim N Tashlitsky
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Ilya A Osterman
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, 143025, Russia
| | - Natalia V Sumbatyan
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.
| |
Collapse
|
23
|
Blair JMA, Zeth K, Bavro VN, Sancho-Vaello E. The role of bacterial transport systems in the removal of host antimicrobial peptides in Gram-negative bacteria. FEMS Microbiol Rev 2022; 46:6617596. [PMID: 35749576 PMCID: PMC9629497 DOI: 10.1093/femsre/fuac032] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 05/23/2022] [Accepted: 06/22/2022] [Indexed: 01/09/2023] Open
Abstract
Antibiotic resistance is a global issue that threatens our progress in healthcare and life expectancy. In recent years, antimicrobial peptides (AMPs) have been considered as promising alternatives to the classic antibiotics. AMPs are potentially superior due to their lower rate of resistance development, since they primarily target the bacterial membrane ('Achilles' heel' of the bacteria). However, bacteria have developed mechanisms of AMP resistance, including the removal of AMPs to the extracellular space by efflux pumps such as the MtrCDE or AcrAB-TolC systems, and the internalization of AMPs to the cytoplasm by the Sap transporter, followed by proteolytic digestion. In this review, we focus on AMP transport as a resistance mechanism compiling all the experimental evidence for the involvement of efflux in AMP resistance in Gram-negative bacteria and combine this information with the analysis of the structures of the efflux systems involved. Finally, we expose some open questions with the aim of arousing the interest of the scientific community towards the AMPs-efflux pumps interactions. All the collected information broadens our understanding of AMP removal by efflux pumps and gives some clues to assist the rational design of AMP-derivatives as inhibitors of the efflux pumps.
Collapse
Affiliation(s)
- Jessica M A Blair
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Kornelius Zeth
- Department of Science and Environment, Roskilde University, Universitetsvej 1, 4000 Roskilde, Denmark
| | - Vassiliy N Bavro
- School of Life Sciences, University of Essex, Colchester, CO4 3SQ, United Kingdom
| | - Enea Sancho-Vaello
- Corresponding author. College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom. E-mail:
| |
Collapse
|
24
|
|
25
|
Loveland AB, Svidritskiy E, Susorov D, Lee S, Park A, Zvornicanin S, Demo G, Gao FB, Korostelev AA. Ribosome inhibition by C9ORF72-ALS/FTD-associated poly-PR and poly-GR proteins revealed by cryo-EM. Nat Commun 2022; 13:2776. [PMID: 35589706 PMCID: PMC9120013 DOI: 10.1038/s41467-022-30418-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 04/29/2022] [Indexed: 12/15/2022] Open
Abstract
Toxic dipeptide-repeat (DPR) proteins are produced from expanded G4C2 repeats in the C9ORF72 gene, the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Two DPR proteins, poly-PR and poly-GR, repress cellular translation but the molecular mechanism remains unknown. Here we show that poly-PR and poly-GR of ≥20 repeats inhibit the ribosome's peptidyl-transferase activity at nanomolar concentrations, comparable to specific translation inhibitors. High-resolution cryogenic electron microscopy (cryo-EM) reveals that poly-PR and poly-GR block the polypeptide tunnel of the ribosome, extending into the peptidyl-transferase center (PTC). Consistent with these findings, the macrolide erythromycin, which binds in the tunnel, competes with poly-PR and restores peptidyl-transferase activity. Our results demonstrate that strong and specific binding of poly-PR and poly-GR in the ribosomal tunnel blocks translation, revealing the structural basis of their toxicity in C9ORF72-ALS/FTD.
Collapse
Affiliation(s)
- Anna B Loveland
- RNA Therapeutics Institute, UMass Chan Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Egor Svidritskiy
- RNA Therapeutics Institute, UMass Chan Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Denis Susorov
- RNA Therapeutics Institute, UMass Chan Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Soojin Lee
- Department of Neurology, UMass Chan Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Alexander Park
- RNA Therapeutics Institute, UMass Chan Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Sarah Zvornicanin
- RNA Therapeutics Institute, UMass Chan Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Gabriel Demo
- RNA Therapeutics Institute, UMass Chan Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
- Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Fen-Biao Gao
- Department of Neurology, UMass Chan Medical School, 368 Plantation Street, Worcester, MA, 01605, USA.
| | - Andrei A Korostelev
- RNA Therapeutics Institute, UMass Chan Medical School, 368 Plantation Street, Worcester, MA, 01605, USA.
| |
Collapse
|
26
|
Panteleev PV, Safronova VN, Kruglikov RN, Bolosov IA, Bogdanov IV, Ovchinnikova TV. A Novel Proline-Rich Cathelicidin from the Alpaca Vicugna pacos with Potency to Combat Antibiotic-Resistant Bacteria: Mechanism of Action and the Functional Role of the C-Terminal Region. MEMBRANES 2022; 12:membranes12050515. [PMID: 35629841 PMCID: PMC9146984 DOI: 10.3390/membranes12050515] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/04/2022] [Accepted: 05/09/2022] [Indexed: 02/04/2023]
Abstract
Over recent years, a growing number of bacterial species have become resistant to clinically relevant antibiotics. Proline-rich antimicrobial peptides (PrAMPs) having a potent antimicrobial activity and a negligible toxicity toward mammalian cells attract attention as new templates for the development of antibiotic drugs. Here, we mined genomes of all living Camelidae species and found a novel family of Bac7-like proline-rich cathelicidins which inhibited bacterial protein synthesis. The N-terminal region of a novel peptide from the alpaca Vicugna pacos named VicBac is responsible for inhibition of bacterial protein synthesis with an IC50 value of 0.5 µM in the E. coli cell-free system whereas the C-terminal region allows the peptide to penetrate bacterial membranes effectively. We also found that the full-length VicBac did not induce bacterial resistance after a two-week selection experiment, unlike the N-terminal truncated analog, which depended on the SbmA transport system. Both pro- and anti-inflammatory action of VicBac and its N-terminal truncated variant on various human cell types was found by multiplex immunoassay. The presence of the C-terminal tail in the natural VicBac does not provide for specific immune-modulatory effects in vitro but enhances the observed impact compared with the truncated analog. The pronounced antibacterial activity of VicBac, along with its moderate adverse effects on mammalian cells, make this molecule a promising scaffold for the development of peptide antibiotics.
Collapse
|
27
|
Wieland M, Holm M, Rundlet EJ, Morici M, Koller TO, Maviza TP, Pogorevc D, Osterman IA, Müller R, Blanchard SC, Wilson DN. The cyclic octapeptide antibiotic argyrin B inhibits translation by trapping EF-G on the ribosome during translocation. Proc Natl Acad Sci U S A 2022; 119:e2114214119. [PMID: 35500116 PMCID: PMC9171646 DOI: 10.1073/pnas.2114214119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 03/16/2022] [Indexed: 11/18/2022] Open
Abstract
Argyrins are a family of naturally produced octapeptides that display promising antimicrobial activity against Pseudomonas aeruginosa. Argyrin B (ArgB) has been shown to interact with an elongated form of the translation elongation factor G (EF-G), leading to the suggestion that argyrins inhibit protein synthesis by interfering with EF-G binding to the ribosome. Here, using a combination of cryo-electron microscopy (cryo-EM) and single-molecule fluorescence resonance energy transfer (smFRET), we demonstrate that rather than interfering with ribosome binding, ArgB rapidly and specifically binds EF-G on the ribosome to inhibit intermediate steps of the translocation mechanism. Our data support that ArgB inhibits conformational changes within EF-G after GTP hydrolysis required for translocation and factor dissociation, analogous to the mechanism of fusidic acid, a chemically distinct antibiotic that binds a different region of EF-G. These findings shed light on the mechanism of action of the argyrin-class antibiotics on protein synthesis as well as the nature and importance of rate-limiting, intramolecular conformational events within the EF-G-bound ribosome during late-steps of translocation.
Collapse
Affiliation(s)
- Maximiliane Wieland
- Institute for Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany
| | - Mikael Holm
- St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Emily J. Rundlet
- St. Jude Children's Research Hospital, Memphis, TN 38105
- Weill Cornell Medicine, Tri-Institutional PhD Program in Chemical Biology, New York, NY 10065
| | - Martino Morici
- Institute for Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany
| | - Timm O. Koller
- Institute for Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany
| | - Tinashe P. Maviza
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
| | - Domen Pogorevc
- Department Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research, Saarland University, 66123 Saarbrücken,Germany
| | - Ilya A. Osterman
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Rolf Müller
- Department Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research, Saarland University, 66123 Saarbrücken,Germany
| | | | - Daniel N. Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany
| |
Collapse
|
28
|
Borovsky D, Rougé P, Shatters RG. The Ribosome Is the Ultimate Receptor for Trypsin Modulating Oostatic Factor (TMOF). Biomolecules 2022; 12:biom12040577. [PMID: 35454167 PMCID: PMC9028786 DOI: 10.3390/biom12040577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 02/06/2023] Open
Abstract
Aedes aegypti Trypsin Modulating Oostatic Factor (AeaTMOF). a mosquito decapeptide that controls trypsin biosynthesis in female and larval mosquitoes. enters the gut epithelial cells of female mosquitoes using ABC-tmfA receptor/importer. To study the ultimate targeted receptor after AeaTMOF enters the cell, AeaTMOF was incubated in vitro with either Escherichia coli or Spodoptera frugiperda protein-expressing extracts containing 70S and 80S ribosomes, respectively. The effect of AeaTMOF on luciferase biosynthesis in vitro using 70S ribosomes was compared with that of oncocin112 (1–13), a ribosome-binding antibacterial peptide. The IC50 of 1 μM and 2 μM, respectively, for both peptides was determined. Incubation with a protein-expressing system and S. frugiperda 80S ribosomes determined an IC50 of 1.8 μM for Aedes aegypti larval late trypsin biosynthesis. Incubation of purified E. coli ribosome with increasing concentration of AeaTMOF shows that the binding of AeaTMOF to the bacterial ribosome exhibits a high affinity (KD = 23 ± 3.4 nM, Bmax = 0.553 ± 0.023 pmol/μg ribosome and Kassoc = 4.3 × 107 M−1). Molecular modeling and docking experiments show that AeaTMOF binds bacterial and Drosophila ribosome (50S and 60S, respectively) at the entrance of the ribosome exit tunnel, blocking the tRNA entrance and preventing protein biosynthesis. Recombinant E. coli cells that express only ABC-tmfA importer are inhibited by AeaTMOF but not by oncocin112 (1–13). These results suggest that the ribosome is the ultimate targeted receptor of AeaTMOF.
Collapse
Affiliation(s)
- Dov Borovsky
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz, Aurora, CO 80045, USA
- Correspondence:
| | - Pierre Rougé
- UMR 152 Pharma-Dev, Faculté des Sciences Pharmaceutiques, Université Toulouse 3, CEDEX 09, F-31062 Toulouse, France;
| | - Robert G. Shatters
- USDA ARS, U.S. Horticultural Research Laboratory, Subtropical Insects and Horticulture Research Unit, 2001 Rock Road, Fort Pierce, FL 34945, USA;
| |
Collapse
|
29
|
Ludwig T, Krizsan A, Mohammed GK, Hoffmann R. Antimicrobial Activity and 70S Ribosome Binding of Apidaecin-Derived Api805 with Increased Bacterial Uptake Rate. Antibiotics (Basel) 2022; 11:antibiotics11040430. [PMID: 35453182 PMCID: PMC9025336 DOI: 10.3390/antibiotics11040430] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 03/21/2022] [Accepted: 03/21/2022] [Indexed: 02/07/2023] Open
Abstract
In view of the global spread of multiresistant bacteria and the occurrence of panresistant bacteria, there is an urgent need for antimicrobials with novel modes of action. A promising class is antimicrobial peptides (AMPs), including them proline-rich AMPs (PrAMPs), which target the 70S ribosome to inhibit protein translation. Here, we present a new designer peptide, Api805, combining the N- and C-terminal sequences of PrAMPs Api137 and drosocin, respectively. Api805 was similarly active against two Escherichia coli B strains but was inactive against E. coli K12 strain BW25113. These different activities could not be explained by the dissociation constants measured for 70S ribosome preparations from E. coli K12 and B strains. Mutations in the SbmA transporter that PrAMPs use to pass the inner membrane or proteolytic degradation of Api805 by lysate proteases could not explain this either. Interestingly, Api805 seems not to bind to the known binding sites of PrAMPs at the 70S ribosome and inhibited in vitro protein translation, independent of release factors, most likely using a “multimodal effect”. Interestingly, Api805 entered the E. coli B strain Rosetta faster and at larger quantities than the E. coli K-12 strain BW25113, which may be related to the different LPS core structure. In conclusion, slight structural changes in PrAMPs significantly altered their binding sites and mechanisms of action, allowing for the design of different antibiotic classes.
Collapse
Affiliation(s)
- Tobias Ludwig
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany; (T.L.); (A.K.); (G.K.M.)
- Center for Biotechnology and Biomedicine (BBZ), Universität Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany
| | - Andor Krizsan
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany; (T.L.); (A.K.); (G.K.M.)
- Center for Biotechnology and Biomedicine (BBZ), Universität Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany
| | - Gubran Khalil Mohammed
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany; (T.L.); (A.K.); (G.K.M.)
- Center for Biotechnology and Biomedicine (BBZ), Universität Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany
| | - Ralf Hoffmann
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany; (T.L.); (A.K.); (G.K.M.)
- Center for Biotechnology and Biomedicine (BBZ), Universität Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany
- Correspondence:
| |
Collapse
|
30
|
Dewangan RP, Verma DP, Verma NK, Gupta A, Pant G, Mitra K, Habib S, Ghosh JK. Spermine-Conjugated Short Proline-Rich Lipopeptides as Broad-Spectrum Intracellular Targeting Antibacterial Agents. J Med Chem 2022; 65:5433-5448. [PMID: 35297625 DOI: 10.1021/acs.jmedchem.1c01809] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Toward the design of new proline-rich peptidomimetics, a short peptide segment, present in several proline-rich antimicrobial peptides (AMPs), was selected. Fatty acids of varying lengths and spermine were conjugated at the N- and C-terminals of the peptide, respectively. Spermine-conjugated lipopeptides, C10-PR-Spn and C12-PR-Spn, exhibited minimum inhibitory concentrations within 1.5-6.2 μM against the tested pathogens including resistant bacteria and insignificant hemolytic activity against human red blood cells up to 100 μM concentrations and demonstrated resistance against trypsin digestion. C10-PR-Spn and C12-PR-Spn showed synergistic antimicrobial activity against multidrug-resistant methicillin-resistant Staphylococcus aureus with several tested antibiotics. These lipopeptides did not permeabilize bacterial membrane-mimetic lipid vesicles or damage the Escherichia coli membrane like the nonmembrane-lytic AMP, buforin-II. The results suggested that C10-PR-Spn and C12-PR-Spn could interact with the 70S ribosome of E. coli and inhibit its protein synthesis. C10-PR-Spn and C12-PR-Spn demonstrated superior clearance of bacteria from the spleen, liver, and kidneys of mice, infected with S. aureus ATCC 25923 compared to levofloxacin.
Collapse
Affiliation(s)
- Rikeshwer Prasad Dewangan
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh 226031, India
| | - Devesh Pratap Verma
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh 226031, India
| | - Neeraj Kumar Verma
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh 226031, India
| | - Ankit Gupta
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh 226031, India
| | - Garima Pant
- Electron Microscopy Unit, SAIF Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Kalyan Mitra
- Electron Microscopy Unit, SAIF Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Saman Habib
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh 226031, India
| | - Jimut Kanti Ghosh
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh 226031, India
| |
Collapse
|
31
|
Brakel A, Krizsan A, Itzenga R, Kraus CN, Otvos L, Hoffmann R. Influence of Substitutions in the Binding Motif of Proline-Rich Antimicrobial Peptide ARV-1502 on 70S Ribosome Binding and Antimicrobial Activity. Int J Mol Sci 2022; 23:ijms23063150. [PMID: 35328571 PMCID: PMC8950706 DOI: 10.3390/ijms23063150] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/07/2022] [Accepted: 03/11/2022] [Indexed: 01/10/2023] Open
Abstract
Proline-rich antimicrobial peptides (PrAMPs) are promising candidates to treat bacterial infections. The designer peptide ARV-1502 exhibits strong antimicrobial effects against Enterobacteriaceae both in vitro and in vivo. Since the inhibitory effects of ARV-1502 reported for the 70 kDa heat-shock protein DnaK do not fully explain the antimicrobial activity of its 176 substituted analogs, we further studied their effect on the bacterial 70S ribosome of Escherichia coli, a known target of PrAMPs. ARV-1502 analogues, substituted in positions 3, 4, and 8 to 12 (underlined) of the binding motif D3KPRPYLPRP12 with aspartic acid, lysine, serine, phenylalanine or leucine, were tested in a competitive fluorescence polarization (FP) binding screening assay using 5(6)-carboxyfluorescein-labeled (Cf-) ARV-1502 and the 70S ribosome isolated from E. coli BW25113. While their effect on ribosomal protein expression was studied for green fluorescent protein (GFP) in a cell-free expression system (in vitro translation), the importance of known PrAMP transporters SbmA and MdtM was investigated using E. coli BW25113 and the corresponding knockout mutants. The dissociation constant (Kd) of 201 ± 16 nmol/L obtained for Cf-ARV-1502 suggests strong binding to the E. coli 70S ribosome. An inhibitory binding assay indicated that the binding site overlaps with those of other PrAMPs including Onc112 and pyrrhocoricin as well as the non-peptidic antibiotics erythromycin and chloramphenicol. All these drugs and drug candidates bind to the exit-tunnel of the 70S ribosome. Substitutions of the C-terminal fragment of the binding motif YLPRP reduced binding. At the same time, inhibition of GFP expression increased with net peptide charge. Interestingly, the MIC values of wild-type and ΔsbmA and ΔmdtM knockout mutants indicated that substitutions in the ribosomal binding motif altered also the bacterial uptake, which was generally improved by incorporation of hydrophobic residues. In conclusion, most substituted ARV-1502 analogs bound weaker to the 70S ribosome than ARV-1502 underlining the importance of the YLPRP binding motif. The weaker ribosomal binding correlated well with decreased antimicrobial activity in vitro. Substituted ARV-1502 analogs with a higher level of hydrophobicity or positive net charge improved the ribosome binding, inhibition of translation, and bacterial uptake.
Collapse
Affiliation(s)
- Alexandra Brakel
- Faculty of Chemistry and Mineralogy, Institute of Bioanalytical Chemistry, Universität Leipzig, 04109 Leipzig, Germany; (A.K.); (R.I.)
- Center for Biotechnology and Biomedicine, Universität Leipzig, 04109 Leipzig, Germany
- Correspondence: (A.B.); (R.H.)
| | - Andor Krizsan
- Faculty of Chemistry and Mineralogy, Institute of Bioanalytical Chemistry, Universität Leipzig, 04109 Leipzig, Germany; (A.K.); (R.I.)
- Center for Biotechnology and Biomedicine, Universität Leipzig, 04109 Leipzig, Germany
| | - Renke Itzenga
- Faculty of Chemistry and Mineralogy, Institute of Bioanalytical Chemistry, Universität Leipzig, 04109 Leipzig, Germany; (A.K.); (R.I.)
- Center for Biotechnology and Biomedicine, Universität Leipzig, 04109 Leipzig, Germany
| | - Carl N. Kraus
- Aceragen Inc., Durham, NC 27709, USA; (C.N.K.); (L.O.J.)
| | - Laszlo Otvos
- Aceragen Inc., Durham, NC 27709, USA; (C.N.K.); (L.O.J.)
- Institute of Medical Microbiology, Semmelweis University, 1085 Budapest, Hungary
| | - Ralf Hoffmann
- Faculty of Chemistry and Mineralogy, Institute of Bioanalytical Chemistry, Universität Leipzig, 04109 Leipzig, Germany; (A.K.); (R.I.)
- Center for Biotechnology and Biomedicine, Universität Leipzig, 04109 Leipzig, Germany
- Correspondence: (A.B.); (R.H.)
| |
Collapse
|
32
|
Landon C, Zhu Y, Mustafi M, Madinier JB, Lelièvre D, Aucagne V, Delmas AF, Weisshaar JC. Real-Time Fluorescence Microscopy on Living E. coli Sheds New Light on the Antibacterial Effects of the King Penguin β-Defensin AvBD103b. Int J Mol Sci 2022; 23:ijms23042057. [PMID: 35216173 PMCID: PMC8880245 DOI: 10.3390/ijms23042057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/31/2022] [Accepted: 02/09/2022] [Indexed: 12/17/2022] Open
Abstract
(1) Antimicrobial peptides (AMPs) are a promising alternative to conventional antibiotics. Among AMPs, the disulfide-rich β-defensin AvBD103b, whose antibacterial activities are not inhibited by salts contrary to most other β-defensins, is particularly appealing. Information about the mechanisms of action is mandatory for the development and approval of new drugs. However, data for non-membrane-disruptive AMPs such as β-defensins are scarce, thus they still remain poorly understood. (2) We used single-cell fluorescence imaging to monitor the effects of a β-defensin (namely AvBD103b) in real time, on living E. coli, and at the physiological concentration of salts. (3) We obtained key parameters to dissect the mechanism of action. The cascade of events, inferred from our precise timing of membrane permeabilization effects, associated with the timing of bacterial growth arrest, differs significantly from the other antimicrobial compounds that we previously studied in the same physiological conditions. Moreover, the AvBD103b mechanism does not involve significant stereo-selective interaction with any chiral partner, at any step of the process. (4) The results are consistent with the suggestion that after penetrating the outer membrane and the cytoplasmic membrane, AvBD103b interacts non-specifically with a variety of polyanionic targets, leading indirectly to cell death.
Collapse
Affiliation(s)
- Céline Landon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; (Y.Z.); (M.M.); (J.C.W.)
- Center for Molecular Biophysics, CNRS, 45071 Orléans, France; (J.-B.M.); (D.L.); (V.A.); (A.F.D.)
- Correspondence:
| | - Yanyu Zhu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; (Y.Z.); (M.M.); (J.C.W.)
| | - Mainak Mustafi
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; (Y.Z.); (M.M.); (J.C.W.)
| | - Jean-Baptiste Madinier
- Center for Molecular Biophysics, CNRS, 45071 Orléans, France; (J.-B.M.); (D.L.); (V.A.); (A.F.D.)
| | - Dominique Lelièvre
- Center for Molecular Biophysics, CNRS, 45071 Orléans, France; (J.-B.M.); (D.L.); (V.A.); (A.F.D.)
| | - Vincent Aucagne
- Center for Molecular Biophysics, CNRS, 45071 Orléans, France; (J.-B.M.); (D.L.); (V.A.); (A.F.D.)
| | - Agnes F. Delmas
- Center for Molecular Biophysics, CNRS, 45071 Orléans, France; (J.-B.M.); (D.L.); (V.A.); (A.F.D.)
| | - James C. Weisshaar
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; (Y.Z.); (M.M.); (J.C.W.)
| |
Collapse
|
33
|
Vazquez-Laslop N, Sharma CM, Mankin A, Buskirk AR. Identifying Small Open Reading Frames in Prokaryotes with Ribosome Profiling. J Bacteriol 2022; 204:e0029421. [PMID: 34339296 PMCID: PMC8765392 DOI: 10.1128/jb.00294-21] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Small proteins encoded by open reading frames (ORFs) shorter than 50 codons (small ORFs [sORFs]) are often overlooked by annotation engines and are difficult to characterize using traditional biochemical techniques. Ribosome profiling has tremendous potential to empirically improve the annotations of prokaryotic genomes. Recent improvements in ribosome profiling methods for bacterial model organisms have revealed many new sORFs in well-characterized genomes. Antibiotics that trap ribosomes just after initiation have played a key role in these developments by allowing the unambiguous identification of the start codons (and, hence, the reading frame) for novel ORFs. Here, we describe these new methods and highlight critical controls and considerations for adapting ribosome profiling to different prokaryotic species.
Collapse
Affiliation(s)
- Nora Vazquez-Laslop
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Cynthia M. Sharma
- Molecular Infection Biology II, Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Alexander Mankin
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Allen R. Buskirk
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| |
Collapse
|
34
|
Kolano L, Knappe D, Berg A, Berg T, Hoffmann R. Effect of amino acid substitutions on 70S ribosomal binding, cellular uptake, and antimicrobial activity of oncocin Onc112. Chembiochem 2021; 23:e202100609. [PMID: 34902208 PMCID: PMC9306569 DOI: 10.1002/cbic.202100609] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Indexed: 11/06/2022]
Abstract
Proline‐rich antimicrobial peptides (PrAMPs) are promising candidates for the treatment of infections caused by high‐priority human pathogens. Their mode of action consists of (I) passive diffusion across the outer membrane, (II) active transport through the inner membrane, and (III) inhibition of protein biosynthesis by blocking the exit tunnel of the 70S ribosome. We tested whether in vitro data on ribosomal binding and bacterial uptake could predict the antibacterial activity of PrAMPs against Gram‐negative and Gram‐positive bacteria. Ribosomal binding and bacterial uptake rates were measured for 47 derivatives of PrAMP Onc112 and compared to the minimal inhibitory concentrations (MIC) of each peptide. Ribosomal binding was evaluated for ribosome extracts from four Gram‐negative bacteria. Bacterial uptake was assessed by quantifying each peptide in the supernatants of bacterial cultures. Oncocin analogues with a higher net positive charge appeared to be more active, although their ribosome binding and uptake rates were not necessarily better than for Onc112. The data suggest a complex mode of action influenced by further factors improving or reducing the antibacterial activity, including diffusion through membranes, transport mechanism, secondary targets, off‐target binding, intracellular distribution, and membrane effects. Relying only on in vitro binding and uptake data may not be sufficient for the rational development of more active analogues.
Collapse
Affiliation(s)
- Lisa Kolano
- Universität Leipzig Fakultät für Chemie und Mineralogie: Universitat Leipzig Fakultat fur Chemie und Mineralogie, Chemie und Mineralogie, GERMANY
| | - Daniel Knappe
- Universität Leipzig Fakultät für Chemie und Mineralogie: Universitat Leipzig Fakultat fur Chemie und Mineralogie, Chemie und Mineralogie, GERMANY
| | - Angela Berg
- Universität Leipzig Fakultät für Chemie und Mineralogie: Universitat Leipzig Fakultat fur Chemie und Mineralogie, Chemie und Mineralogie, GERMANY
| | - Thorsten Berg
- Universität Leipzig Fakultät für Chemie und Mineralogie: Universitat Leipzig Fakultat fur Chemie und Mineralogie, Chemie und Mineralogie, GERMANY
| | - Ralf Hoffmann
- Institut für Bioanalytische Chemie, Biotechnologisch-Biomedizinisches Zentrum, Deutscher Platz 5, 04103, Leipzig, GERMANY
| |
Collapse
|
35
|
Shirokikh NE. Translation complex stabilization on messenger RNA and footprint profiling to study the RNA responses and dynamics of protein biosynthesis in the cells. Crit Rev Biochem Mol Biol 2021; 57:261-304. [PMID: 34852690 DOI: 10.1080/10409238.2021.2006599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
During protein biosynthesis, ribosomes bind to messenger (m)RNA, locate its protein-coding information, and translate the nucleotide triplets sequentially as codons into the corresponding sequence of amino acids, forming proteins. Non-coding mRNA features, such as 5' and 3' untranslated regions (UTRs), start sites or stop codons of different efficiency, stretches of slower or faster code and nascent polypeptide interactions can alter the translation rates transcript-wise. Most of the homeostatic and signal response pathways of the cells converge on individual mRNA control, as well as alter the global translation output. Among the multitude of approaches to study translational control, one of the most powerful is to infer the locations of translational complexes on mRNA based on the mRNA fragments protected by these complexes from endonucleolytic hydrolysis, or footprints. Translation complex profiling by high-throughput sequencing of the footprints allows to quantify the transcript-wise, as well as global, alterations of translation, and uncover the underlying control mechanisms by attributing footprint locations and sizes to different configurations of the translational complexes. The accuracy of all footprint profiling approaches critically depends on the fidelity of footprint generation and many methods have emerged to preserve certain or multiple configurations of the translational complexes, often in challenging biological material. In this review, a systematic summary of approaches to stabilize translational complexes on mRNA for footprinting is presented and major findings are discussed. Future directions of translation footprint profiling are outlined, focusing on the fidelity and accuracy of inference of the native in vivo translation complex distribution on mRNA.
Collapse
Affiliation(s)
- Nikolay E Shirokikh
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| |
Collapse
|
36
|
Mao Y, Seravalli J, Smith TG, Morton M, Tanner JJ, Becker DF. Evidence for Proline Catabolic Enzymes in the Metabolism of Thiazolidine Carboxylates. Biochemistry 2021; 60:3610-3620. [PMID: 34752700 DOI: 10.1021/acs.biochem.1c00625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thiazolidine carboxylates such as thiazolidine-4-carboxylate (T4C) and thiazolidine-2-carboxylate (T2C) are naturally occurring sulfur analogues of proline. These compounds have been observed to have both beneficial and toxic effects in cells. Given that proline dehydrogenase has been proposed to be a key enzyme in the oxidative metabolism of thioprolines, we characterized T4C and T2C as substrates of proline catabolic enzymes using proline utilization A (PutA), which is a bifunctional enzyme with proline dehydrogenase (PRODH) and l-glutamate-γ-semialdehyde dehydrogenase (GSALDH) activities. PutA is shown here to catalyze the FAD-dependent PRODH oxidation of both T4C and T2C with catalytic efficiencies significantly higher than with proline. Stopped-flow experiments also demonstrate that l-T4C and l-T2C reduce PutA-bound FAD at rates faster than proline. Unlike proline, however, oxidation of T4C and T2C does not generate a substrate for NAD+-dependent GSALDH. Instead, PutA/PRODH oxidation of T4C leads to cysteine formation, whereas oxidation of T2C generates an apparently stable Δ4-thiazoline-2-carboxylate species. Our results provide new insights into the metabolism of T2C and T4C.
Collapse
Affiliation(s)
- Yizi Mao
- Department of Biochemistry, Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588, United States
| | - Javier Seravalli
- Department of Biochemistry, Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588, United States
| | - Thomas G Smith
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588, United States
| | - Martha Morton
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588, United States
| | - John J Tanner
- Departments of Biochemistry and Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Donald F Becker
- Department of Biochemistry, Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588, United States
| |
Collapse
|
37
|
Bin Hafeez A, Jiang X, Bergen PJ, Zhu Y. Antimicrobial Peptides: An Update on Classifications and Databases. Int J Mol Sci 2021; 22:11691. [PMID: 34769122 PMCID: PMC8583803 DOI: 10.3390/ijms222111691] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/24/2021] [Accepted: 10/25/2021] [Indexed: 02/06/2023] Open
Abstract
Antimicrobial peptides (AMPs) are distributed across all kingdoms of life and are an indispensable component of host defenses. They consist of predominantly short cationic peptides with a wide variety of structures and targets. Given the ever-emerging resistance of various pathogens to existing antimicrobial therapies, AMPs have recently attracted extensive interest as potential therapeutic agents. As the discovery of new AMPs has increased, many databases specializing in AMPs have been developed to collect both fundamental and pharmacological information. In this review, we summarize the sources, structures, modes of action, and classifications of AMPs. Additionally, we examine current AMP databases, compare valuable computational tools used to predict antimicrobial activity and mechanisms of action, and highlight new machine learning approaches that can be employed to improve AMP activity to combat global antimicrobial resistance.
Collapse
Affiliation(s)
- Ahmer Bin Hafeez
- Centre of Biotechnology and Microbiology, University of Peshawar, Peshawar 25120, Pakistan;
| | - Xukai Jiang
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; (X.J.); (P.J.B.)
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, China
| | - Phillip J. Bergen
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; (X.J.); (P.J.B.)
| | - Yan Zhu
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; (X.J.); (P.J.B.)
| |
Collapse
|
38
|
DeJong MP, Ritter SC, Fransen KA, Tresnak DT, Golinski AW, Hackel BJ. A Platform for Deep Sequence-Activity Mapping and Engineering Antimicrobial Peptides. ACS Synth Biol 2021; 10:2689-2704. [PMID: 34506711 DOI: 10.1021/acssynbio.1c00314] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Developing potent antimicrobials, and platforms for their study and engineering, is critical as antibiotic resistance grows. A high-throughput method to quantify antimicrobial peptide and protein (AMP) activity across a broad continuum would be powerful to elucidate sequence-activity landscapes and identify potent mutants. Yet the complexity of antimicrobial activity has largely constrained the scope and mechanistic bandwidth of AMP variant analysis. We developed a platform to efficiently perform sequence-activity mapping of AMPs via depletion (SAMP-Dep): a bacterial host culture is transformed with an AMP mutant library, induced to intracellularly express AMPs, grown under selective pressure, and deep sequenced to quantify mutant depletion. The slope of mutant growth rate versus induction level indicates potency. Using SAMP-Dep, we mapped the sequence-activity landscape of 170 000 mutants of oncocin, a proline-rich AMP, for intracellular activity against Escherichia coli. Clonal validation supported the platform's sensitivity and accuracy. The mapped landscape revealed an extended oncocin pharmacophore contrary to earlier structural studies, clarified the C-terminus role in internalization, identified functional epistasis, and guided focused, successful synthetic peptide library design, yielding a mutant with 2-fold enhancement in both intracellular and extracellular activity. The efficiency of SAMP-Dep poises the platform to transform AMP engineering, characterization, and discovery.
Collapse
Affiliation(s)
- Matthew P. DeJong
- Department of Chemical Engineering and Materials Science, University of Minnesota − Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Seth C. Ritter
- Department of Chemical Engineering and Materials Science, University of Minnesota − Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Katharina A. Fransen
- Department of Chemical Engineering and Materials Science, University of Minnesota − Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Daniel T. Tresnak
- Department of Chemical Engineering and Materials Science, University of Minnesota − Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Alexander W. Golinski
- Department of Chemical Engineering and Materials Science, University of Minnesota − Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Benjamin J. Hackel
- Department of Chemical Engineering and Materials Science, University of Minnesota − Twin Cities, Minneapolis, Minnesota 55455, United States
| |
Collapse
|
39
|
Pacor S, Benincasa M, Musso MV, Krce L, Aviani I, Pallavicini A, Scocchi M, Gerdol M, Mardirossian M. The proline-rich myticalins from Mytilus galloprovincialis display a membrane-permeabilizing antimicrobial mode of action. Peptides 2021; 143:170594. [PMID: 34118363 DOI: 10.1016/j.peptides.2021.170594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/19/2021] [Accepted: 06/03/2021] [Indexed: 12/15/2022]
Abstract
Bivalve mollusks are continuously exposed to potentially pathogenic microorganisms living in the marine environment. Not surprisingly, these filter-feeders developed a robust innate immunity to protect themselves, which includes a broad panel of antimicrobial peptides. Among these, myticalins represent a recently discovered family of linear cationic peptides expressed in the gills of Mytilus galloprovincialis. Even though myticalins and insect and mammalian proline-rich antimicrobial peptides (PrAMPs) share a similar amino acid composition, we here show that none of the tested mussel peptides use a non-lytic mode of action relying on the bacterial transporter SbmA. On the other hand, all the tested myticalins perturbed and permeabilized the membranes of E. coli BW25113, as shown by flow-cytometry and atomic force microscopy. Circular dichroism spectra revealed that most myticalins did not adopt recognizable secondary structures in the presence of amphipathic environments, such as biological membranes. To explore possible uses of myticalins for biotech, we assessed their biocompatibility with a human cell line. Non-negligible cytotoxic effects displayed by myticalins indicate that their optimization would be required before their further use as lead compounds in the development of new antibiotics.
Collapse
Affiliation(s)
- Sabrina Pacor
- Department of Life Sciences, Via Licio Giorgieri 5, University of Trieste, 34127 Trieste, Italy.
| | - Monica Benincasa
- Department of Life Sciences, Via Licio Giorgieri 5, University of Trieste, 34127 Trieste, Italy.
| | - Maria Valentina Musso
- Department of Life Sciences, Via Licio Giorgieri 5, University of Trieste, 34127 Trieste, Italy.
| | - Lucija Krce
- Department of Physics, Faculty of Science, University of Split, Soba B3-18, Ruđera Boškovića 33, 21000 Split, Croatia.
| | - Ivica Aviani
- Department of Physics, Faculty of Science, University of Split, Soba B3-18, Ruđera Boškovića 33, 21000 Split, Croatia.
| | - Alberto Pallavicini
- Department of Life Sciences, Via Licio Giorgieri 5, University of Trieste, 34127 Trieste, Italy.
| | - Marco Scocchi
- Department of Life Sciences, Via Licio Giorgieri 5, University of Trieste, 34127 Trieste, Italy.
| | - Marco Gerdol
- Department of Life Sciences, Via Licio Giorgieri 5, University of Trieste, 34127 Trieste, Italy.
| | - Mario Mardirossian
- Department of Medical Sciences, University of Trieste, Laboratorio Clinica Odontostomatologica, Piazza dell'Ospitale 1, 34125 Trieste, Italy.
| |
Collapse
|
40
|
Abstract
Many integral membrane proteins form oligomeric complexes, but the assembly of these structures is poorly understood. Here, we show that the assembly of OmpC, a trimeric porin that resides in the Escherichia coli outer membrane (OM), can be reconstituted in vitro. Although we observed the insertion of both urea-denatured and in vitro-synthesized OmpC into pure lipid vesicles at physiological pH, the protein assembled only into dead-end dimers. In contrast, in vitro-synthesized OmpC was inserted into proteoliposomes that contained the barrel assembly machinery (Bam) complex, a conserved heterooligomer that catalyzes protein integration into the bacterial OM, and folded into heat-stable trimers by passing through a short-lived dimeric intermediate. Interestingly, complete OmpC assembly was also dependent on the addition of lipopolysaccharide (LPS), a glycolipid located exclusively in the OM. Our results strongly suggest that trimeric porins form through a stepwise process that requires the integration of the protein into the OM in an assembly-competent state. Furthermore, our results provide surprising evidence that interaction with LPS is required not only for trimerization but also for the productive insertion of individual subunits into the lipid bilayer.
Collapse
|
41
|
Patriarca EJ, Cermola F, D’Aniello C, Fico A, Guardiola O, De Cesare D, Minchiotti G. The Multifaceted Roles of Proline in Cell Behavior. Front Cell Dev Biol 2021; 9:728576. [PMID: 34458276 PMCID: PMC8397452 DOI: 10.3389/fcell.2021.728576] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 07/23/2021] [Indexed: 12/13/2022] Open
Abstract
Herein, we review the multifaceted roles of proline in cell biology. This peculiar cyclic imino acid is: (i) A main precursor of extracellular collagens (the most abundant human proteins), antimicrobial peptides (involved in innate immunity), salivary proteins (astringency, teeth health) and cornifins (skin permeability); (ii) an energy source for pathogenic bacteria, protozoan parasites, and metastatic cancer cells, which engage in extracellular-protein degradation to invade their host; (iii) an antistress molecule (an osmolyte and chemical chaperone) helpful against various potential harms (UV radiation, drought/salinity, heavy metals, reactive oxygen species); (iv) a neural metabotoxin associated with schizophrenia; (v) a modulator of cell signaling pathways such as the amino acid stress response and extracellular signal-related kinase pathway; (vi) an epigenetic modifier able to promote DNA and histone hypermethylation; (vii) an inducer of proliferation of stem and tumor cells; and (viii) a modulator of cell morphology and migration/invasiveness. We highlight how proline metabolism impacts beneficial tissue regeneration, but also contributes to the progression of devastating pathologies such as fibrosis and metastatic cancer.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Gabriella Minchiotti
- Stem Cell Fate Laboratory, Institute of Genetics and Biophysics “A. Buzzati Traverso”, Consiglio Nazionale delle Ricerche, Naples, Italy
| |
Collapse
|
42
|
Armas F, Di Stasi A, Mardirossian M, Romani AA, Benincasa M, Scocchi M. Effects of Lipidation on a Proline-Rich Antibacterial Peptide. Int J Mol Sci 2021; 22:7959. [PMID: 34360723 PMCID: PMC8347091 DOI: 10.3390/ijms22157959] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/21/2021] [Accepted: 07/22/2021] [Indexed: 01/04/2023] Open
Abstract
The emergence of multidrug-resistant bacteria is a worldwide health problem. Antimicrobial peptides have been recognized as potential alternatives to conventional antibiotics, but still require optimization. The proline-rich antimicrobial peptide Bac7(1-16) is active against only a limited number of Gram-negative bacteria. It kills bacteria by inhibiting protein synthesis after its internalization, which is mainly supported by the bacterial transporter SbmA. In this study, we tested two different lipidated forms of Bac7(1-16) with the aim of extending its activity against those bacterial species that lack SbmA. We linked a C12-alkyl chain or an ultrashort cationic lipopeptide Lp-I to the C-terminus of Bac7(1-16). Both the lipidated Bac-C12 and Bac-Lp-I forms acquired activity at low micromolar MIC values against several Gram-positive and Gram-negative bacteria. Moreover, unlike Bac7(1-16), Bac-C12, and Bac-Lp-I did not select resistant mutants in E. coli after 14 times of exposure to sub-MIC concentrations of the respective peptide. We demonstrated that the extended spectrum of activity and absence of de novo resistance are likely related to the acquired capability of the peptides to permeabilize cell membranes. These results indicate that C-terminal lipidation of a short proline-rich peptide profoundly alters its function and mode of action and provides useful insights into the design of novel broad-spectrum antibacterial agents.
Collapse
Affiliation(s)
- Federica Armas
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (F.A.); (A.D.S.); (M.M.); (M.B.)
- Area Science Park, Padriciano, 34149 Trieste, Italy
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore 138602, Singapore
| | - Adriana Di Stasi
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (F.A.); (A.D.S.); (M.M.); (M.B.)
| | - Mario Mardirossian
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (F.A.); (A.D.S.); (M.M.); (M.B.)
- Department of Medical Sciences, University of Trieste, 34129 Trieste, Italy
| | | | - Monica Benincasa
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (F.A.); (A.D.S.); (M.M.); (M.B.)
| | - Marco Scocchi
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (F.A.); (A.D.S.); (M.M.); (M.B.)
| |
Collapse
|
43
|
Khairullina ZZ, Tereshchenkov AG, Zavyalova SA, Komarova ES, Lukianov DA, Tashlitsky VN, Osterman IA, Sumbatyan NV. Interaction of Chloramphenicol Cationic Peptide Analogues with the Ribosome. BIOCHEMISTRY (MOSCOW) 2021; 85:1443-1457. [PMID: 33280584 DOI: 10.1134/s0006297920110127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Virtual screening of all possible tripeptide analogues of chloramphenicol was performed using molecular docking to evaluate their affinity to bacterial ribosomes. Chloramphenicol analogues that demonstrated the lowest calculated energy of interaction with ribosomes were synthesized. Chloramphenicol amine (CAM) derivatives, which contained specific peptide fragments from the proline-rich antimicrobial peptides were produced. It was demonstrated using displacement of the fluorescent erythromycin analogue from its complex with ribosomes that the novel peptide analogues of chloramphenicol were able to bind bacterial ribosome; all the designed tripeptide analogues and one of the chloramphenicol amine derivatives containing fragment of the proline-rich antimicrobial peptides exhibited significantly greater affinity to Escherichia coli ribosome than chloramphenicol. Correlation between the calculated and experimentally evaluated levels of the ligand efficiencies was observed. In vitro protein biosynthesis inhibition assay revealed, that the RAW-CAM analogue shows activity at the level of chloramphenicol. These data were confirmed by the chemical probing assay, according to which binding pattern of this analogue in the nascent peptide exit tunnel was similar to chloramphenicol.
Collapse
Affiliation(s)
- Z Z Khairullina
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - A G Tereshchenkov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - S A Zavyalova
- Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
| | - E S Komarova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119992, Russia.,Skolkovo Institute of Science and Technology, Moscow, 143025, Russia
| | - D A Lukianov
- Skolkovo Institute of Science and Technology, Moscow, 143025, Russia
| | - V N Tashlitsky
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - I A Osterman
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.,Skolkovo Institute of Science and Technology, Moscow, 143025, Russia
| | - N V Sumbatyan
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.
| |
Collapse
|
44
|
Khodaparast L, Wu G, Khodaparast L, Schmidt BZ, Rousseau F, Schymkowitz J. Bacterial Protein Homeostasis Disruption as a Therapeutic Intervention. Front Mol Biosci 2021; 8:681855. [PMID: 34150852 PMCID: PMC8206779 DOI: 10.3389/fmolb.2021.681855] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/04/2021] [Indexed: 12/15/2022] Open
Abstract
Cells have evolved a complex molecular network, collectively called the protein homeostasis (proteostasis) network, to produce and maintain proteins in the appropriate conformation, concentration and subcellular localization. Loss of proteostasis leads to a reduction in cell viability, which occurs to some degree during healthy ageing, but is also the root cause of a group of diverse human pathologies. The accumulation of proteins in aberrant conformations and their aggregation into specific beta-rich assemblies are particularly detrimental to cell viability and challenging to the protein homeostasis network. This is especially true for bacteria; it can be argued that the need to adapt to their changing environments and their high protein turnover rates render bacteria particularly vulnerable to the disruption of protein homeostasis in general, as well as protein misfolding and aggregation. Targeting bacterial proteostasis could therefore be an attractive strategy for the development of novel antibacterial therapeutics. This review highlights advances with an antibacterial strategy that is based on deliberately inducing aggregation of target proteins in bacterial cells aiming to induce a lethal collapse of protein homeostasis. The approach exploits the intrinsic aggregation propensity of regions residing in the hydrophobic core regions of the polypeptide sequence of proteins, which are genetically conserved because of their essential role in protein folding and stability. Moreover, the molecules were designed to target multiple proteins, to slow down the build-up of resistance. Although more research is required, results thus far allow the hope that this strategy may one day contribute to the arsenal to combat multidrug-resistant bacterial infections.
Collapse
Affiliation(s)
- Laleh Khodaparast
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Guiqin Wu
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Ladan Khodaparast
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Béla Z Schmidt
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Frederic Rousseau
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
| |
Collapse
|
45
|
Upert G, Luther A, Obrecht D, Ermert P. Emerging peptide antibiotics with therapeutic potential. MEDICINE IN DRUG DISCOVERY 2021; 9:100078. [PMID: 33398258 PMCID: PMC7773004 DOI: 10.1016/j.medidd.2020.100078] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/15/2020] [Accepted: 12/27/2020] [Indexed: 02/09/2023] Open
Abstract
This review covers some of the recent progress in the field of peptide antibiotics with a focus on compounds with novel or established mode of action and with demonstrated efficacy in animal infection models. Novel drug discovery approaches, linear and macrocyclic peptide antibiotics, lipopeptides like the polymyxins as well as peptides addressing targets located in the plasma membrane or in the outer membrane of bacterial cells are discussed.
Collapse
Key Words
- ADMET, absorption, distribution, metabolism and excretion – toxicity in pharmacokinetics
- AMP, antimicrobial peptide
- AMR, antimicrobial resistance
- ATCC, ATCC cell collection
- Antibiotic
- BAM, β-barrel assembly machinery
- CC50, cytotoxic concentration to kill 50% of cells
- CD, circular dichroism
- CFU, colony forming unit
- CLSI, clinical and laboratory standards institute
- CMS, colistin methane sulfonate
- DMPC, 1,2-dimyristoyl-sn-glycero-3-phosphocholine
- ESKAPE, acronym encompassing six bacterial pathogens (often carrying antibiotic resistance): Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumonia, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp
- FDA, U. S. Food and Drug Administration
- HABP, hospital acquired bacterial pneumonia
- HDP, host-defense peptide
- HEK293, human embryonic kidney 293 cells
- HK-2, human kidney 2 cells (proximal tubular cell line)
- HepG2, human hepatocellular carcinoma cell line
- Hpg, 4-hydroxy-phenyl glycine
- ITC, isothermal titration calorimetry
- KPC, Klebsiella pneumoniae metallo-β-lactamase C resistant
- LPS, lipopolysaccharide
- LptA, lipopolysaccharide transport protein A
- LptC, lipopolysaccharide transport protein C
- LptD, lipopolysaccharide transport protein D
- MDR, multidrug-resistant
- MH-I, Müller-Hinton broth I
- MH-II, Müller-Hinton broth II (cation adjusted)
- MIC, minimal inhibitory concentration
- MRSA, methicilline-resistant S. aureus
- MSSA, methicilline-sensitive S. aureus
- MoA, mechanism (mode) of action
- NDM-1, New Delhi metallo-β-lactamase resistant
- NOAEL, no adverse effect level
- ODL, odilorhabdin
- OMPTA (outer membrane targeting antibiotic)
- OMPTA, outer membrane targeting antibiotic
- Omp, outer membrane protein
- PBMC, peripheral mononuclear blood cell
- PBP, penicillin-binding protein
- PBS, phosphate-buffered saline
- PK, pharmacokinetics
- POPC, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
- POPG, 2-oleoyl-1-palmitoyl-sn-glycero-3-phospho-(1-glycerol)
- PrAMPs, polyproline antimicrobial peptides
- RBC, red blood cell
- SAR, structure-activity relationship
- SPR, surface plasmon resonance
- SPase I, signal peptidase I
- VABP, ventilator associated bacterial pneumonia
- VIM-1, beta-lactamase 2 (K. pneumoniae)
- VISA, vancomycin-intermediate S. aureus
- VRE, vancomycin-resistant enterococcus
- WHO, World Health Organization
- WT, wild type
- WTA, wall teichoic acid
- XDR, extremely drug-resistant
- antimicrobial peptide
- antimicrobial resistance
- bid, bis in die (two times a day)
- i.p., intraperitoneal
- i.v., intravenous
- lipopeptide
- mITT population, minimal intend-to-treat population
- peptide antibiotic
- s.c., subcutaneous
Collapse
Affiliation(s)
- Gregory Upert
- Polyphor Ltd, Hegenheimermattweg 125, 4123 Allschwil, Switzerland
| | - Anatol Luther
- Bachem AG, Hauptstrasse 114, 4416 Bubendorf, Switzerland
| | - Daniel Obrecht
- Polyphor Ltd, Hegenheimermattweg 125, 4123 Allschwil, Switzerland
| | - Philipp Ermert
- Polyphor Ltd, Hegenheimermattweg 125, 4123 Allschwil, Switzerland
| |
Collapse
|
46
|
Zhang L, He J, Bai L, Ruan S, Yang T, Luo Y. Ribosome-targeting antibacterial agents: Advances, challenges, and opportunities. Med Res Rev 2021; 41:1855-1889. [PMID: 33501747 DOI: 10.1002/med.21780] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/08/2020] [Accepted: 12/19/2020] [Indexed: 02/05/2023]
Abstract
Ribosomes, which synthesize proteins, are critical organelles for the survival and growth of bacteria. About 60% of approved antibiotics discovered so far combat pathogenic bacteria by targeting ribosomes. However, several issues, such as drug resistance and toxicity, have impeded the clinical use of ribosome-targeting antibiotics. Moreover, the complexity of the bacteria ribosome structure has retarded the discovery of new ribosome-targeting agents that are considered as the key to the drug-resistance and toxicity. To deal with these challenges, efforts such as medicinal chemistry optimization, combination treatment, and new drug delivery system have been developed. But not enough, the development of structural biology and new screening methods bring powerful tools, such as cryo-electron microscopy technology, advanced computer-aided drug design, and cell-free in vitro transcription/translation systems, for the discovery of novel ribosome-targeting antibiotics. Thus, in this paper, we overview the research on different aspects of bacterial ribosomes, especially focus on discussing the challenges in the discovery of ribosome-targeting antibacterial drugs and advances made to address issues such as drug-resistance and selectivity, which, we believe, provide perspectives for the discovery of novel antibiotics.
Collapse
Affiliation(s)
- Laiying Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Jun He
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Lang Bai
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Shihua Ruan
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Tao Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China.,Laboratory of Human Diseases and Immunotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China.,Institute of Immunology and Inflammation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Youfu Luo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| |
Collapse
|
47
|
Proline-rich antimicrobial peptide Api137 is bactericidal in porcine blood infected ex vivo with a porcine or human Klebsiella pneumoniae strain. J Glob Antimicrob Resist 2020; 24:127-135. [PMID: 33373733 DOI: 10.1016/j.jgar.2020.12.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 12/04/2020] [Accepted: 12/18/2020] [Indexed: 11/20/2022] Open
Abstract
OBJECTIVES Klebsiella pneumoniae is an emerging invasive pathogen in humans and pigs. Resistance against multiple antibiotics in this species is a major health concern and the development of new antibiotics is urgently needed. The objective of this study was to investigate the effects of proline-rich antimicrobial peptides (PrAMPs) on the survival of K. pneumoniae strains in porcine blood. METHODS We established a bactericidal assay with K. pneumoniae in fresh blood drawn from 4-week-old piglets. PrAMPs, namely the apidaecins Api137 and Api802 as well as the oncocin Onc112, were added to ex vivo-infected whole blood samples in order to study their bactericidal effects and, in the case of Api137, also immune responses. RESULTS A porcine invasive and a human iucA+rmpA+ K. pneumoniae strain showed prominent proliferation in porcine blood. Application of Api137 resulted in a dose-dependent prominent bactericidal effect killing the invasive porcine K. pneumoniae strain. Addition of 8 μg/mL Api137 also resulted in complete killing of the human iucA+rmpA+ strain. Cytotoxicity, haemolysis and induction of the pro-inflammatory cytokine tumour necrosis factor-alpha (TNFα) in K. pneumoniae-infected porcine blood treated with Api137 was comparable with values obtained after application of 10 μg/mL cefquinome. CONCLUSION We describe a new non-rodent model for invasive K. pneumoniae bacteraemia and present promising data for the PrAMP Api137 for the control of infection with hypervirulent K. pneumoniae strains.
Collapse
|
48
|
Limbrick EM, Graf M, Derewacz DK, Nguyen F, Spraggins JM, Wieland M, Ynigez-Gutierrez AE, Reisman BJ, Zinshteyn B, McCulloch KM, Iverson TM, Green R, Wilson DN, Bachmann BO. Bifunctional Nitrone-Conjugated Secondary Metabolite Targeting the Ribosome. J Am Chem Soc 2020; 142:18369-18377. [PMID: 32709196 DOI: 10.1021/jacs.0c04675] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Many microorganisms possess the capacity for producing multiple antibiotic secondary metabolites. In a few notable cases, combinations of secondary metabolites produced by the same organism are used in important combination therapies for treatment of drug-resistant bacterial infections. However, examples of conjoined roles of bioactive metabolites produced by the same organism remain uncommon. During our genetic functional analysis of oxidase-encoding genes in the everninomicin producer Micromonospora carbonacea var. aurantiaca, we discovered previously uncharacterized antibiotics everninomicin N and O, comprised of an everninomicin fragment conjugated to the macrolide rosamicin via a rare nitrone moiety. These metabolites were determined to be hydrolysis products of everninomicin P, a nitrone-linked conjugate likely the result of nonenzymatic condensation of the rosamicin aldehyde and the octasaccharide everninomicin F, possessing a hydroxylamino sugar moiety. Rosamicin binds the erythromycin macrolide binding site approximately 60 Å from the orthosomycin binding site of everninomicins. However, while individual ribosomal binding sites for each functional half of everninomicin P are too distant for bidentate binding, ligand displacement studies demonstrated that everninomicin P competes with rosamicin for ribosomal binding. Chemical protection studies and structural analysis of everninomicin P revealed that everninomicin P occupies both the macrolide- and orthosomycin-binding sites on the 70S ribosome. Moreover, resistance mutations within each binding site were overcome by the inhibition of the opposite functional antibiotic moiety binding site. These data together demonstrate a strategy for coupling orthogonal antibiotic pharmacophores, a surprising tolerance for substantial covalent modification of each antibiotic, and a potential beneficial strategy to combat antibiotic resistance.
Collapse
Affiliation(s)
- Emilianne M Limbrick
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Michael Graf
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg 20146, Germany
| | - Dagmara K Derewacz
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Fabian Nguyen
- Department of Biochemistry, University of Munich, 81377 Munich, Germany
| | - Jeffrey M Spraggins
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States.,Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37205, United States.,Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - Maximiliane Wieland
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg 20146, Germany
| | | | - Benjamin J Reisman
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Boris Zinshteyn
- Department of Molecular Biology and Genetics, Johns Hopkins University. Baltimore, Maryland 21205, United States
| | - Kathryn M McCulloch
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - T M Iverson
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37205, United States.,Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, United States.,Vanderbilt Center for Structural Biology, Nashville, Tennessee 37232, United States
| | - Rachel Green
- Department of Molecular Biology and Genetics, Johns Hopkins University. Baltimore, Maryland 21205, United States.,Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Daniel N Wilson
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg 20146, Germany
| | - Brian O Bachmann
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States.,Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37205, United States.,Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, United States.,Vanderbilt Institute of Chemical Biology, Nashville, Tennessee 37205, United States
| |
Collapse
|
49
|
Huan Y, Kong Q, Mou H, Yi H. Antimicrobial Peptides: Classification, Design, Application and Research Progress in Multiple Fields. Front Microbiol 2020; 11:582779. [PMID: 33178164 PMCID: PMC7596191 DOI: 10.3389/fmicb.2020.582779] [Citation(s) in RCA: 593] [Impact Index Per Article: 148.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 09/23/2020] [Indexed: 12/12/2022] Open
Abstract
Antimicrobial peptides (AMPs) are a class of small peptides that widely exist in nature and they are an important part of the innate immune system of different organisms. AMPs have a wide range of inhibitory effects against bacteria, fungi, parasites and viruses. The emergence of antibiotic-resistant microorganisms and the increasing of concerns about the use of antibiotics resulted in the development of AMPs, which have a good application prospect in medicine, food, animal husbandry, agriculture and aquaculture. This review introduces the progress of research on AMPs comprehensively and systematically, including their classification, mechanism of action, design methods, environmental factors affecting their activity, application status, prospects in various fields and problems to be solved. The research progress on antivirus peptides, especially anti-coronavirus (COVID-19) peptides, has been introduced given the COVID-19 pandemic worldwide in 2020.
Collapse
Affiliation(s)
| | - Qing Kong
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | | | | |
Collapse
|
50
|
Sancho-Vaello E, Gil-Carton D, François P, Bonetti EJ, Kreir M, Pothula KR, Kleinekathöfer U, Zeth K. The structure of the antimicrobial human cathelicidin LL-37 shows oligomerization and channel formation in the presence of membrane mimics. Sci Rep 2020; 10:17356. [PMID: 33060695 PMCID: PMC7562864 DOI: 10.1038/s41598-020-74401-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 09/26/2020] [Indexed: 12/22/2022] Open
Abstract
The human cathelicidin LL-37 serves a critical role in the innate immune system defending bacterial infections. LL-37 can interact with molecules of the cell wall and perforate cytoplasmic membranes resulting in bacterial cell death. To test the interactions of LL-37 and bacterial cell wall components we crystallized LL-37 in the presence of detergents and obtained the structure of a narrow tetrameric channel with a strongly charged core. The formation of a tetramer was further studied by cross-linking in the presence of detergents and lipids. Using planar lipid membranes a small but defined conductivity of this channel could be demonstrated. Molecular dynamic simulations underline the stability of this channel in membranes and demonstrate pathways for the passage of water molecules. Time lapse studies of E. coli cells treated with LL-37 show membrane discontinuities in the outer membrane followed by cell wall damage and cell death. Collectively, our results open a venue to the understanding of a novel AMP killing mechanism and allows the rational design of LL-37 derivatives with enhanced bactericidal activity.
Collapse
Affiliation(s)
- Enea Sancho-Vaello
- Unidad de Biofisica, Centro Mixto Consejo Superior de Investigaciones Cientificas-Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC, UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia, Spain.,Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - David Gil-Carton
- Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia Edificio 800, 48160, Derio, Spain
| | - Patrice François
- Genomic Research Laboratory, Department of Medical Specialities, Geneva University Hospitals, University of Geneva, Genève, Switzerland
| | - Eve-Julie Bonetti
- Genomic Research Laboratory, Department of Medical Specialities, Geneva University Hospitals, University of Geneva, Genève, Switzerland
| | - Mohamed Kreir
- Nanion Technologies GmbH, Gabrielenstraße 9, 80636, Munich, Germany.,Janssen Pharmaceutica NV, Janssen R&D, Nonclinical Safety, Beerse, Belgium
| | - Karunakar Reddy Pothula
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759, Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759, Bremen, Germany
| | - Kornelius Zeth
- Department of Science and Environment, Roskilde University, Universitetsvej 1, 4000, Roskilde, Denmark.
| |
Collapse
|