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MacNair CR, Rutherford ST, Tan MW. Alternative therapeutic strategies to treat antibiotic-resistant pathogens. Nat Rev Microbiol 2024; 22:262-275. [PMID: 38082064 DOI: 10.1038/s41579-023-00993-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2023] [Indexed: 04/19/2024]
Abstract
Resistance threatens to render antibiotics - which are essential for modern medicine - ineffective, thus posing a threat to human health. The discovery of novel classes of antibiotics able to overcome resistance has been stalled for decades, with the developmental pipeline relying almost entirely on variations of existing chemical scaffolds. Unfortunately, this approach has been unable to keep pace with resistance evolution, necessitating new therapeutic strategies. In this Review, we highlight recent efforts to discover non-traditional antimicrobials, specifically describing the advantages and limitations of antimicrobial peptides and macrocycles, antibodies, bacteriophages and antisense oligonucleotides. These approaches have the potential to stem the tide of resistance by expanding the physicochemical property space and target spectrum occupied by currently approved antibiotics.
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Affiliation(s)
- Craig R MacNair
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Steven T Rutherford
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Man-Wah Tan
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA.
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2
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Story S, Bhaduri S, Ganguly S, Dakarapu R, Wicks SL, Bhadra J, Kwange S, Arya DP. Understanding Antisense Oligonucleotide Efficiency in Inhibiting Prokaryotic Gene Expression. ACS Infect Dis 2024; 10:971-987. [PMID: 38385613 DOI: 10.1021/acsinfecdis.3c00645] [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] [Indexed: 02/23/2024]
Abstract
Oligonucleotides offer a unique opportunity for sequence specific regulation of gene expression in bacteria. A fundamental question to address is the choice of oligonucleotide, given the large number of options available. Different modifications varying in RNA binding affinities and cellular uptake are available but no comprehensive comparisons have been performed. Herein, the efficiency of blocking expression of β-galactosidase (β-Gal) in E. coli was evaluated utilizing different antisense oligomers (ASOs). Fluorescein (FAM)-labeled oligomers were used to understand their differences in bacterial uptake. Flow cytometry analysis revealed significant differences in uptake, with high fluorescence seen in cells treated with FAM-labeled peptidic nucleic acid (PNA), phosphorodiamidate morpholino oligonucleotide (PMO) and phosphorothioate (PS) oligomers, and low fluorescence observed in cells treated with phosphodiester (PO) oligomers. Thermal denaturation (Tm) of oligomer:RNA duplexes and isothermal titration calorimetry (ITC) studies reveal that ASO binding to target RNA demonstrates a good correlation between Tm and Kd values. There was no correlation between Kd values and reduction of β-Gal activity in bacterial cells. However, cell-free translation assays demonstrated a direct relationship between Kd values and inhibition of gene expression by antisense oligomers, with tight binding oligomers such as LNA being the most efficient. Membrane active compounds such as polymyxin B and A22 further improved the cellular uptake of FAM-PNA and FAM-PS oligomers in wild-type E. coli cells. PNA and PMO were most effective in cellular uptake and reducing β-Gal activity as compared to oligomers with PS or those with PO linkages. Overall, cell uptake of the oligomers is shown as the key determinant in predicting their differences in bacterial antisense inhibition, and the RNA affinity is the key determinant in inhibition of gene expression in cell free systems.
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Affiliation(s)
- Sandra Story
- NUBAD, LLC, Greenville, South Carolina 29605, United States
| | | | - Sudakshina Ganguly
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
| | | | - Sarah L Wicks
- NUBAD, LLC, Greenville, South Carolina 29605, United States
| | - Jhuma Bhadra
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
| | - Simeon Kwange
- NUBAD, LLC, Greenville, South Carolina 29605, United States
| | - Dev P Arya
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
- NUBAD, LLC, Greenville, South Carolina 29605, United States
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3
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El-Fateh M, Chatterjee A, Zhao X. A systematic review of peptide nucleic acids (PNAs) with antibacterial activities: Efficacy, potential and challenges. Int J Antimicrob Agents 2024; 63:107083. [PMID: 38185398 DOI: 10.1016/j.ijantimicag.2024.107083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 12/11/2023] [Accepted: 12/30/2023] [Indexed: 01/09/2024]
Abstract
Peptide nucleic acids (PNAs) are synthetic molecules that are like DNA/RNA, but with different building blocks. PNAs target and bind to mRNAs and disrupt the function of a targeted gene, hence they have been studied as potential antibacterials. The aim of this systematic review was to provide an in-depth analysis of the current status of PNAs as antibacterial agents, define the characteristics of the effective PNA constructs, and address the gap in advancing PNAs to become clinically competent agents. Following the PRISMA model, four electronic databases were searched: Web of Science, PubMed, SciFinder and Scopus. A total of 627 articles published between 1994 and 2023 were found. After screening and a rigorous selection process using explicit inclusion and exclusion criteria, 65 scientific articles were selected, containing 656 minimum inhibitory concentration (MIC) data. The antibacterial activity of PNAs was assessed against 20 bacterial species. The most studied Gram-negative and Gram-positive bacteria were Escherichia coli (n=266) and Staphylococcus aureus (n=53), respectively. In addition, the effect of PNA design, including construct length, binding location, and carrier agents, on antibacterial activity was shown. Finally, antibacterial test models to assess the inhibitory effects of PNAs were examined, emphasising gaps and prospects. This systematic review provides a comprehensive assessment of the potential of PNAs as antibacterial agents and offers valuable insights for researchers and clinicians seeking novel therapeutic strategies in the context of increasing rates of antibiotic-resistant bacteria.
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Affiliation(s)
- Mohamed El-Fateh
- Department of Animal Science, McGill University, Sainte-Anne-de-Bellevue, QC, Canada, H9X3V9; Department of Hygiene and Zoonoses, Faculty of Veterinary Medicine, Mansoura University, 35516, El-Dakhelia, Egypt; Antimicrobial Regeneration Consortium Labs, Louisville, CO, 80027, USA
| | - Anushree Chatterjee
- Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80303, USA; Antimicrobial Regeneration Consortium Labs, Louisville, CO, 80027, USA
| | - Xin Zhao
- Department of Animal Science, McGill University, Sainte-Anne-de-Bellevue, QC, Canada, H9X3V9; Antimicrobial Regeneration Consortium Labs, Louisville, CO, 80027, USA.
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4
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Tsylents U, Burmistrz M, Wojciechowska M, Stępień J, Maj P, Trylska J. Iron uptake pathway of Escherichia coli as an entry route for peptide nucleic acids conjugated with a siderophore mimic. Front Microbiol 2024; 15:1331021. [PMID: 38357356 PMCID: PMC10864483 DOI: 10.3389/fmicb.2024.1331021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/09/2024] [Indexed: 02/16/2024] Open
Abstract
Bacteria secrete various iron-chelators (siderophores), which scavenge Fe3+ from the environment, bind it with high affinity, and retrieve it inside the cell. After the Fe3+ uptake, bacteria extract the soluble iron(II) from the siderophore. Ferric siderophores are transported inside the cell via the TonB-dependent receptor system. Importantly, siderophore uptake paths have been also used by sideromycins, natural antibiotics. Our goal is to hijack the transport system for hydroxamate-type siderophores to deliver peptide nucleic acid oligomers into Escherichia coli cells. As siderophore mimics we designed and synthesized linear and cyclic Nδ-acetyl-Nδ-hydroxy-l-ornithine based peptides. Using circular dichroism spectroscopy, we found that iron(III) is coordinated by the linear trimer with hydroxamate groups but not by the cyclic peptide. The internal flexibility of the linear siderophore oxygen atoms and their interactions with Fe3+ were confirmed by all-atom molecular dynamics simulations. Using flow cytometry we found that the designed hydroxamate trimer transports PNA oligomers inside the E. coli cells. Growth recovery assays on various E. coli mutants suggest the pathway of this transport through the FhuE outer-membrane receptor, which is responsible for the uptake of the natural iron chelator, ferric-coprogen. This pathway also involves the FhuD periplasmic binding protein. Docking of the siderophores to the FhuE and FhuD receptor structures showed that binding of the hydroxamate trimer is energetically favorable corroborating the experimentally suggested uptake path. Therefore, this siderophore mimic, as well as its conjugate with PNA, is most probably internalized through the hydroxamate pathway.
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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.
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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.)
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Plotniece A, Sobolev A, Supuran CT, Carta F, Björkling F, Franzyk H, Yli-Kauhaluoma J, Augustyns K, Cos P, De Vooght L, Govaerts M, Aizawa J, Tammela P, Žalubovskis R. Selected strategies to fight pathogenic bacteria. J Enzyme Inhib Med Chem 2023; 38:2155816. [PMID: 36629427 PMCID: PMC9848314 DOI: 10.1080/14756366.2022.2155816] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Natural products and analogues are a source of antibacterial drug discovery. Considering drug resistance levels emerging for antibiotics, identification of bacterial metalloenzymes and the synthesis of selective inhibitors are interesting for antibacterial agent development. Peptide nucleic acids are attractive antisense and antigene agents representing a novel strategy to target pathogens due to their unique mechanism of action. Antisense inhibition and development of antisense peptide nucleic acids is a new approach to antibacterial agents. Due to the increased resistance of biofilms to antibiotics, alternative therapeutic options are necessary. To develop antimicrobial strategies, optimised in vitro and in vivo models are needed. In vivo models to study biofilm-related respiratory infections, device-related infections: ventilator-associated pneumonia, tissue-related infections: chronic infection models based on alginate or agar beads, methods to battle biofilm-related infections are discussed. Drug delivery in case of antibacterials often is a serious issue therefore this review includes overview of drug delivery nanosystems.
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Affiliation(s)
- Aiva Plotniece
- Latvian Institute of Organic Synthesis, Riga, Latvia,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Riga Stradiņš University, Riga, Latvia,CONTACT Aiva Plotniece Latvian Institute of Organic Synthesis, Riga, Latvia
| | | | - Claudiu T. Supuran
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Firenze, Italy
| | - Fabrizio Carta
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Firenze, Italy
| | - Fredrik Björkling
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, Center for Peptide-Based Antibiotics, University of Copenhagen, Copenhagen East, Denmark
| | - Henrik Franzyk
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, Center for Peptide-Based Antibiotics, University of Copenhagen, Copenhagen East, Denmark
| | - Jari Yli-Kauhaluoma
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, Drug Research Program, University of Helsinki, Helsinki, Finland
| | - Koen Augustyns
- Infla-Med, Centre of Excellence, University of Antwerp, Antwerp, Belgium,Laboratory of Medicinal Chemistry, University of Antwerp, Antwerp, Belgium
| | - Paul Cos
- Department of Pharmaceutical Sciences, Laboratory for Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Antwerp, Belgium
| | - Linda De Vooght
- Department of Pharmaceutical Sciences, Laboratory for Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Antwerp, Belgium
| | - Matthias Govaerts
- Department of Pharmaceutical Sciences, Laboratory for Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Antwerp, Belgium
| | - Juliana Aizawa
- Department of Pharmaceutical Sciences, Laboratory for Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Antwerp, Belgium
| | - Päivi Tammela
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, Drug Research Program, University of Helsinki, Helsinki, Finland
| | - Raivis Žalubovskis
- Latvian Institute of Organic Synthesis, Riga, Latvia,Faculty of Materials Science and Applied Chemistry, Institute of Technology of Organic Chemistry, Riga Technical University, Riga, Latvia
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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.
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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.
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8
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Selvaraj SP, Chen JY. Conjugation of antimicrobial peptides to enhance therapeutic efficacy. Eur J Med Chem 2023; 259:115680. [PMID: 37515922 DOI: 10.1016/j.ejmech.2023.115680] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/05/2023] [Accepted: 07/23/2023] [Indexed: 07/31/2023]
Abstract
The growing prevalence of antimicrobial resistance (AMR) has brought with it a continual increase in the numbers of deaths from multidrug-resistant (MDR) infections. Since the current arsenal of antibiotics has become increasingly ineffective, there exists an urgent need for discovery and development of novel antimicrobials. Antimicrobial peptides (AMPs) are considered to be a promising class of molecules due to their broad-spectrum activities and low resistance rates compared with other types of antibiotics. Since AMPs also often play major roles in elevating the host immune response, the molecules may also be called "host defense peptides." Despite the great promise of AMPs, the majority remain unsuitable for clinical use due to issues of structural instability, degradation by proteases, and/or toxicity to host cells. Moreover, AMP activities in vivo can be influenced by many factors, such as interaction with blood and serum biomolecules, physiological salt concentrations or different pH values. To overcome these limitations, structural modifications can be made to the AMP. Among several modifications, physical and chemical conjugation of AMP to other biomolecules is widely considered an effective strategy. In this review, we discuss structural modification strategies related to conjugation of AMPs and their possible effects on mode of action. The conjugation of fatty acids, glycans, antibiotics, photosensitizers, polymers, nucleic acids, nanoparticles, and immobilization to biomaterials are highlighted.
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Affiliation(s)
- Sanjay Prasad Selvaraj
- Molecular and Biological Agricultural Science Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 11529, Taiwan; Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, 402, Taiwan
| | - Jyh-Yih Chen
- Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, 23-10 Dahuen Rd, Jiaushi, Ilan, 262, Taiwan; The iEGG and Animal Biotechnology Center and the Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung, 402, Taiwan.
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9
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Tsylents U, Siekierska I, Trylska J. Peptide nucleic acid conjugates and their antimicrobial applications-a mini-review. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:533-544. [PMID: 37610696 PMCID: PMC10618302 DOI: 10.1007/s00249-023-01673-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 07/07/2023] [Accepted: 07/10/2023] [Indexed: 08/24/2023]
Abstract
Peptide nucleic acid (PNA) is a nucleic acid mimic with high specificity and binding affinity to natural DNA or RNA, as well as resistance to enzymatic degradation. PNA sequences can be designed to selectively silence gene expression, which makes PNA a promising tool for antimicrobial applications. However, the poor membrane permeability of PNA remains the main limiting factor for its applications in cells. To overcome this obstacle, PNA conjugates with different molecules have been developed. This mini-review focuses on covalently linked conjugates of PNA with cell-penetrating peptides, aminosugars, aminoglycoside antibiotics, and non-peptidic molecules that were tested, primarily as PNA carriers, in antibacterial and antiviral applications. The chemistries of the conjugation and the applied linkers are also discussed.
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Affiliation(s)
- Uladzislava Tsylents
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097, Warsaw, Poland
| | - Izabela Siekierska
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097, Warsaw, Poland
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097, Warsaw, Poland.
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10
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Hans AC, Becker PM, Haußmann J, Suhr S, Wanner DM, Lederer V, Willig F, Frey W, Sarkar B, Kästner J, Peters R. A Practical and Robust Zwitterionic Cooperative Lewis Acid/Acetate/Benzimidazolium Catalyst for Direct 1,4-Additions. Angew Chem Int Ed Engl 2023; 62:e202217519. [PMID: 36651714 DOI: 10.1002/anie.202217519] [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: 11/28/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/19/2023]
Abstract
A catalyst type is disclosed allowing for exceptional efficiency in direct 1,4-additions. The catalyst is a zwitterionic entity, in which acetate binds to CuII , which is formally negatively charged and serving as counterion for benzimidazolium. All 3 functionalities are involved in the catalytic activation. For maleimides productivity was increased by a factor >300 compared to literature (TONs up to 6700). High stereoselectivity and productivity was attained for a broad range of other Michael acceptors as well. The polyfunctional catalyst is accessible in only 4 steps from N-Ph-benzimidazole with an overall yield of 96 % and robust during catalysis. This allowed to reuse the same catalyst multiple times with nearly constant efficiency. Mechanistic studies, in particular by DFT, give a detailed picture how the catalyst operates. The benzimidazolium unit stabilizes the coordinated enolate nucleophile and prevents that acetate/acetic acid dissociate from the catalyst.
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Affiliation(s)
- Andreas C Hans
- Universität Stuttgart, Institut für Organische Chemie, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Patrick M Becker
- Universität Stuttgart, Institut für Theoretische Chemie, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Johanna Haußmann
- Universität Stuttgart, Institut für Organische Chemie, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Simon Suhr
- Universität Stuttgart, Institut für Anorganische Chemie, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Daniel M Wanner
- Universität Stuttgart, Institut für Organische Chemie, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Vera Lederer
- Universität Stuttgart, Institut für Organische Chemie, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Felix Willig
- Universität Stuttgart, Institut für Organische Chemie, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Wolfgang Frey
- Universität Stuttgart, Institut für Organische Chemie, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Biprajit Sarkar
- Universität Stuttgart, Institut für Anorganische Chemie, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Johannes Kästner
- Universität Stuttgart, Institut für Theoretische Chemie, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - René Peters
- Universität Stuttgart, Institut für Organische Chemie, Pfaffenwaldring 55, 70569, Stuttgart, Germany
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11
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Zhang Y, Håkansson J, Fan Y, Andrén OCJ, San Jacinto García J, Qin L, Umerska A, Hutchinson DJ, Lüchow M, Mahlapuu M, Malkoch M. Dendritic Nanogels Directed Dual-Encapsulation Topical Delivery System of Antimicrobial Peptides Targeting Skin Infections. Macromol Biosci 2023; 23:e2200433. [PMID: 36639138 DOI: 10.1002/mabi.202200433] [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: 10/15/2022] [Revised: 12/15/2022] [Indexed: 01/15/2023]
Abstract
Antimicrobial peptides (AMPs) are promising antibacterial agents in the fight against multidrug resistant pathogens. However, their application to skin infections is limited by the absence of a realizable topical delivery strategy. Herein, a hybrid hierarchical delivery system for topical delivery of AMPs is accomplished through the incorporation of AMPs into dendritic nanogels (DNGs) and their subsequent embedding into poloxamer gel. The high level of control over the crosslink density and the number of chosen functionalities makes DNGs ideal capsules with tunable loading capacity for DPK-060, a human kininogen-derived AMP. Once embedded into the poloxamer gel, DPK-060 encapsulated in DNGs displays a slower release rate compared to those entrapped directly in the gels. In vitro EpiDerm Skin Irritation Tests show good biocompatibility, while MIC and time-kill curves reveal the potency of the peptide toward Staphylococcus aureus. Anti-infection tests on ex vivo pig skin and in vivo mouse infection models demonstrate that formulations with 0.5% and 1% AMPs significantly inhibit the growth of S. aureus. Similar outcomes are observed for an in vivo mouse surgical site infection model. Importantly, when normalizing the bacteria inhibition to released/free DPK-060 at the wound site, all formulations display superior efficacy compared to DPK-060 in solution.
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Affiliation(s)
- Yuning Zhang
- Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, Stockholm, SE-100 44, Sweden.,Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Institute of Immunology, The First Hospital, Jilin University, Changchun, 130061, P. R. China
| | - Joakim Håkansson
- Biological Function Unit, RISE Research Institutes of Sweden, Methodology, Textile and Medical Devices, Borås, SE-501 15, Sweden.,Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, P.O. Box 440, Gothenburg, SE-40530, Sweden
| | - Yanmiao Fan
- Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, Stockholm, SE-100 44, Sweden
| | - Oliver C J Andrén
- Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, Stockholm, SE-100 44, Sweden
| | - Jorge San Jacinto García
- Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, Stockholm, SE-100 44, Sweden
| | - Liguo Qin
- Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, Stockholm, SE-100 44, Sweden.,Institute of Design Science and Basic Components, School of Mechanical Engineering, Xi'an Jiaotong University, Xi'an, 710049, P. R. China
| | - Anita Umerska
- Biological Function Unit, RISE Research Institutes of Sweden, Methodology, Textile and Medical Devices, Borås, SE-501 15, Sweden
| | - Daniel J Hutchinson
- Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, Stockholm, SE-100 44, Sweden
| | - Mads Lüchow
- Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, Stockholm, SE-100 44, Sweden
| | | | - Michael Malkoch
- Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, Stockholm, SE-100 44, Sweden
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12
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Goltermann L, Zhang M, Ebbensgaard AE, Fiodorovaite M, Yavari N, Løbner-Olesen A, Nielsen PE. Effects of LPS Composition in Escherichia coli on Antibacterial Activity and Bacterial Uptake of Antisense Peptide-PNA Conjugates. Front Microbiol 2022; 13:877377. [PMID: 35794919 PMCID: PMC9251361 DOI: 10.3389/fmicb.2022.877377] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/18/2022] [Indexed: 11/13/2022] Open
Abstract
The physical and chemical properties of the outer membrane of Gram-negative bacteria including Escherichia coli have a significant impact on the antibacterial activity and uptake of antibiotics, including antimicrobial peptides and antisense peptide-peptide nucleic acid (PNA) conjugates. Using a defined subset of E. coli lipopolysaccharide (LPS) and envelope mutants, components of the LPS-core, which provide differential susceptibility toward a panel of bacterial penetrating peptide (BPP)-PNA conjugates, were identified. Deleting the outer core of the LPS and perturbing the inner core only sensitized the bacteria toward (KFF)3K-PNA conjugates, but not toward conjugates carrying arginine-based BPPs. Interestingly, the chemical composition of the outer LPS core as such, rather than overall hydrophobicity or surface charge, appears to determine the susceptibility to different BPP-PNA conjugates thereby clearly demonstrating the complexity and specificity of the interaction with the LPS/outer membrane. Notably, mutants with outer membrane changes conferring polymyxin resistance did not show resistance toward the BPP-PNA conjugates, thereby eliminating one possible route of resistance for these molecules. Finally, envelope weakening, through deletion of membrane proteins such as OmpA as well as some proteins previously identified as involved in cationic antimicrobial peptide uptake, did not significantly influence BPP-PNA conjugate activity.
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Affiliation(s)
- Lise Goltermann
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, Center for Peptide-Based Antibiotics, The Panum Institute, University of Copenhagen, Copenhagen, Denmark
- *Correspondence: Lise Goltermann
| | - Meiqin Zhang
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, Center for Peptide-Based Antibiotics, The Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Marija Fiodorovaite
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, Center for Peptide-Based Antibiotics, The Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | - Niloofar Yavari
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, Center for Peptide-Based Antibiotics, The Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | - Anders Løbner-Olesen
- Section for Functional Genomics, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Peter E. Nielsen
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, Center for Peptide-Based Antibiotics, The Panum Institute, University of Copenhagen, Copenhagen, Denmark
- Peter E. Nielsen
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13
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Iubatti M, Gabas IM, Cavaco LM, Mood EH, Lim E, Bonanno F, Yavari N, Brolin C, Nielsen PE. Antisense Peptide Nucleic Acid-Diaminobutanoic Acid Dendron Conjugates with SbmA-Independent Antimicrobial Activity against Gram-Negative Bacteria. ACS Infect Dis 2022; 8:1098-1106. [PMID: 35436109 PMCID: PMC9112330 DOI: 10.1021/acsinfecdis.2c00089] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Precision antisense antibacterial agents may be developed into novel antibiotics in the fight against multidrug-resistant Gram-negative bacteria. In this study, a series of diaminobutanoic acid (DAB) dendrons are presented as novel carriers for the delivery of antisense antibacterial peptide nucleic acids (PNAs). The dendron-PNA conjugates targeting the essential acpP gene exhibit specific antisense antimicrobial bactericidal activity against Escherichia coli and Klebsiella pneumoniae at one-digit micromolar concentrations, while showing low toxicity to human cells. One compound selected from a structure-activity relationship series showed high stability in mouse and human serum (t1/2 ≫ 24 h) as well as in vivo activity against a multidrug-resistant, extended spectrum beta-lactamase-producing E. coli in a murine peritonitis model. The compound was also well tolerated in mice upon i.v. administration up to a dose of 20 mg/kg, and in vivo fluorescence imaging indicated clearance via renal excretion with slight accumulation in the kidneys and liver. Thus, DAB-based dendrons constitute a promising new chemistry platform for development of effective delivery agents for antibacterial drugs with possible in vivo use.
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Affiliation(s)
- Mirko Iubatti
- Center for Peptide-based Antibiotics, Department of Cellular and Molecular Medicine, The Panum Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen 2200, Denmark
| | - Isabel Maicas Gabas
- Center for Peptide-based Antibiotics, Department of Cellular and Molecular Medicine, The Panum Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen 2200, Denmark
| | - Lina M. Cavaco
- Department for Bacteria Parasites and Fungi, Statens Serum Institut, Copenhagen 2200, Denmark
| | - Elnaz Harifi Mood
- Center for Peptide-based Antibiotics, Department of Cellular and Molecular Medicine, The Panum Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen 2200, Denmark
| | - Ernest Lim
- Center for Peptide-based Antibiotics, Department of Cellular and Molecular Medicine, The Panum Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen 2200, Denmark
| | - Federica Bonanno
- Center for Peptide-based Antibiotics, Department of Cellular and Molecular Medicine, The Panum Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen 2200, Denmark
| | - Niloofar Yavari
- Center for Peptide-based Antibiotics, Department of Cellular and Molecular Medicine, The Panum Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen 2200, Denmark
| | - Camilla Brolin
- Center for Peptide-based Antibiotics, Department of Cellular and Molecular Medicine, The Panum Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen 2200, Denmark
| | - Peter E. Nielsen
- Center for Peptide-based Antibiotics, Department of Cellular and Molecular Medicine, The Panum Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen 2200, Denmark
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14
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Patil NA, Thombare VJ, Li R, He X, Lu J, Yu HH, Wickremasinghe H, Pamulapati K, Azad MAK, Velkov T, Roberts KD, Li J. An Efficient Approach for the Design and Synthesis of Antimicrobial Peptide-Peptide Nucleic Acid Conjugates. Front Chem 2022; 10:843163. [PMID: 35372270 PMCID: PMC8964499 DOI: 10.3389/fchem.2022.843163] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 02/16/2022] [Indexed: 01/23/2023] Open
Abstract
Peptide-Peptide Nucleic Acid (PNA) conjugates targeting essential bacterial genes have shown significant potential in developing novel antisense antimicrobials. The majority of efforts in this area are focused on identifying different PNA targets and the selection of peptides to deliver the peptide-PNA conjugates to Gram-negative bacteria. Notably, the selection of a linkage strategy to form peptide-PNA conjugate plays an important role in the effective delivery of PNAs. Recently, a unique Cysteine- 2-Cyanoisonicotinamide (Cys-CINA) click chemistry has been employed for the synthesis of cyclic peptides. Considering the high selectivity of this chemistry, we investigated the efficiency of Cys-CINA conjugation to synthesize novel antimicrobial peptide-PNA conjugates. The PNA targeting acyl carrier protein gene (acpP), when conjugated to the membrane-active antimicrobial peptides (polymyxin), showed improvement in antimicrobial activity against multidrug-resistant Gram-negative Acinetobacter baumannii. Thus, indicating that the Cys-CINA conjugation is an effective strategy to link the antisense oligonucleotides with antimicrobial peptides. Therefore, the Cys-CINA conjugation opens an exciting prospect for antimicrobial drug development.
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Affiliation(s)
- Nitin A. Patil
- Infection and Immunity Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
- *Correspondence: Nitin A. Patil,
| | - Varsha J. Thombare
- Department of Biochemistry and Pharmacology, The University of Melbourne, Melbourne, VIC, Australia
| | - Rong Li
- Infection and Immunity Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
| | - Xiaoji He
- Infection and Immunity Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
| | - Jing Lu
- Infection and Immunity Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
- Department of Biochemistry and Pharmacology, The University of Melbourne, Melbourne, VIC, Australia
| | - Heidi H. Yu
- Infection and Immunity Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
| | - Hasini Wickremasinghe
- Infection and Immunity Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
| | - Kavya Pamulapati
- Infection and Immunity Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
| | - Mohammad A. K. Azad
- Infection and Immunity Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
| | - Tony Velkov
- Department of Biochemistry and Pharmacology, The University of Melbourne, Melbourne, VIC, Australia
| | - Kade D. Roberts
- Infection and Immunity Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
| | - Jian Li
- Infection and Immunity Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
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15
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Halloy F, Biscans A, Bujold KE, Debacker A, Hill AC, Lacroix A, Luige O, Strömberg R, Sundstrom L, Vogel J, Ghidini A. Innovative developments and emerging technologies in RNA therapeutics. RNA Biol 2022; 19:313-332. [PMID: 35188077 PMCID: PMC8865321 DOI: 10.1080/15476286.2022.2027150] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
RNA-based therapeutics are emerging as a powerful platform for the treatment of multiple diseases. Currently, the two main categories of nucleic acid therapeutics, antisense oligonucleotides and small interfering RNAs (siRNAs), achieve their therapeutic effect through either gene silencing, splicing modulation or microRNA binding, giving rise to versatile options to target pathogenic gene expression patterns. Moreover, ongoing research seeks to expand the scope of RNA-based drugs to include more complex nucleic acid templates, such as messenger RNA, as exemplified by the first approved mRNA-based vaccine in 2020. The increasing number of approved sequences and ongoing clinical trials has attracted considerable interest in the chemical development of oligonucleotides and nucleic acids as drugs, especially since the FDA approval of the first siRNA drug in 2018. As a result, a variety of innovative approaches is emerging, highlighting the potential of RNA as one of the most prominent therapeutic tools in the drug design and development pipeline. This review seeks to provide a comprehensive summary of current efforts in academia and industry aimed at fully realizing the potential of RNA-based therapeutics. Towards this, we introduce established and emerging RNA-based technologies, with a focus on their potential as biosensors and therapeutics. We then describe their mechanisms of action and their application in different disease contexts, along with the strengths and limitations of each strategy. Since the nucleic acid toolbox is rapidly expanding, we also introduce RNA minimal architectures, RNA/protein cleavers and viral RNA as promising modalities for new therapeutics and discuss future directions for the field.
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Affiliation(s)
- François Halloy
- Department of Paediatrics, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Annabelle Biscans
- Oligonucleotide Chemistry, Discovery Sciences, BioPharmaceuticals R&d, AstraZeneca, Gothenburg, Sweden
| | - Katherine E. Bujold
- Department of Chemistry & Chemical Biology, McMaster University, (Ontario), Canada
| | | | - Alyssa C. Hill
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, Eth Zürich, Zürich, Switzerland
| | - Aurélie Lacroix
- Sixfold Bioscience, Translation & Innovation Hub, London, UK
| | - Olivia Luige
- Department of Biosciences and Nutrition, Karolinska Institutet, Sweden
| | - Roger Strömberg
- Department of Biosciences and Nutrition, Karolinska Institutet, Sweden
| | - Linda Sundstrom
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&d, AstraZeneca, Gothenburg, Sweden
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research (Hiri), Helmholtz Center for Infection Research (Hzi), Würzburg, Germany
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Alice Ghidini
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&d, AstraZeneca, Gothenburg, Sweden
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16
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Potentiating the Anti-Tuberculosis Efficacy of Peptide Nucleic Acids through Combinations with Permeabilizing Drugs. Microbiol Spectr 2022; 10:e0126221. [PMID: 35171048 PMCID: PMC8849056 DOI: 10.1128/spectrum.01262-21] [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] [Indexed: 11/24/2022] Open
Abstract
The emergence of antimicrobial resistance warrants for the development of improved treatment approaches. In this regard, peptide nucleic acids (PNAs) have shown great promise, exhibiting antibiotic properties through the targeting of cellular nucleic acids. We aimed to study the efficacy of PNA as an anti-tuberculosis agent. Since the efficacy of PNA is limited by its low penetration into the cell, we also investigated combinatorial treatments using permeabilizing drugs to improve PNA efficacy. Various concentrations of anti-inhA PNA, permeabilizing drugs, and their combinations were screened against extracellular and intracellular mycobacteria.0.625 to 5 μM anti-inhA PNA was observed to merely inhibit the growth of extracellular M. smegmatis, while low intracellular bacterial load was reduced by 2 or 2.5 log-fold when treated with 2.5 or 5 μM PNA, respectively. Anti-inhA PNA against M. tuberculosis H37Ra exhibited bactericidal properties at 2.5 and 5 μM and enabled a slight reduction in intracellular M. tuberculosis at concentrations from 2.5 to 20 μM. Of the permeabilizing drugs tested, ethambutol showed the most permeabilizing potential and ultimately potentiated anti-inhA PNA to the greatest extent, reducing its efficacious concentration to 1.25 μM against both M. smegmatis and M. tuberculosis. Furthermore, an enhanced clearance of 1.3 log-fold was observed for ethambutol-anti-inhA PNA combinations against intracellular M. tuberculosis. Thus, permeabilizing drug-PNA combinations indeed exhibit improved efficacies. We therefore propose that anti-inhA PNA could improve therapy even when applied in minute doses as an addition to the current anti-tuberculosis drug regimen. IMPORTANCE Peptide nucleic acids have great potential in therapeutics as anti-gene/anti-sense agents. However, their limited uptake in cells has curtailed their widespread application. Through this study, we explore a PNA-drug combinatorial strategy to improve the efficacy of PNAs and reduce their effective concentrations. This work also focuses on improving tuberculosis treatment, which is hindered by the emergence of antimicrobial-resistant strains of Mycobacterium tuberculosis. It is observed that the antibacterial efficacy of anti-inhA PNA is enhanced when it is combined with permeabilizing drugs, particularly ethambutol. This indicates that the addition of even small concentrations of anti-inhA PNA to the current TB regimen could potentiate their therapeutic efficiency. We hypothesize that this system would also overcome isoniazid resistance, since the resistance mutations lie outside the designed anti-inhA PNA target site.
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17
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Luo Y, Song Y. Mechanism of Antimicrobial Peptides: Antimicrobial, Anti-Inflammatory and Antibiofilm Activities. Int J Mol Sci 2021; 22:ijms222111401. [PMID: 34768832 PMCID: PMC8584040 DOI: 10.3390/ijms222111401] [Citation(s) in RCA: 129] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/08/2021] [Accepted: 10/20/2021] [Indexed: 12/13/2022] Open
Abstract
Antimicrobial peptides (AMPs) are regarded as a new generation of antibiotics. Besides antimicrobial activity, AMPs also have antibiofilm, immune-regulatory, and other activities. Exploring the mechanism of action of AMPs may help in the modification and development of AMPs. Many studies were conducted on the mechanism of AMPs. The present review mainly summarizes the research status on the antimicrobial, anti-inflammatory, and antibiofilm properties of AMPs. This study not only describes the mechanism of cell wall action and membrane-targeting action but also includes the transmembrane mechanism of intracellular action and intracellular action targets. It also discusses the dual mechanism of action reported by a large number of investigations. Antibiofilm and anti-inflammatory mechanisms were described based on the formation of biofilms and inflammation. This study aims to provide a comprehensive review of the multiple activities and coordination of AMPs in vivo, and to fully understand AMPs to realize their therapeutic prospect.
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Affiliation(s)
- Ying Luo
- College of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China;
| | - Yuzhu Song
- College of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China;
- Medical College, Kunming University of Science and Technology, Kunming 650500, China
- Correspondence: ; Tel.: +86-871-65939528
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18
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Landeros JM, Cruz‐Hernández C, Juaristi E. α‐Amino Acids and α,β‐Dipeptides Intercalated into Hydrotalcite: Efficient Catalysts in the Asymmetric Michael Addition Reaction of Aldehydes to
N
‐Substituted Maleimides. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100877] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- José M. Landeros
- Departamento de Química, Centro de Investigación y de Estudios Avanzados Instituto Politécnico Nacional Avenida IPN #2508 07360 Ciudad de México Mexico
| | - Carlos Cruz‐Hernández
- Departamento de Química, Centro de Investigación y de Estudios Avanzados Instituto Politécnico Nacional Avenida IPN #2508 07360 Ciudad de México Mexico
| | - Eusebio Juaristi
- Departamento de Química, Centro de Investigación y de Estudios Avanzados Instituto Politécnico Nacional Avenida IPN #2508 07360 Ciudad de México Mexico
- El Colegio Nacional Luis González Obregón 23, Centro Histórico 06020 Ciudad de México Mexico
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19
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Wang C, Hong T, Cui P, Wang J, Xia J. Antimicrobial peptides towards clinical application: Delivery and formulation. Adv Drug Deliv Rev 2021; 175:113818. [PMID: 34090965 DOI: 10.1016/j.addr.2021.05.028] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 05/14/2021] [Accepted: 05/30/2021] [Indexed: 02/07/2023]
Abstract
Antimicrobial peptides hold promise to supplement small molecules antibiotics and combat the multidrug resistant microbes. There are however technical hurdles towards the clinical applications, largely due to the inherent limitations of peptides including stability, cytotoxicity and bioavailability. Here we review recent studies concerning the delivery and formulation of antimicrobial peptides, by categorizing the different strategies as driven by physical interactions or chemical conjugation reactions, and carriers ranging from inorganic based ones (including gold, silver and silica based solid nanoparticles) to organic ones (including micelle, liposome and hydrogel) are covered. Besides, targeted delivery of antimicrobial peptides or using antimicrobial peptides as the targeting moiety, and responsive release of the peptides after delivery are also reviewed. Lastly, strategies towards the increase of oral bioavailability, from both physical or chemical methods, are highlighted. Altogether, this article provides a comprehensive review of the recent progress of the delivery and formulation of antimicrobial peptides towards clinical application.
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Affiliation(s)
- Cheng Wang
- Jiangsu Key Laboratory of Advanced Catalytic Materials and Technology, School of Pharmacy, Changzhou University, Changzhou, Jiangsu 213164, China
| | - Tingting Hong
- Jiangsu Key Laboratory of Advanced Catalytic Materials and Technology, School of Pharmacy, Changzhou University, Changzhou, Jiangsu 213164, China
| | - Pengfei Cui
- Jiangsu Key Laboratory of Advanced Catalytic Materials and Technology, School of Pharmacy, Changzhou University, Changzhou, Jiangsu 213164, China
| | - Jianhao Wang
- Jiangsu Key Laboratory of Advanced Catalytic Materials and Technology, School of Pharmacy, Changzhou University, Changzhou, Jiangsu 213164, China.
| | - Jiang Xia
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region.
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20
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Shemyakin IG, Firstova VV, Fursova NK, Abaev IV, Filippovich SY, Ignatov SG, Dyatlov IA. Next-Generation Antibiotics, Bacteriophage Endolysins, and Nanomaterials for Combating Pathogens. BIOCHEMISTRY (MOSCOW) 2021; 85:1374-1388. [PMID: 33280580 DOI: 10.1134/s0006297920110085] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
This review presents various strategies to fight causative agents of infectious diseases. Species-specific programmable RNA-containing antibiotics open up new possibilities for creating next-generation of personalized drugs based on microbiome editing and can serve as a new tool for selective elimination of pathogenic bacterial species while keeping intact the rest of microbiota. Another promising approach in combating bacterial infections is genome editing using the CRISPR-Cas systems. Expanding knowledge on the molecular mechanisms of innate immunity has been actively used for developing new antimicrobials. However, obvious risks of using antibiotic adjuvants aimed at activation of the host immune system include development of the autoimmune response with subsequent organ damage. To avoid these risks, it is essential to elucidate action mechanisms of the specific ligands and signal molecules used as components of the hybrid antibiotics. Bacteriophage endolysins are also considered as effective antimicrobials against antibiotic-resistant bacteria, metabolically inactive persisters, and microbial biofilms. Despite significant advances in the design of implants with antibacterial properties, the problem of postoperative infections still remains. Different nanomodifications of the implant surface have been designed to reduce bacterial contamination. Here, we review bactericidal, fungicidal, and immunomodulating properties of compounds used for the implant surface nanomodifications, such as silver, boron nitride nanomaterials, nanofibers, and nanogalvanic materials.
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Affiliation(s)
- I G Shemyakin
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, 142279, Russia
| | - V V Firstova
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, 142279, Russia.
| | - N K Fursova
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, 142279, Russia
| | - I V Abaev
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, 142279, Russia
| | - S Yu Filippovich
- Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
| | - S G Ignatov
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, 142279, Russia
| | - I A Dyatlov
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, 142279, Russia
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21
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Popella L, Jung J, Popova K, Ðurica-Mitić S, Barquist L, Vogel J. Global RNA profiles show target selectivity and physiological effects of peptide-delivered antisense antibiotics. Nucleic Acids Res 2021; 49:4705-4724. [PMID: 33849070 PMCID: PMC8096218 DOI: 10.1093/nar/gkab242] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/18/2021] [Accepted: 03/24/2021] [Indexed: 12/13/2022] Open
Abstract
Antisense peptide nucleic acids (PNAs) inhibiting mRNAs of essential genes provide a straight-forward way to repurpose our knowledge of bacterial regulatory RNAs for development of programmable species-specific antibiotics. While there is ample proof of PNA efficacy, their target selectivity and impact on bacterial physiology are poorly understood. Moreover, while antibacterial PNAs are typically designed to block mRNA translation, effects on target mRNA levels are not well-investigated. Here, we pioneer the use of global RNA-seq analysis to decipher PNA activity in a transcriptome-wide manner. We find that PNA-based antisense oligomer conjugates robustly decrease mRNA levels of the widely-used target gene, acpP, in Salmonella enterica, with limited off-target effects. Systematic analysis of several different PNA-carrier peptides attached not only shows different bactericidal efficiency, but also activation of stress pathways. In particular, KFF-, RXR- and Tat-PNA conjugates especially induce the PhoP/Q response, whereas the latter two additionally trigger several distinct pathways. We show that constitutive activation of the PhoP/Q response can lead to Tat-PNA resistance, illustrating the utility of RNA-seq for understanding PNA antibacterial activity. In sum, our study establishes an experimental framework for the design and assessment of PNA antimicrobials in the long-term quest to use these for precision editing of microbiota.
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Affiliation(s)
- Linda Popella
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
| | - Jakob Jung
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
| | - Kristina Popova
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
| | - Svetlana Ðurica-Mitić
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany.,Faculty of Medicine, University of Würzburg, D-97080 Würzburg, Germany
| | - Jörg Vogel
- Institute of Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany.,Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany.,Faculty of Medicine, University of Würzburg, D-97080 Würzburg, Germany
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22
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Liang X, Liu M, Komiyama M. Recognition of Target Site in Various Forms of DNA and RNA by Peptide Nucleic Acid (PNA): From Fundamentals to Practical Applications. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210086] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, P. R. China
| | - Mengqin Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Makoto Komiyama
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
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23
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Li R, He S, Yin K, Zhang B, Yi Y, Zhang M, Pei N, Huang L. Effects of N-terminal modifications on the stability of antimicrobial peptide SAMP-A4 analogues against protease degradation. J Pept Sci 2021; 27:e3352. [PMID: 34028137 DOI: 10.1002/psc.3352] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 05/10/2021] [Accepted: 05/12/2021] [Indexed: 02/06/2023]
Abstract
Infections with multidrug-resistant (MDR) pathogens are increasingly concerning for public health. Synthesized antimicrobial peptide A4 (SAMP-A4), a peptide computationally designed by our research team, is a potential drug candidate. However, the antimicrobial peptide SAMP-A4 is easily degraded in serum. To obtain SAMP-A4 analogues with high biostability, chemical modifications at its N-terminus, including fatty acid conjugation, glycosylation and PEGylation, were carried out. The results showed that the introduction of hydrophobic fatty acids at the N-terminus of SAMP-A4 is better than hydrophilic glycosylation and PEGylation. With increasing fatty acid chain length, the stability of SAMP-A4 analogues in serum and trypsin solutions is significantly improved, and the activities against MDR bacteria and Candida are significantly enhanced. There is no obvious change in haemolysis even when hexanoic acid is coupled with SAMP-A4, so the resulting analogue SAMP-A4-C6, SAMP-A4 conjugated with hexanoic acid, is the most likely of the analogues to become a drug.
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Affiliation(s)
- Ruifang Li
- College of Biological Engineering, Henan University of Technology, Zhengzhou, China
| | - Songlin He
- College of Biological Engineering, Henan University of Technology, Zhengzhou, China
| | - Kedong Yin
- College of Information Science and Engineering, Henan University of Technology, Zhengzhou, China
| | - Beibei Zhang
- College of Biological Engineering, Henan University of Technology, Zhengzhou, China
| | - Yanjie Yi
- College of Biological Engineering, Henan University of Technology, Zhengzhou, China
| | - Meng Zhang
- College of Biological Engineering, Henan University of Technology, Zhengzhou, China
| | - Nanqi Pei
- College of Biological Engineering, Henan University of Technology, Zhengzhou, China
| | - Liang Huang
- College of Biological Engineering, Henan University of Technology, Zhengzhou, China
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24
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Abstract
The activity of many antibiotics depends on the initial density of cells used in bacterial growth inhibition assays. This phenomenon, termed the inoculum effect, can have important consequences for the therapeutic efficacy of the drugs, because bacterial loads vary by several orders of magnitude in clinically relevant infections. Antimicrobial peptides are a promising class of molecules in the fight against drug-resistant bacteria because they act mainly by perturbing the cell membranes rather than by inhibiting intracellular targets. Here, we report a systematic characterization of the inoculum effect for this class of antibacterial compounds. Minimum inhibitory concentration values were measured for 13 peptides (including all-D enantiomers) and peptidomimetics, covering more than seven orders of magnitude in inoculated cell density. In most cases, the inoculum effect was significant for cell densities above the standard inoculum of 5 × 105 cells/mL, while for lower densities the active concentrations remained essentially constant, with values in the micromolar range. In the case of membrane-active peptides, these data can be rationalized by considering a simple model, taking into account peptide-cell association, and hypothesizing that a threshold number of cell-bound peptide molecules is required in order to cause bacterial killing. The observed effect questions the clinical utility of activity and selectivity determinations performed at a fixed, standardized cell density. A routine evaluation of the dependence of the activity of antimicrobial peptides and peptidomimetics on the inoculum should be considered.
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25
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Shaikh AY, Björkling F, Nielsen PE, Franzyk H. Optimized Synthesis of Fmoc/Boc‐Protected PNA Monomers and their Assembly into PNA Oligomers. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Ashif Y. Shaikh
- Center for Peptide-based Antibiotics, Department of Drug Design and Pharmacology Faculty of Heath and Medical Sciences University of Copenhagen Jagtvej 162 2100 Copenhagen Denmark
| | - Fredrik Björkling
- Center for Peptide-based Antibiotics, Department of Drug Design and Pharmacology Faculty of Heath and Medical Sciences University of Copenhagen Jagtvej 162 2100 Copenhagen Denmark
| | - Peter E. Nielsen
- Center for Peptide-based Antibiotics, Department of Cellular and Molecular Medicine, The Panum Institute, Faculty of Heath and Medical Sciences University of Copenhagen Blegdamsvej 3 2200 Copenhagen Denmark
| | - Henrik Franzyk
- Center for Peptide-based Antibiotics, Department of Drug Design and Pharmacology Faculty of Heath and Medical Sciences University of Copenhagen Jagtvej 162 2100 Copenhagen Denmark
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26
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Martínez-Guitián M, Vázquez-Ucha JC, Álvarez-Fraga L, Conde-Pérez K, Bou G, Poza M, Beceiro A. Antisense inhibition of lpxB gene expression in Acinetobacter baumannii by peptide-PNA conjugates and synergy with colistin. J Antimicrob Chemother 2021; 75:51-59. [PMID: 31586411 DOI: 10.1093/jac/dkz409] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 08/28/2019] [Accepted: 09/03/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND LpxB is an enzyme involved in the biosynthesis pathway of lipid A, a component of LPS. OBJECTIVES To evaluate the lpxB gene in Acinetobacter baumannii as a potential therapeutic target and to propose antisense agents such as peptide nucleic acids (PNAs) as a tool to combat bacterial infection, either alone or in combination with known antimicrobial therapies. METHODS RNA-seq analysis of the A. baumannii ATCC 17978 strain in a murine pneumonia model was performed to study the in vivo expression of lpxB. Protein expression was studied in the presence or absence of anti-lpxB (KFF)3K-PNA (pPNA). Time-kill curve analyses and protection assays of infected A549 cells were performed. The chequerboard technique was used to test for synergy between pPNA and colistin. A Galleria mellonella infection model was used to test the in vivo efficacy of pPNA. RESULTS The lpxB gene was overexpressed during pneumonia. Treatment with a specific pPNA inhibited LpxB expression in vitro, decreased survival of the ATCC 17978 strain and increased the survival rate of infected A549 cells. Synergy was observed between pPNA and colistin in colistin-susceptible strains. In vivo assays confirmed that a combination treatment of anti-lpxB pPNA and colistin was more effective than colistin in monotherapy. CONCLUSIONS The lpxB gene is essential for A. baumannii survival. Anti-lpxB pPNA inhibits LpxB expression, causing bacterial death. This pPNA showed synergy with colistin and increased the survival rate in G. mellonella. The data suggest that antisense pPNA molecules blocking the lpxB gene could be used as antibacterial agents.
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Affiliation(s)
- Marta Martínez-Guitián
- Servicio de Microbiología do Complexo Hospitalario Universitario da Coruña (CHUAC), Instituto de Investigación Biomédica da Coruña (INIBIC), Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña (UDC), A Coruña, Spain
| | - Juan Carlos Vázquez-Ucha
- Servicio de Microbiología do Complexo Hospitalario Universitario da Coruña (CHUAC), Instituto de Investigación Biomédica da Coruña (INIBIC), Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña (UDC), A Coruña, Spain
| | - Laura Álvarez-Fraga
- Servicio de Microbiología do Complexo Hospitalario Universitario da Coruña (CHUAC), Instituto de Investigación Biomédica da Coruña (INIBIC), Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña (UDC), A Coruña, Spain
| | - Kelly Conde-Pérez
- Servicio de Microbiología do Complexo Hospitalario Universitario da Coruña (CHUAC), Instituto de Investigación Biomédica da Coruña (INIBIC), Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña (UDC), A Coruña, Spain
| | - Germán Bou
- Servicio de Microbiología do Complexo Hospitalario Universitario da Coruña (CHUAC), Instituto de Investigación Biomédica da Coruña (INIBIC), Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña (UDC), A Coruña, Spain
| | - Margarita Poza
- Servicio de Microbiología do Complexo Hospitalario Universitario da Coruña (CHUAC), Instituto de Investigación Biomédica da Coruña (INIBIC), Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña (UDC), A Coruña, Spain
| | - Alejandro Beceiro
- Servicio de Microbiología do Complexo Hospitalario Universitario da Coruña (CHUAC), Instituto de Investigación Biomédica da Coruña (INIBIC), Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña (UDC), A Coruña, Spain
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27
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Targeting of the Essential acpP, ftsZ, and rne Genes in Carbapenem-Resistant Acinetobacter baumannii by Antisense PNA Precision Antibacterials. Biomedicines 2021; 9:biomedicines9040429. [PMID: 33921011 PMCID: PMC8071358 DOI: 10.3390/biomedicines9040429] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 03/31/2021] [Accepted: 04/08/2021] [Indexed: 12/12/2022] Open
Abstract
Infections by carbapenem-resistant A. baumannii (CRAB), a widespread nosocomial pathogen, are becoming increasingly difficult to prevent and treat. Therefore, there is an urgent need for discovery of novel antibiotics against CRAB. Programmable, precision antisense antibiotics, e.g., based on the nucleic acid mimic PNA (peptide nucleic acid) have shown promise in this respect in the form of PNA-BPP (bacteria penetrating peptide) conjugates targeting essential bacterial genes. In the present study, we designed and synthesized a series of PNA-BPPs targeting the translation initiation region of the ftsZ, acpP, or rne gene of CRAB strains. The antimicrobial activity of the compounds and effects on gene expression level was compared to that of analogous mismatch PNA controls. Three antisense conjugates (KFF)3K-eg1-(acpP)PNA (5639), (KFF)3K-eg1-(ftsZ)PNA (5612), and (KFF)3-K-eg1-(rne)PNA (5656) exhibited complete growth inhibition against several CRAB strains at 1-2, 2-8, and 2 µM, respectively, and the compounds were bactericidal at 1-2× MIC. The bactericidal effect was correlated to reduction of target gene mRNA level using RT-qPCR, and the compounds showed no bacterial membrane disruption activity at 1-2× MIC. PNA5612 was tested against a series of 12 CRAB isolates and all were sensitive at 2-8 µM. In addition, the conjugates exhibited no cellular toxicity in the HepG2 cell line (up to 20 μM) and did not shown significant antibacterial activity against other Gram negatives (E. coli, P. aeruginosa). These results provide a starting point for discovery of antisense precision designer antibiotics for specific treatment of CRAB infections.
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28
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Chen W, Dong B, Liu W, Liu Z. Recent Advances in Peptide Nucleic Acids as Antibacterial Agents. Curr Med Chem 2021; 28:1104-1125. [PMID: 32484766 DOI: 10.2174/0929867327666200602132504] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 05/06/2020] [Accepted: 05/13/2020] [Indexed: 11/22/2022]
Abstract
The emergence of antibiotic-resistant bacteria and the slow progress in searching for new antimicrobial agents makes it hard to treat bacterial infections and cause problems for the healthcare system worldwide, including high costs, prolonged hospitalizations, and increased mortality. Therefore, the discovery of effective antibacterial agents is of great importance. One attractive alternative is antisense peptide nucleic acid (PNA), which inhibits or eliminates gene expression by binding to the complementary messenger RNA (mRNA) sequence of essential genes or the accessible and functionally important regions of the ribosomal RNA (rRNA). Following 30 years of development, PNAs have played an extremely important role in the treatment of Gram-positive, Gram-negative, and acidfast bacteria due to their desirable stability of hybrid complex with target RNA, the strong affinity for target mRNA/rRNA, and the stability against nucleases. PNA-based antisense antibiotics can strongly inhibit the growth of pathogenic and antibiotic-resistant bacteria in a sequence-specific and dose-dependent manner at micromolar concentrations. However, several fundamental challenges, such as intracellular delivery, solubility, physiological stability, and clearance still need to be addressed before PNAs become broadly applicable in clinical settings. In this review, we summarize the recent advances in PNAs as antibacterial agents and the challenges that need to be overcome in the future.
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Affiliation(s)
- Wei Chen
- Hunan Key Laboratory for Super Microstructure and Ultrafast Process, School of Physics and Electronics Central South University, Changsha 410083, China
| | - Bo Dong
- Hunan Key Laboratory for Super Microstructure and Ultrafast Process, School of Physics and Electronics Central South University, Changsha 410083, China
| | - Wenen Liu
- Department of Clinical Laboratory, Xiangya Hospital of Central South University, Changsha 410008, China
| | - Zhengchun Liu
- Hunan Key Laboratory for Super Microstructure and Ultrafast Process, School of Physics and Electronics Central South University, Changsha 410083, China
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29
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de Oliveira Costa B, Franco OL. Cryptic Host Defense Peptides: Multifaceted Activity and Prospects for Medicinal Chemistry. Curr Top Med Chem 2021; 20:1274-1290. [PMID: 32209042 DOI: 10.2174/1568026620666200325112425] [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] [Received: 11/11/2019] [Revised: 02/03/2020] [Accepted: 02/24/2020] [Indexed: 01/22/2023]
Abstract
Host defense peptides (HDPs) comprise a heterogeneous group of evolutionarily conserved and biologically active small molecules that are produced by different organisms. HDPs are widely researched because they often have multiple biological activities, for example antimicrobial, immunomodulatory and anticancer activity. In this context, in this review we focus on cryptic HDPs, molecules derived specifically from proteolytic processing of endogenous precursor proteins. Here, we explore the biological activity of such molecules and we further discuss the development of optimized sequences based on these natural cryptic HDPs. In addition, we present clinical-phase studies of cryptic HDPs (natural or optimized), and point out the possible applicability of these molecules in medicinal chemistry.
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Affiliation(s)
- Bruna de Oliveira Costa
- S-inova Biotech, Graduate Program in Biotechnology, Universidade Catolica Dom Bosco, Campo Grande, MS, Brazil
| | - Octávio Luiz Franco
- S-inova Biotech, Graduate Program in Biotechnology, Universidade Catolica Dom Bosco, Campo Grande, MS, Brazil.,Department of Genomic Sciences and Biotechnology, Center for Analysis of Proteomics and Biochemistry, Catholic University of Brasília, Brasília, DF, Brazil.,Department of Molecular Pathology, Faculty of Medicine, University of Brasília, Brasília-DF, Brazil
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30
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Fmoc-Based Assembly of PNA Oligomers: Manual and Microwave-Assisted Automated Synthesis. Methods Mol Biol 2021; 2105:1-16. [PMID: 32088861 DOI: 10.1007/978-1-0716-0243-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Exploration of PNA-peptide conjugates as potential antisense antibiotics necessitates a fast and efficient synthesis protocols for amounts that facilitate determination of structure-activity relationships and in vivo studies in animal infection models. Fmoc/Boc-protected PNA monomers are here used for assembly of oligomers by optimized protocols involving either a manual synthesis method at room temperature or automated microwave-assisted coupling of monomers on a peptide synthesizer.
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31
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Ghosh S, Cotta KB, Hande AA, Fernandes M, Mehra S. PNA-mediated efflux inhibition as a therapeutic strategy towards overcoming drug resistance in Mycobacterium smegmatis. Microb Pathog 2021; 151:104737. [PMID: 33453316 DOI: 10.1016/j.micpath.2021.104737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 01/06/2021] [Accepted: 01/07/2021] [Indexed: 11/27/2022]
Abstract
The emergence of antibiotic-resistant strains of Mycobacterium tuberculosis and the decelerating development of new and effective antibiotics has impaired the treatment of tuberculosis (TB). Efflux pump inhibitors (EPIs) have the potential to improve the efficacy of existing anti-TB drugs although with toxicity limitations. Peptide nucleic acids (PNAs), oligonucleotide mimics, by virtue of their high nucleic acid binding specificity have the capability to overcome this drawback. We, therefore, investigated the efflux pump inhibitory properties of a PNA designed against an efflux pump of Mycobacterium smegmatis. LfrA, an efflux pump found in M. smegmatis, is majorly involved in conferring innate drug resistance to this strain and, therefore, was selected as a target for gene silencing via PNA. qRT-PCR and EtBr assays confirmed the EPI activity of the anti-lfrA PNA. On testing the effect of the anti-lfrA PNA on the bactericidal activity of a fluoroquinolone, norfloxacin, we observed that 5 μM of anti-lfrA PNA in combination with norfloxacin led to an enhanced killing of up to 2.5 log-fold against wild-type and a lab-generated multidrug resistant strain, exemplifying its potential in countering resistance. Improved efficacy was also observed against intra-macrophage mycobacteria, where the drug-PNA combination enhanced bacterial clearance by 1.3 log-fold. Further, no toxicity was observed with PNA concentrations up to 4 times higher than the efficacious anti-lfrA PNA concentration. Thus, PNA, as an adjuvant, presents a novel and viable approach to rejuvenate anti-TB therapeutics.
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Affiliation(s)
| | - Karishma Berta Cotta
- Centre for Research in Nanotechnology and Science, IIT Bombay, Powai, Mumbai, India
| | - Aniket A Hande
- Université de Pau et des Pays de l'Adour E2S UPPA, CNRS, IPREM, Pau, France
| | - Moneesha Fernandes
- Organic Chemistry Division, CSIR-National Chemical Laboratory, Pune, India
| | - Sarika Mehra
- WRCB, IIT Bombay, Powai, Mumbai, Maharashtra, India; Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, India.
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32
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Vogel J. An RNA biology perspective on species-specific programmable RNA antibiotics. Mol Microbiol 2020; 113:550-559. [PMID: 32185839 DOI: 10.1111/mmi.14476] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 01/20/2020] [Accepted: 01/21/2020] [Indexed: 12/14/2022]
Abstract
Our body is colonized by a vast array of bacteria the sum of which forms our microbiota. The gut alone harbors >1,000 bacterial species. An understanding of their individual or synergistic contributions to human health and disease demands means to interfere with their functions on the species level. Most of the currently available antibiotics are broad-spectrum, thus too unspecific for a selective depletion of a single species of interest from the microbiota. Programmable RNA antibiotics in the form of short antisense oligonucleotides (ASOs) promise to achieve precision manipulation of bacterial communities. These ASOs are coupled to small peptides that carry them inside the bacteria to silence mRNAs of essential genes, for example, to target antibiotic-resistant pathogens as an alternative to standard antibiotics. There is already proof-of-principle with diverse bacteria, but many open questions remain with respect to true species specificity, potential off-targeting, choice of peptides for delivery, bacterial resistance mechanisms and the host response. While there is unlikely a one-fits-all solution for all microbiome species, I will discuss how recent progress in bacterial RNA biology may help to accelerate the development of programmable RNA antibiotics for microbiome editing and other applications.
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Affiliation(s)
- Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Würzburg, Germany.,RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
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33
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Chen Z, Nie D, Hu Y, Li M, Hou Z, Mao X, Luo X, Xue X. Efficient Delivery of Antisense Oligonucleotides by an Amphipathic Cell-Penetrating Peptide in Acinetobacter baumannii. Curr Drug Deliv 2020; 16:728-736. [PMID: 31244437 DOI: 10.2174/1567201816666190627141931] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 04/08/2019] [Accepted: 06/10/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Carbapenem-resistant Acinetobacter baumannii (A. baumannii) was on the top of the list of the most threatening bacteria published by the WHO in 2017. Antisense oligonucleotides (ASOs) based therapy is a promising strategy for combating Multi-Drug Resistant (MDR) bacteria because of its high specificity, easy design and lower induction of resistance, but poor cellular uptake by bacteria has restricted the further utilization of this therapy. METHODS Here, we used CADY, a secondary amphipathic peptide of 20 residues that could successfully carry siRNA into mammalian cells, to prepare CADY/ASOs nanoparticles (CADY-NPs) targeting acpP (encoding acyl carrier protein), and evaluated the uptake features, the inhibitory effects of CADY-NPs on gene expression and the growth of MDR-A. baumannii. RESULTS We found that CADY-NPs could be quickly internalized by drug-sensitive and MDR-A. baumannii in an energy independent manner, which could be restrained by chlorpromazine (an inhibitor of clathrin mediated endocytosis) significantly. In addition, CADY-NPs targeting acpP concentrationdependently retarded the growth of MDR-A. baumannii, which was associated with the decreased expression of targeted genes in A. baumannii. CONCLUSION In conclusion, our research is the first to demonstrate that CADY can deliver ASOs into bacteria and provide a novel strategy for the treatment of MDR-A. baumannii.
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Affiliation(s)
- Zhou Chen
- Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, No. 169, Changle West Road, Xi'an 710032, China
| | - Dan Nie
- Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, No. 169, Changle West Road, Xi'an 710032, China
| | - Yue Hu
- Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, No. 169, Changle West Road, Xi'an 710032, China
| | - Mingkai Li
- Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, No. 169, Changle West Road, Xi'an 710032, China
| | - Zheng Hou
- Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, No. 169, Changle West Road, Xi'an 710032, China
| | - Xinggang Mao
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, No. 169, Changle West Road, Xi'an, Shaanxi Province, China
| | - Xiaoxing Luo
- Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, No. 169, Changle West Road, Xi'an 710032, China
| | - Xiaoyan Xue
- Department of Pharmacology, School of Pharmacy, Fourth Military Medical University, No. 169, Changle West Road, Xi'an 710032, China
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Antibacterial Peptide Nucleic Acids-Facts and Perspectives. Molecules 2020; 25:molecules25030559. [PMID: 32012929 PMCID: PMC7038079 DOI: 10.3390/molecules25030559] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 01/20/2020] [Accepted: 01/22/2020] [Indexed: 12/13/2022] Open
Abstract
Antibiotic resistance is an escalating, worldwide problem. Due to excessive use of antibiotics, multidrug-resistant bacteria have become a serious threat and a major global healthcare problem of the 21st century. This fact creates an urgent need for new and effective antimicrobials. The common strategies for antibiotic discovery are based on either modifying existing antibiotics or screening compound libraries, but these strategies have not been successful in recent decades. An alternative approach could be to use gene-specific oligonucleotides, such as peptide nucleic acid (PNA) oligomers, that can specifically target any single pathogen. This approach broadens the range of potential targets to any gene with a known sequence in any bacterium, and could significantly reduce the time required to discover new antimicrobials or their redesign, if resistance arises. We review the potential of PNA as an antibacterial molecule. First, we describe the physicochemical properties of PNA and modifications of the PNA backbone and nucleobases. Second, we review the carriers used to transport PNA to bacterial cells. Furthermore, we discuss the PNA targets in antibacterial studies focusing on antisense PNA targeting bacterial mRNA and rRNA.
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Goltermann L, Nielsen PE. PNA Antisense Targeting in Bacteria: Determination of Antibacterial Activity (MIC) of PNA-Peptide Conjugates. Methods Mol Biol 2020; 2105:231-239. [PMID: 32088874 DOI: 10.1007/978-1-0716-0243-0_14] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Antisense PNA-peptide conjugates targeting essential bacterial genes have shown interesting potential for discovery of novel precision antibiotics. In this context, the minimal inhibitory concentration (MIC) assay is used to assess and compare the antimicrobial activity of natural as well as synthetic antimicrobial compounds. Here, we describe the determination of the minimal inhibitory concentration of peptide-PNA conjugates against Escherichia coli. This method can be expanded to include minimal bactericidal concentration (MBC) determination and kill-curve kinetics.
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Affiliation(s)
- Lise Goltermann
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Peter E Nielsen
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Shang Z, Chan SY, Song Q, Li P, Huang W. The Strategies of Pathogen-Oriented Therapy on Circumventing Antimicrobial Resistance. RESEARCH (WASHINGTON, D.C.) 2020; 2020:2016201. [PMID: 33083786 PMCID: PMC7539235 DOI: 10.34133/2020/2016201] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 08/02/2020] [Indexed: 12/23/2022]
Abstract
The emerging antimicrobial resistance (AMR) poses serious threats to the global public health. Conventional antibiotics have been eclipsed in combating with drug-resistant bacteria. Moreover, the developing and deploying of novel antimicrobial drugs have trudged, as few new antibiotics are being developed over time and even fewer of them can hit the market. Alternative therapeutic strategies to resolve the AMR crisis are urgently required. Pathogen-oriented therapy (POT) springs up as a promising approach in circumventing antibiotic resistance. The tactic underling POT is applying antibacterial compounds or materials directly to infected regions to treat specific bacteria species or strains with goals of improving the drug efficacy and reducing nontargeting and the development of drug resistance. This review exemplifies recent trends in the development of POTs for circumventing AMR, including the adoption of antibiotic-antibiotic conjugates, antimicrobial peptides, therapeutic monoclonal antibodies, nanotechnologies, CRISPR-Cas systems, and microbiota modulations. Employing these alternative approaches alone or in combination shows promising advantages for addressing the growing clinical embarrassment of antibiotics in fighting drug-resistant bacteria.
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Affiliation(s)
- Zifang Shang
- Frontiers Science Center for Flexible Electronics (FSCFE), Xi'an Institute of Flexible Electronics (IFE) & Xi'an Institute of Biomedical Materials and Engineering (IBME), Northwestern Polytechnical University (NPU), Xi'an 710072, China
| | - Siew Yin Chan
- Frontiers Science Center for Flexible Electronics (FSCFE), Xi'an Institute of Flexible Electronics (IFE) & Xi'an Institute of Biomedical Materials and Engineering (IBME), Northwestern Polytechnical University (NPU), Xi'an 710072, China
| | - Qing Song
- Frontiers Science Center for Flexible Electronics (FSCFE), Xi'an Institute of Flexible Electronics (IFE) & Xi'an Institute of Biomedical Materials and Engineering (IBME), Northwestern Polytechnical University (NPU), Xi'an 710072, China
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) and Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications (NUPT), Nanjing 210023, China
| | - Peng Li
- Frontiers Science Center for Flexible Electronics (FSCFE), Xi'an Institute of Flexible Electronics (IFE) & Xi'an Institute of Biomedical Materials and Engineering (IBME), Northwestern Polytechnical University (NPU), Xi'an 710072, China
| | - Wei Huang
- Frontiers Science Center for Flexible Electronics (FSCFE), Xi'an Institute of Flexible Electronics (IFE) & Xi'an Institute of Biomedical Materials and Engineering (IBME), Northwestern Polytechnical University (NPU), Xi'an 710072, China
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) and Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications (NUPT), Nanjing 210023, China
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University (NanjingTech), Nanjing 211816, China
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37
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Kawano M, Morohashi S, Oda K, Ishikawa M, Fujita S, Saito M. Artificial small RNA-mediated growth inhibition in Escherichia coli and Salmonella enterica serovar Typhimurium. Biochem Biophys Res Commun 2019; 521:577-583. [PMID: 31679698 DOI: 10.1016/j.bbrc.2019.10.060] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 10/05/2019] [Indexed: 11/25/2022]
Abstract
We developed a synthetic RNA approach to identify growth inhibition sequences by cloning random 24-nucleotide (nt) sequences into an arabinose-inducible expression vector. This vector expressed a small RNA (sRNA) of ∼140 nt containing a 24 nt random sequence insert. After transforming Escherichia coli with the vector, 10 out of 954 transformants showed strong growth defect phenotypes and two clones caused cell lysis. We then examined growth inhibition phenotypes in the Salmonella Typhimurium LT2 strain using the twelve sRNAs that exerted an inhibitory effect on E. coli growth. Three of these clones showed strong growth inhibition phenotypes in S. Typhimurium LT2. The most effective sRNA contained the same insert (N1) in both bacteria. The 24 nt random sequence insert of N1 was abundant in guanine residues (ten out of 24 nt), and other random sequences causing growth defects were also highly enriched for guanine (G) nucleotides. We, therefore, generated clones that express sRNAs containing a stretch of 16 to 24 continuous guanine sequences (poly-G16, -G18, -G20, -G22, and -G24). All of these clones induced growth inhibition in both liquid and agar plate media and the poly-G20 clone showed the strongest effect in E. coli. These results demonstrate that our sRNA expression system can be used to identify nucleotide sequences that are potential candidates for oligonucleotide antimicrobial drugs.
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Affiliation(s)
- Mitsuoki Kawano
- Department of Human Nutrition, Faculty of Contemporary Life Science, Chugokugakuen University, Okayama, Japan; Department of Microbiology, Kawasaki Medical School, Kurashiki, Japan.
| | - Shota Morohashi
- Laboratory of Gene Regulation Study, Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
| | - Kohei Oda
- Laboratory of Gene Regulation Study, Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
| | - Masataka Ishikawa
- Laboratory of Gene Regulation Study, Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
| | - Shouta Fujita
- Laboratory of Gene Regulation Study, Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
| | - Mineki Saito
- Department of Microbiology, Kawasaki Medical School, Kurashiki, Japan
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Non-Lytic Antibacterial Peptides That Translocate Through Bacterial Membranes to Act on Intracellular Targets. Int J Mol Sci 2019; 20:ijms20194877. [PMID: 31581426 PMCID: PMC6801614 DOI: 10.3390/ijms20194877] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 09/12/2019] [Accepted: 09/14/2019] [Indexed: 11/28/2022] Open
Abstract
The advent of multidrug resistance among pathogenic bacteria has attracted great attention worldwide. As a response to this growing challenge, diverse studies have focused on the development of novel anti-infective therapies, including antimicrobial peptides (AMPs). The biological properties of this class of antimicrobials have been thoroughly investigated, and membranolytic activities are the most reported mechanisms by which AMPs kill bacteria. Nevertheless, an increasing number of works have pointed to a different direction, in which AMPs are seen to be capable of displaying non-lytic modes of action by internalizing bacterial cells. In this context, this review focused on the description of the in vitro and in vivo antibacterial and antibiofilm activities of non-lytic AMPs, including indolicidin, buforin II PR-39, bactenecins, apidaecin, and drosocin, also shedding light on how AMPs interact with and further translocate through bacterial membranes to act on intracellular targets, including DNA, RNA, cell wall and protein synthesis.
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39
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Jasiński M, Miszkiewicz J, Feig M, Trylska J. Thermal Stability of Peptide Nucleic Acid Complexes. J Phys Chem B 2019; 123:8168-8177. [PMID: 31491077 DOI: 10.1021/acs.jpcb.9b05168] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Peptide nucleic acid (PNA) is a neutral nucleic acid analogue that base pairs with itself and natural nucleic acids. PNA-nucleic acid complexes are more thermally stable than the corresponding complexes of natural nucleic acids. In addition, PNA is biostable and thus used in many antisense and antigene applications to block functional RNA or DNA via sequence-specific interactions. We have recently developed force field parameters for molecular dynamics (MD) simulations of PNA and PNA-involving duplexes with natural nucleic acids. In this work, we provide the first application of this force field to biologically relevant PNA sequences and their complexes with RNA. We investigated thermal stabilities of short PNA-PNA, PNA-RNA, and RNA-RNA duplexes using UV-monitored thermal denaturation experiments and MD simulations at ambient and elevated temperatures. The simulations show a two-state melting transition and reproduce the thermal stability from melting experiments, with PNA-PNA being the most and RNA-RNA the least stable. The PNA-PNA duplex also displays the highest activation energy for melting. The atomistic details of unfolding of PNA duplexes suggest that all PNA-PNA bases melt concomitantly, whereas the RNA-RNA and PNA-RNA are destabilized from the termini toward the central part of the duplexes.
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Affiliation(s)
| | | | - Michael Feig
- Department of Biochemistry and Molecular Biology , Michigan State University , 603 Wilson Road , East Lansing , Michigan 48824 , United States
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40
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Arciola CR, Campoccia D, Montanaro L. Implant infections: adhesion, biofilm formation and immune evasion. Nat Rev Microbiol 2019; 16:397-409. [PMID: 29720707 DOI: 10.1038/s41579-018-0019-y] [Citation(s) in RCA: 1037] [Impact Index Per Article: 207.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Medical device-associated infections account for a large proportion of hospital-acquired infections. A variety of opportunistic pathogens can cause implant infections, depending on the type of the implant and on the anatomical site of implantation. The success of these versatile pathogens depends on rapid adhesion to virtually all biomaterial surfaces and survival in the hostile host environment. Biofilm formation on implant surfaces shelters the bacteria and encourages persistence of infection. Furthermore, implant-infecting bacteria can elude innate and adaptive host defences as well as biocides and antibiotic chemotherapies. In this Review, we explore the fundamental pathogenic mechanisms underlying implant infections, highlighting orthopaedic implants and Staphylococcus aureus as a prime example, and discuss innovative targets for preventive and therapeutic strategies.
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Affiliation(s)
- Carla Renata Arciola
- Research Unit on Implant Infections, Rizzoli Orthopaedic Institute, Bologna, Italy. .,Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy.
| | - Davide Campoccia
- Research Unit on Implant Infections, Rizzoli Orthopaedic Institute, Bologna, Italy
| | - Lucio Montanaro
- Research Unit on Implant Infections, Rizzoli Orthopaedic Institute, Bologna, Italy.,Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
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41
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Kalani BS, Najafi M, Mohammadzadeh R, Razavi S, Ohadi E, Irajian G. Targeting Listeria monocytogenes consensus sequence of internalin genes using an antisense molecule. Microb Pathog 2019; 136:103689. [PMID: 31445122 DOI: 10.1016/j.micpath.2019.103689] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/17/2019] [Accepted: 08/21/2019] [Indexed: 12/20/2022]
Abstract
As an intracellular pathogen, Listeria monocytogenes can enter host cells where it can replicate and escape detection and eradication by the host immune response making the clearance of infection very challenging. Furthermore, with the advent of antimicrobial resistance, the need for alternative targets is inevitable. Internalin proteins are crucial to this bacterium as they contribute to bacterial entry to the systemic circulation. In this study, we targeted a highly conserved region of these proteins by an antisense sequence that was covalently conjugated to the cell penetrating peptides (CPP) to overcome the challenging delivery barriers. Then, we evaluated the efficiency of this construct in vitro. We also assessed the antigenicity, cytotoxicity, and probability of apoptosis induction by this construct. The studied CPP-PNA inhibited bacterial growth and suppressed the mRNA expression of internalins in a dose-dependent manner. In addition, at all studied concentrations, CPP-PNA significantly reduced the invasion rate of L. monocytogenes in the examined cell lines. Moreover, different concentrations of CPP-PNA did not have a significant antigenic, cytotoxic, and apoptotic properties compared to the control. These results suggest the effectiveness of CPP-antisense in targeting the mRNAs of internalins for various research, therapeutic and preventive purposes. However, additional research is required to evaluate the potency, safety, and pharmacokinetics of this compound for the prevention and treatment of listeriosis.
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Affiliation(s)
- Behrooz Sadeghi Kalani
- Microbial Biotechnology Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Najafi
- Department of Biochemistry, Iran University of Medical Sciences, Tehran, Iran
| | - Rokhsareh Mohammadzadeh
- Microbial Biotechnology Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Shabnam Razavi
- Microbial Biotechnology Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Elnaz Ohadi
- Microbial Biotechnology Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Gholamreza Irajian
- Microbial Biotechnology Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
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42
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Kusuma KD, Payne M, Ung AT, Bottomley AL, Harry EJ. FtsZ as an Antibacterial Target: Status and Guidelines for Progressing This Avenue. ACS Infect Dis 2019; 5:1279-1294. [PMID: 31268666 DOI: 10.1021/acsinfecdis.9b00055] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The disturbing increase in the number of bacterial pathogens that are resistant to multiple, or sometimes all, current antibiotics highlights the desperate need to pursue the discovery and development of novel classes of antibacterials. The wealth of knowledge available about the bacterial cell division machinery has aided target-driven approaches to identify new inhibitor compounds. The main division target being pursued is the highly conserved and essential protein FtsZ. Despite very active research on FtsZ inhibitors for several years, this protein is not yet targeted by any commercial antibiotic. Here, we discuss the suitability of FtsZ as an antibacterial target for drug development and review progress achieved in this area. We use hindsight to highlight the gaps that have slowed progress in FtsZ inhibitor development and to suggest guidelines for concluding that FtsZ is actually the target of these molecules, a key missing link in several studies. In moving forward, a multidisciplinary, communicative, and collaborative process, with sharing of research expertise, is critical if we are to succeed.
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43
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Baker KR, Jana B, Hansen AM, Vissing KJ, Nielsen HM, Franzyk H, Guardabassi L. Repurposing azithromycin and rifampicin against Gram-negative pathogens by combination with peptide potentiators. Int J Antimicrob Agents 2019; 53:868-872. [DOI: 10.1016/j.ijantimicag.2018.10.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 10/11/2018] [Accepted: 10/30/2018] [Indexed: 10/27/2022]
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44
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Goltermann L, Yavari N, Zhang M, Ghosal A, Nielsen PE. PNA Length Restriction of Antibacterial Activity of Peptide-PNA Conjugates in Escherichia coli Through Effects of the Inner Membrane. Front Microbiol 2019; 10:1032. [PMID: 31178830 PMCID: PMC6542938 DOI: 10.3389/fmicb.2019.01032] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 04/24/2019] [Indexed: 01/10/2023] Open
Abstract
Peptide Nucleic Acid (PNA)-peptide conjugates targeting essential bacterial genes are showing promise as antisense antimicrobials in drug discovery. Optimization has focused on selection of target genes and exact localization around the ribosome binding site, but surprisingly a length optimum around 10-12 nucleobases has been found. Addressing this observation, we have investigated the relationship between PNA-length, PNA-RNA duplex stability and antimicrobial activity in E. coli in more detail. For PNAs of identical length of ten nucleobases the expected reverse correlation between the thermal stability (Tm) of the PNA-RNA duplex and the MIC for single mismatched PNAs was found. Also the expected direct correlation between the length of the PNA and the PNA-RNA duplex stability was found. Nonetheless, 10-mer PNAs [in a 6-18 mer extension series of (KFF)3K- and (RXR)4 conjugates] were the most active as antisense antimicrobials in both wild type E. coli MG1655 and AS19, suggesting that the size constraint is related to the bacterial uptake of PNA-peptide conjugates. This conclusion was supported by flow cytometry data showing higher bacterial uptake of shorter PNA fluorophore labeled conjugates. Interestingly, the size-limited uptake seems independent on outer membrane integrity (AS19), and thus the results suggest that the inner membrane limits the molecular size for peptide-PNA passage.
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Affiliation(s)
- Lise Goltermann
- Department of Cellular and Molecular Medicine, Center for Peptide-Based Antibiotics, The Panum Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Niloofar Yavari
- Department of Cellular and Molecular Medicine, Center for Peptide-Based Antibiotics, The Panum Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Meiqin Zhang
- Department of Cellular and Molecular Medicine, Center for Peptide-Based Antibiotics, The Panum Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anubrata Ghosal
- Department of Cellular and Molecular Medicine, Center for Peptide-Based Antibiotics, The Panum Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Peter E Nielsen
- Department of Cellular and Molecular Medicine, Center for Peptide-Based Antibiotics, The Panum Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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45
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Hansen AM, Bonke G, Hogendorf WFJ, Björkling F, Nielsen J, Kongstad KT, Zabicka D, Tomczak M, Urbas M, Nielsen PE, Franzyk H. Microwave-assisted solid-phase synthesis of antisense acpP peptide nucleic acid-peptide conjugates active against colistin- and tigecycline-resistant E. coli and K. pneumoniae. Eur J Med Chem 2019; 168:134-145. [PMID: 30807888 DOI: 10.1016/j.ejmech.2019.02.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 02/05/2019] [Accepted: 02/07/2019] [Indexed: 11/26/2022]
Abstract
Recent discovery of potent antibacterial antisense PNA-peptide conjugates encouraged development of a fast and efficient synthesis protocol that facilitates structure-activity studies. The use of an Fmoc/Boc protection scheme for both PNA monomers and amino acid building blocks in combination with microwave-assisted solid-phase synthesis proved to be a convenient procedure for continuous assembly of antisense PNA-peptide conjugates. A validated antisense PNA oligomer (CTCATACTCT; targeting mRNA of the acpP gene) was linked to N-terminally modified drosocin (i.e., RXR-PRPYSPRPTSHPRPIRV; X = aminohexanoic acid) or to a truncated Pip1 peptide (i.e., RXRRXR-IKILFQNRRMKWKK; X = aminohexanoic acid), and determination of the antibacterial effects of the resulting conjugates allowed assessment of the influence of different linkers as well as differences between the L- and D-forms of the peptides. The drosocin-derived compound without a linker moiety exhibited highest antibacterial activity against both wild-type Escherichia coli and Klebsiella pneumoniae (MICs in the range 2-4 μg/mL ∼ 0.3-0.7 μM), while analogues displaying an ethylene glycol (eg1) moiety or a polar maleimide linker also possessed activity toward wild-type K. pneumoniae (MICs of 4-8 μg/mL ∼ 0.6-1.3 μM). Against two colistin-resistant E. coli strains the linker-deficient compound proved most potent (with MICs in the range 2-4 μg/mL ∼ 0.3-0.7 μM). The truncated all-L Pip1 peptide had moderate inherent activity against E. coli, and this was unaltered or reduced upon conjugation to the antisense PNA oligomer. By contrast, this peptide was 8-fold less potent against K. pneumoniae, but in this case some PNA-peptide conjugates exhibited potent antisense activity (MICs of 2-8 μg/mL ∼ 0.3-1.2 μM). Most interestingly, the antibacterial activity of the D-form peptide itself was 2- to 16-fold higher than that of the L-form, even for the colistin- and tigecycline-resistant E. coli strains (MIC of 1-2 μg/mL ∼ 0.25-0.5 μM). Low activity was found for conjugates with a two-mismatch PNA sequence corroborating an antisense mode of action. Conjugates containing a D-form peptide were also significantly less active. In conclusion, we have designed and synthesized antisense PNA-drosocin conjugates with potent antibacterial activity against colistin- and tigecycline-resistant E. coli and K. pneumonia without concomitant hemolytic properties. In addition, a truncated D-form of Pip1 was identified as a peptide exhibiting potent activity against both wild-type and multidrug-resistant E. coli, P. aeruginosa, and A. baumannii (MICs within the range 1-4 μg/mL ∼ 0.25-1 μM) as well as toward wild-type Staphylococcus aureus (MIC of 2-4 μg/mL ∼ 0.5-1.0 μM).
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Affiliation(s)
- Anna Mette Hansen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, DK-2100, Denmark
| | - Gitte Bonke
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, DK-2100, Denmark
| | - Wouter Frederik Johan Hogendorf
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, DK-2100, Denmark
| | - Fredrik Björkling
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, DK-2100, Denmark
| | - John Nielsen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, DK-2100, Denmark
| | - Kenneth T Kongstad
- 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
| | - Peter E Nielsen
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2100, Denmark
| | - Henrik Franzyk
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, DK-2100, Denmark.
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Yang G, Huang T, Wang Y, Wang H, Li Y, Yu K, Dong L. Sustained Release of Antimicrobial Peptide from Self-Assembling Hydrogel Enhanced Osteogenesis. JOURNAL OF BIOMATERIALS SCIENCE-POLYMER EDITION 2018; 29:1812-1824. [PMID: 30035666 DOI: 10.1080/09205063.2018.1504191] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Biomaterials have been widely used in bone infection and osteomyelitis resulting from their versatile functionalities. As far as we know, the appearance of osteomyelitis was mainly caused by bacteria. Therefore, a biomaterial that can cure bone infection and promote osteogenesis may become an ideal candidate for the treatment of osteomyelitis. Cationic antimicrobial peptides (AMPs) have been proved to have an excellent ability to kill bacteria, fungi, viruses, and parasites. However, the application of AMPs in bone infection and osteomyelitis is quite limited. Here, we designed a new hydrogel that has an inhibitory effect on the proliferation of S. aureus and enhances osteogenesis. RADA16 self-assembling peptide has been applied for AMPs delivery. In this study, we demonstrated that RADA16 could form a stable structure and afford the sustained release of AMPs. The interwoven nanofiber morphology was detected by field emission scanning electron microscopy. The sustained release study revealed that the release of AMPs could be obtained until 28 days. In vitro research showed this new self-assembling hydrogel could promote the proliferation of bone mesenchymal stem cells (BMSCs) and inhibited the growth of S. aureus. More importantly, the results in vivo also proved that RADA16-AMP self-assembling peptide had an excellent effect on bone formation. Our findings implied that we successfully combined RADA16 and AMPs together and laid the foundation for the application of this new hydrogel and open new avenues for biomaterials.
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Affiliation(s)
- Guoli Yang
- a Department of Implantology , Stomatology Hospital, School of Medicine, Zhejiang University , Hangzhou , P. R. China
| | - Tingben Huang
- a Department of Implantology , Stomatology Hospital, School of Medicine, Zhejiang University , Hangzhou , P. R. China
| | - Ying Wang
- c Department of Oral Medicine , Stomatology Hospital, School of Medicine, Zhejiang University , Hangzhou , P. R. China
| | - Huiming Wang
- b Department of Oral and Maxillofacial Surgery , Stomatology Hospital, School of Medicine, Zhejiang University , Hangzhou , P. R. China
| | - Yongzheng Li
- a Department of Implantology , Stomatology Hospital, School of Medicine, Zhejiang University , Hangzhou , P. R. China
| | - Ke Yu
- a Department of Implantology , Stomatology Hospital, School of Medicine, Zhejiang University , Hangzhou , P. R. China
| | - Lingling Dong
- c Department of Oral Medicine , Stomatology Hospital, School of Medicine, Zhejiang University , Hangzhou , P. R. China
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Jasiński M, Feig M, Trylska J. Improved Force Fields for Peptide Nucleic Acids with Optimized Backbone Torsion Parameters. J Chem Theory Comput 2018; 14:3603-3620. [PMID: 29791152 DOI: 10.1021/acs.jctc.8b00291] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Peptide nucleic acids are promising nucleic acid analogs for antisense therapies as they can form stable duplex and triplex structures with DNA and RNA. Computational studies of PNA-containing duplexes and triplexes are an important component for guiding their design, yet existing force fields have not been well validated and parametrized with modern computational capabilities. We present updated CHARMM and Amber force fields for PNA that greatly improve the stability of simulated PNA-containing duplexes and triplexes in comparison with experimental structures and allow such systems to be studied on microsecond time scales. The force field modifications focus on reparametrized PNA backbone torsion angles to match high-level quantum mechanics reference energies for a model compound. The microsecond simulations of PNA-PNA, PNA-DNA, PNA-RNA, and PNA-DNA-PNA complexes also allowed a comprehensive analysis of hydration and ion interactions with such systems.
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Affiliation(s)
- Maciej Jasiński
- Department of Biochemistry and Molecular Biology , Michigan State University , East Lansing , Michigan 48824 , United States.,Centre of New Technologies , University of Warsaw , Warsaw , Poland
| | - Michael Feig
- Department of Biochemistry and Molecular Biology , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Joanna Trylska
- Centre of New Technologies , University of Warsaw , Warsaw , Poland
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48
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Xue XY, Mao XG, Zhou Y, Chen Z, Hu Y, Hou Z, Li MK, Meng JR, Luo XX. Advances in the delivery of antisense oligonucleotides for combating bacterial infectious diseases. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2018; 14:745-758. [PMID: 29341934 DOI: 10.1016/j.nano.2017.12.026] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 12/12/2017] [Accepted: 12/31/2017] [Indexed: 12/22/2022]
Abstract
Discovery and development of new antibacterial drugs against multidrug resistant bacterial strains have become more and more urgent. Antisense oligonucleotides (ASOs) show immense potential to control the spread of resistant microbes due to its high specificity of action, little risk to human gene expression, and easy design and synthesis to target any possible gene. However, efficient delivery of ASOs to their action sites with enough concentration remains a major obstacle, which greatly hampers their clinical application. In this study, we reviewed current progress on delivery strategies of ASOs into bacteria, focused on various non-virus gene vectors, including cell penetrating peptides, lipid nanoparticles, bolaamphiphile-based nanoparticles, DNA nanostructures and Vitamin B12. The current review provided comprehensive understanding and novel perspective for the future application of ASOs in combating bacterial infections.
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Affiliation(s)
- Xiao-Yan Xue
- Department of Pharmacology, School of Pharmacy, The Fourth Military Medical University, Xi'an, China.
| | - Xing-Gang Mao
- Department of Neurosurgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, China
| | - Ying Zhou
- Department of Pharmacology, Xi'an Medical University, Xi'an, China
| | - Zhou Chen
- Department of Pharmacology, School of Pharmacy, The Fourth Military Medical University, Xi'an, China
| | - Yue Hu
- Department of Pharmacology, School of Pharmacy, The Fourth Military Medical University, Xi'an, China
| | - Zheng Hou
- Department of Pharmacology, School of Pharmacy, The Fourth Military Medical University, Xi'an, China
| | - Ming-Kai Li
- Department of Pharmacology, School of Pharmacy, The Fourth Military Medical University, Xi'an, China
| | - Jing-Ru Meng
- Department of Pharmacology, School of Pharmacy, The Fourth Military Medical University, Xi'an, China
| | - Xiao-Xing Luo
- Department of Pharmacology, School of Pharmacy, The Fourth Military Medical University, Xi'an, China.
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49
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Hegarty JP, Stewart DB. Advances in therapeutic bacterial antisense biotechnology. Appl Microbiol Biotechnol 2017; 102:1055-1065. [PMID: 29209794 DOI: 10.1007/s00253-017-8671-0] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 11/16/2017] [Accepted: 11/17/2017] [Indexed: 12/15/2022]
Abstract
Antisense therapeutics are a biotechnological form of antibiotic therapy using chemical analogues of short single-stranded nucleic acid sequences modified to form stable oligomers. These molecules are termed antisense oligonucleotides (ASOs) because their sequence is complementary, via Watson-Crick specific base pairing, to their target messenger RNA (mRNA). ASOs modify gene expression in this sequence-dependent manner by binding to its complementary mRNA and inhibiting its translation into protein through steric blockage and/or through RNase degradation of the ASO/RNA duplex. The widespread use of conventional antibiotics has led to the increasing emergence of multiple drug-resistant pathogenic bacteria. There is an urgent need to develop alternative therapeutic strategies to reduce the morbidity and mortality associated with bacterial infections, and until recently, the use of ASOs as therapeutic agents has been essentially limited to eukaryotic cells, with ASOs as antibacterials having been largely unexplored primarily due to the poor uptake efficiency of antisense molecules by bacteria. There are conceptual advantages to bacterial antisense antibiotic therapies, including a sequence-dependent approach that allows for a rational design to multiple specific molecular targets. This review summarizes the current knowledge of antisense bacterial biotechnology and highlights the recent progress and the current obstacles in their development for therapeutic applications.
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Affiliation(s)
- John P Hegarty
- College of Medicine, Department of Surgery, The Pennsylvania State University, 500 University Drive, H137, P.O. Box 850, Hershey, PA, 17033-0850, USA
| | - David B Stewart
- College of Medicine, Department of Surgery, The Pennsylvania State University, 500 University Drive, H137, P.O. Box 850, Hershey, PA, 17033-0850, USA.
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50
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Molchanova N, Hansen PR, Franzyk H. Advances in Development of Antimicrobial Peptidomimetics as Potential Drugs. Molecules 2017; 22:E1430. [PMID: 28850098 PMCID: PMC6151827 DOI: 10.3390/molecules22091430] [Citation(s) in RCA: 179] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 08/18/2017] [Accepted: 08/22/2017] [Indexed: 01/19/2023] Open
Abstract
The rapid emergence of multidrug-resistant pathogens has evolved into a global health problem as current treatment options are failing for infections caused by pan-resistant bacteria. Hence, novel antibiotics are in high demand, and for this reason antimicrobial peptides (AMPs) have attracted considerable interest, since they often show broad-spectrum activity, fast killing and high cell selectivity. However, the therapeutic potential of natural AMPs is limited by their short plasma half-life. Antimicrobial peptidomimetics mimic the structure and biological activity of AMPs, but display extended stability in the presence of biological matrices. In the present review, focus is on the developments reported in the last decade with respect to their design, synthesis, antimicrobial activity, cytotoxic side effects as well as their potential applications as anti-infective agents. Specifically, only peptidomimetics with a modular structure of residues connected via amide linkages will be discussed. These comprise the classes of α-peptoids (N-alkylated glycine oligomers), β-peptoids (N-alkylated β-alanine oligomers), β³-peptides, α/β³-peptides, α-peptide/β-peptoid hybrids, α/γ N-acylated N-aminoethylpeptides (AApeptides), and oligoacyllysines (OAKs). Such peptidomimetics are of particular interest due to their potent antimicrobial activity, versatile design, and convenient optimization via assembly by standard solid-phase procedures.
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Affiliation(s)
- Natalia Molchanova
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark.
| | - Paul R Hansen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark.
| | - Henrik Franzyk
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark.
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