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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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Charting the sequence-activity landscape of peptide inhibitors of translation termination. Proc Natl Acad Sci U S A 2021; 118:2026465118. [PMID: 33674389 DOI: 10.1073/pnas.2026465118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Apidaecin (Api), an unmodified 18-amino-acid-long proline-rich antibacterial peptide produced by bees, has been recently described as a specific inhibitor of translation termination. It invades the nascent peptide exit tunnel of the postrelease ribosome and traps the release factors preventing their recycling. Api binds in the exit tunnel in an extended conformation that matches the placement of a nascent polypeptide and establishes multiple contacts with ribosomal RNA (rRNA) and ribosomal proteins. Which of these interactions are critical for Api's activity is unknown. We addressed this problem by analyzing the activity of all possible single-amino-acid substitutions of the Api variants synthesized in the bacterial cell. By conditionally expressing the engineered api gene, we generated Api directly in the bacterial cytosol, thereby bypassing the need for importing the peptide from the medium. The endogenously expressed Api, as well as its N-terminally truncated mutants, retained the antibacterial properties and the mechanism of action of the native peptide. Taking advantage of the Api expression system and next-generation sequencing, we mapped in one experiment all the single-amino-acid substitutions that preserve or alleviate the on-target activity of the Api mutants. Analysis of the inactivating mutations made it possible to define the pharmacophore of Api involved in critical interactions with the ribosome, transfer RNA (tRNA), and release factors. We also identified the Api segment that tolerates a variety of amino acid substitutions; alterations in this segment could be used to improve the pharmacological properties of the antibacterial peptide.
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Kolano L, Knappe D, Volke D, Sträter N, Hoffmann R. Ribosomal Target-Binding Sites of Antimicrobial Peptides Api137 and Onc112 Are Conserved among Pathogens Indicating New Lead Structures To Develop Novel Broad-Spectrum Antibiotics. Chembiochem 2020; 21:2628-2634. [PMID: 32293093 PMCID: PMC7540576 DOI: 10.1002/cbic.202000109] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Indexed: 12/13/2022]
Abstract
Proline‐rich antimicrobial peptides expressed in insects are primarily active against Enterobacteriaceae. Mechanistically, they target the bacterial (70S) ribosome after partially transporter‐based cellular uptake, as revealed for Api137 and Onc112 on Escherichia coli. Following molecular modeling indicating that the Onc112 contact site is conserved among the ribosomes of high‐priority pathogens, the ribosome binding of Api137 and Onc112 was studied. The dissociation constants (Kd) of Onc112 were ∼75 nmol/L for Escherichia coli, Klebsiella pneumoniae, and Acinetobacter baumannii, 36 nmol/L for Pseudomonas aeruginosa, and 102 nmol/L for Staphylococcus aureus, thus indicating a very promising lead structure for developing broad‐spectrum antibiotics. Api137 bound weaker with Kd values ranging from 155 nmol/L to 13 μmol/L. For most bacteria, the antibacterial activities were lower than predicted from the Kd values, which was only partially explained by their ability to enter bacterial cells. Other factors limiting the activity expected from the ribosome binding might be off‐target binding.
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Affiliation(s)
- Lisa Kolano
- Faculty of Chemistry and Mineralogy, Institute of Bioanalytical Chemistry, Deutscher Platz 5, 04103, Leipzig, Germany.,Center for Biotechnology and Biomedicine (BBZ), Deutscher Platz 5, 04103, Leipzig, Germany
| | - Daniel Knappe
- Faculty of Chemistry and Mineralogy, Institute of Bioanalytical Chemistry, Deutscher Platz 5, 04103, Leipzig, Germany.,Center for Biotechnology and Biomedicine (BBZ), Deutscher Platz 5, 04103, Leipzig, Germany.,EnBiotix GmbH, Leipzig, Deutscher Platz 5E, 04103, Leipzig, Germany
| | - Daniela Volke
- Faculty of Chemistry and Mineralogy, Institute of Bioanalytical Chemistry, Deutscher Platz 5, 04103, Leipzig, Germany.,Center for Biotechnology and Biomedicine (BBZ), Deutscher Platz 5, 04103, Leipzig, Germany
| | - Norbert Sträter
- Faculty of Chemistry and Mineralogy, Institute of Bioanalytical Chemistry, Deutscher Platz 5, 04103, Leipzig, Germany.,Center for Biotechnology and Biomedicine (BBZ), Deutscher Platz 5, 04103, Leipzig, Germany
| | - Ralf Hoffmann
- Faculty of Chemistry and Mineralogy, Institute of Bioanalytical Chemistry, Deutscher Platz 5, 04103, Leipzig, Germany.,Center for Biotechnology and Biomedicine (BBZ), Deutscher Platz 5, 04103, Leipzig, Germany
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Mishra B, Reiling S, Zarena D, Wang G. Host defense antimicrobial peptides as antibiotics: design and application strategies. Curr Opin Chem Biol 2017; 38:87-96. [PMID: 28399505 PMCID: PMC5494204 DOI: 10.1016/j.cbpa.2017.03.014] [Citation(s) in RCA: 207] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 03/21/2017] [Accepted: 03/22/2017] [Indexed: 12/16/2022]
Abstract
This review deals with the design and application strategies of new antibiotics based on naturally occurring antimicrobial peptides (AMPs). The initial candidate can be designed based on three-dimensional structure or selected from a library of peptides from natural or laboratory sources followed by optimization via structure-activity relationship studies. There are also advanced application strategies such as induction of AMP expression from host cells by various factors (e.g., metals, amino acids, vitamin D and sunlight), the use of engineered probiotic bacteria to deliver peptides, the design of prodrug and peptide conjugates to improve specific targeting. In addition, combined uses of newly developed AMPs with existing antimicrobial agents may provide a practical avenue for effective management of antibiotic-resistant bacteria (superbugs), including biofilms. Finally, we highlight AMPs already in use or under clinical trials.
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Affiliation(s)
- Biswajit Mishra
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, 986495 Nebraska Medical Center, Omaha, NE 68198-6495, USA
| | - Scott Reiling
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, 986495 Nebraska Medical Center, Omaha, NE 68198-6495, USA
| | - D Zarena
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, 986495 Nebraska Medical Center, Omaha, NE 68198-6495, USA; Department of Physics, JNTUA College of Engineering, Anantapur 515002, India
| | - Guangshun Wang
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, 986495 Nebraska Medical Center, Omaha, NE 68198-6495, USA.
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Li W, Sun Z, O'Brien-Simpson NM, Otvos L, Reynolds EC, Hossain MA, Separovic F, Wade JD. The Effect of Selective D- or N α-Methyl Arginine Substitution on the Activity of the Proline-Rich Antimicrobial Peptide, Chex1-Arg20. Front Chem 2017; 5:1. [PMID: 28154813 PMCID: PMC5243837 DOI: 10.3389/fchem.2017.00001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 01/04/2017] [Indexed: 01/21/2023] Open
Abstract
In vivo pharmacokinetics studies have shown that the proline-rich antimicrobial peptide, A3-APO, which is a discontinuous dimer of the peptide, Chex1-Arg20, undergoes degradation to small fragments at positions Pro6-Arg7 and Val19-Arg20. With the aim of minimizing or abolishing this degradation, a series of Chex1-Arg20 analogs were prepared via Fmoc/tBu solid phase peptide synthesis with D-arginine or, in some cases, peptide backbone Nα-methylated arginine, substitution at these sites. All the peptides were tested for antibacterial activity against the Gram-negative bacterium Klebsiella pneumoniae. The resulting activity of position-7 substitution of Chex1-Arg20 analogs showed that arginine-7 is a crucial residue for maintaining activity against K. pneumoniae. However, arginine-20 substitution had a much less deleterious effect on the antibacterial activity of the peptide. Moreover, none of these peptides displayed any cytotoxicity to HEK and H-4-II-E mammalian cells. These results will aid the development of more effective and stable PrAMPs via judicious amino acid substitutions.
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Affiliation(s)
- Wenyi Li
- Florey Institute of Neuroscience and Mental Health, University of MelbourneParkville, VIC, Australia; School of Chemistry, University of MelbourneParkville, VIC, Australia
| | - Zhe Sun
- Oral Health Cooperative Research Centre, Melbourne Dental School, University of MelbourneParkville, VIC, Australia; Bio21 Institute, University of MelbourneParkville, VIC, Australia
| | - Neil M O'Brien-Simpson
- Oral Health Cooperative Research Centre, Melbourne Dental School, University of MelbourneParkville, VIC, Australia; Bio21 Institute, University of MelbourneParkville, VIC, Australia
| | - Laszlo Otvos
- Department of Biology, Temple University Philadelphia, PA, USA
| | - Eric C Reynolds
- Oral Health Cooperative Research Centre, Melbourne Dental School, University of MelbourneParkville, VIC, Australia; Bio21 Institute, University of MelbourneParkville, VIC, Australia
| | - Mohammed A Hossain
- Florey Institute of Neuroscience and Mental Health, University of MelbourneParkville, VIC, Australia; School of Chemistry, University of MelbourneParkville, VIC, Australia
| | - Frances Separovic
- School of Chemistry, University of MelbourneParkville, VIC, Australia; Bio21 Institute, University of MelbourneParkville, VIC, Australia
| | - John D Wade
- Florey Institute of Neuroscience and Mental Health, University of MelbourneParkville, VIC, Australia; School of Chemistry, University of MelbourneParkville, VIC, Australia
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