1
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K R G, Balenahalli Narasingappa R, Vishnu Vyas G. Unveiling mechanisms of antimicrobial peptide: Actions beyond the membranes disruption. Heliyon 2024; 10:e38079. [PMID: 39386776 PMCID: PMC11462253 DOI: 10.1016/j.heliyon.2024.e38079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 09/07/2024] [Accepted: 09/17/2024] [Indexed: 10/12/2024] Open
Abstract
Antimicrobial peptides (AMPs) are a critical component of the innate immune system, playing a key role in defending against a variety of pathogenic microorganisms. While many AMPs act primarily on the cell membrane of target pathogens, leading to lysis and subsequent cell death, less is known about their nonlytic membrane activity. This nonlytic activity allows AMPs to target and disrupt bacterial cells without causing lysis, leading to bacterial death through alternative mechanisms.Understanding these nonlytic properties of AMPs is crucial, as they present a promising alternative to traditional antibiotics, which can induce bacterial resistance and have adverse effects on human health and the environment. The mechanisms by which AMPs exhibit nonlytic membrane activity are still being explored. However, it is believed that AMPs penetrate the bacterial membrane and interact directly with internal cellular components such as DNA, RNA, and various enzymes essential for microbial survival and replication. This interaction disrupts metabolic homeostasis, ultimately resulting in bacterial death.The nonlytic activity of AMPs also results in minimal damage to host cells and tissues, making them attractive candidates for the development of new, more effective antibiotics. This review emphasizes the mechanisms by which AMPs nonlytically target cellular components, including DNA, proteins, RNA, and other biomolecules, and discusses their clinical significance. Understanding these mechanisms may pave the way for developing alternatives to conventional antibiotics, offering a solution to the growing issue of antibiotic resistance.
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Affiliation(s)
- Gagandeep K R
- Department of Plant Biotechnology, University of Agricultural Sciences, Gandhi Krishi Vignana Kendra, Bengaluru, Karnataka, 560065, India
| | - Ramesh Balenahalli Narasingappa
- Department of Plant Biotechnology, University of Agricultural Sciences, Gandhi Krishi Vignana Kendra, Bengaluru, Karnataka, 560065, India
| | - Gatta Vishnu Vyas
- Department of Plant Biotechnology, University of Agricultural Sciences, Gandhi Krishi Vignana Kendra, Bengaluru, Karnataka, 560065, India
- ICAR-AICRP On Post Harvest Engineering and Technology, University of Agricultural Sciences, Gandhi Krishi Vignana Kendra, Bengaluru, 560065, India
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2
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Huang W, Baliga C, Vázquez-Laslop N, Mankin A. Sequence diversity of apidaecin-like peptides arresting the terminating ribosome. Nucleic Acids Res 2024; 52:8967-8978. [PMID: 38953159 PMCID: PMC11347161 DOI: 10.1093/nar/gkae567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/31/2024] [Accepted: 06/22/2024] [Indexed: 07/03/2024] Open
Abstract
The Proline-rich Antimicrobial Peptide (PrAMP) apidaecin (Api) inhibits translation by binding in the ribosomal nascent peptide exit tunnel, trapping release factors RF1 or RF2, and arresting ribosomes at stop codons. To explore the extent of sequence variations of the native 18-amino acid Api that allows it to preserve its activity, we screened a library of synthetic mutant Api genes expressed in bacterial cells, resulting in nearly 350000 peptide variants with multiple substitutions. By applying orthogonal negative and positive selection strategies, we identified a number of multi-substituted Api variants capable of arresting ribosomes at stop codons. Our findings underscore the critical contribution of specific amino acid residues of the peptide for its on-target function while significantly expanding the variety of PrAMPs acting on the terminating ribosome. Additionally, some of the tested synthesized multi-substituted Api variants exhibit improved antibacterial activity compared to that of the wild type PrAMP and may constitute the starting point to develop clinically useful antimicrobials.
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Affiliation(s)
- Weiping Huang
- Department of Pharmaceutical Sciences and Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Chetana Baliga
- Department of Pharmaceutical Sciences and Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Nora Vázquez-Laslop
- Department of Pharmaceutical Sciences and Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Alexander S Mankin
- Department of Pharmaceutical Sciences and Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
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3
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Collins J, McConnell A, Schmitz ZD, Hackel BJ. Sequence-function mapping of proline-rich antimicrobial peptides. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.28.577586. [PMID: 38352424 PMCID: PMC10862732 DOI: 10.1101/2024.01.28.577586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
Antimicrobial peptides (AMPs) are essential elements of natural cellular combat and candidates as antibiotic therapy. Elevated function may be needed for robust physiological performance. Yet, both pure protein design and combinatorial library discovery are hindered by the complexity of antimicrobial activity. We applied a recently developed high-throughput technique, sequence-activity mapping of AMPs via depletion (SAMP-Dep), to proline-rich AMPs. Robust self-inhibition was achieved for metalnikowin 1 (Met) and apidaecin 1b (Api). SAMP-Dep exhibited high reproducibility with correlation coefficients 0.90 and 0.92, for Met and Api, respectively, between replicates and 0.99 and 0.96 for synonymous genetic variants. Sequence-activity maps were obtained via characterization of 26,000 and 34,000 mutants of Met and Api, respectively. Both AMPs exhibit similar mutational profiles including beneficial mutations at one terminus, the C-terminus for Met and N-terminus for Api, which is consistent with their opposite binding orientations in the ribosome. While Met and Api reside with the family of proline-rich AMPs, different proline sites exhibit substantially different mutational tolerance. Within the PRP motif, proline mutation eliminates activity, whereas non-PRP prolines readily tolerate mutation. Homologous mutations are more tolerated, particularly at alternating sites on one 'face' of the peptide. Important and consistent epistasis was observed following the PRP domain within the segment that extends into the ribosomal exit tunnel for both peptides. Variants identified from the SAMP-Dep platform were produced and exposed toward Gram-negative species exogenously, showing either increased potency or specificity for strains tested. In addition to mapping sequence-activity space for fundamental insight and therapeutic engineering, the results advance the robustness of the SAMP-Dep platform for activity characterization.
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Affiliation(s)
| | | | - Zachary D Schmitz
- Chemical Engineering and Materials Science University of Minnesota, Minneapolis, MN 55455
| | - Benjamin J Hackel
- Biomedical Engineering, Minneapolis, MN 55455
- Chemical Engineering and Materials Science University of Minnesota, Minneapolis, MN 55455
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4
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Collins J, Hackel BJ. Sequence-activity mapping via depletion reveals striking mutational tolerance and elucidates functional motifs in Tur1a antimicrobial peptide. Protein Eng Des Sel 2024; 37:gzae006. [PMID: 38484121 DOI: 10.1093/protein/gzae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 03/27/2024] Open
Abstract
Proline-rich antimicrobial peptides (PrAMPs) are attractive antibiotic candidates that target gram-negative bacteria ribosomes. We elucidated the sequence-function landscape of 43 000 variants of a recently discovered family member, Tur1a, using the validated SAMP-Dep platform that measures intracellular AMP potency in a high-throughput manner via self-depletion of the cellular host. The platform exhibited high replicate reproducibility (ρ = 0.81) and correlation between synonymous genetic variants (R2 = 0.93). Only two segments within Tur1a exhibited stringent mutational requirements to sustain potency: residues 9YLP11 and 19FP20. This includes the aromatic residue in the hypothesized binding domain but not the PRP domain. Along with unexpected mutational tolerance of PRP, the data contrast hypothesized importance of the 1RRIR4 motif and arginines in general. In addition to mutational tolerance of residue segments with presumed significance, 77% of mutations are functionally neutral. Multimutant performance mainly shows compounding effects from removed combinations of prolines and arginines in addition to the two segments of residues showing individual importance. Several variants identified as active from SAMP-Dep were externally produced and maintained activity when applied to susceptible species exogenously.
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Affiliation(s)
- Jonathan Collins
- Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, United States
| | - Benjamin J Hackel
- Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, United States
- Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, United States
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5
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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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6
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Md Fadilah NI, Shahabudin NA, Mohd Razif RA, Sanyal A, Ghosh A, Baharin KI, Ahmad H, Maarof M, Motta A, Fauzi MB. Discovery of bioactive peptides as therapeutic agents for skin wound repair. J Tissue Eng 2024; 15:20417314241280359. [PMID: 39398382 PMCID: PMC11468004 DOI: 10.1177/20417314241280359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Accepted: 08/19/2024] [Indexed: 10/15/2024] Open
Abstract
Short sequences of amino acids called peptides have a wide range of biological functions and the potential to treat a number of diseases. Bioactive peptides can be derived from different sources, including marine organisms, and synthetic design, making them versatile candidates for production of therapeutic agents. Their therapeutic effects span across areas such as antimicrobial activity, cells proliferation and migration, synthesis of collagen, and more. This current review explores the fascinating realm of bioactive peptides as promising therapeutic agents for skin wound healing. This review focuses on the multifaceted biological effects of specific peptides, shedding light on their potential to revolutionize the field of dermatology and regenerative medicine. It delves into how these peptides stimulate collagen synthesis, inhibit inflammation, and accelerate tissue regeneration, ultimately contributing to the effective repair of skin wounds. The findings underscore the significant role several types of bioactive peptides can play in enhancing wound healing processes and offer promising insights for improving the quality of life for individuals with skin injuries and dermatological conditions. The versatility of peptides allows for the development of tailored treatments catering to specific wound types and patient needs. As continuing to delve deeper into the realm of bioactive peptides, there is immense potential for further exploration and innovation. Future endeavors may involve the optimization of peptide formulations, elucidation of underlying molecular and cellular mechanisms.
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Affiliation(s)
- Nur Izzah Md Fadilah
- Department of Tissue Engineering and Regenerative Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Cheras, Kuala Lumpur, Malaysia
- Advance Bioactive Materials-Cells UKM Research Group, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Nurul Aqilah Shahabudin
- Department of Tissue Engineering and Regenerative Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Cheras, Kuala Lumpur, Malaysia
| | - Raniya Adiba Mohd Razif
- Department of Tissue Engineering and Regenerative Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Cheras, Kuala Lumpur, Malaysia
| | - Arka Sanyal
- Department of Biotechnology, KIIT University, Bhubaneswar, India
| | - Anushikha Ghosh
- Department of Biotechnology, KIIT University, Bhubaneswar, India
| | | | - Haslina Ahmad
- Integrated Chemical Biophysics Research, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
| | - Manira Maarof
- Department of Tissue Engineering and Regenerative Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Cheras, Kuala Lumpur, Malaysia
- Advance Bioactive Materials-Cells UKM Research Group, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Antonella Motta
- Department of Industrial Engineering, University of Trento, Trento, Italy
| | - Mh Busra Fauzi
- Department of Tissue Engineering and Regenerative Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Cheras, Kuala Lumpur, Malaysia
- Advance Bioactive Materials-Cells UKM Research Group, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
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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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Gasu EN, Mensah JK, Borquaye LS. Computer-aided design of proline-rich antimicrobial peptides based on the chemophysical properties of a peptide isolated from Olivancillaria hiatula. J Biomol Struct Dyn 2023; 41:8254-8275. [PMID: 36218088 DOI: 10.1080/07391102.2022.2131626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 09/27/2022] [Indexed: 10/17/2022]
Abstract
The chemophysical properties of a peptide isolated from Olivancillaria hiatula were combined with computational tools to design new antimicrobial peptides (AMPs). The in silico peptide design utilized arbitrary sequence shuffling, AMP sequence prediction and alignments such that putative sequences mimicked those of proline-rich AMPs (PrAMPs) and were potentially active against bacteria. Molecular modelling and docking experiments were used to monitor peptide binding to some intracellular targets like bacteria ribosome, DnaK and LasR. Peptide candidates were tested in vitro for antibacterial and antivirulence activities. Chemophysical studies of peptide extract suggested hydrophobic, acidic and proline-rich peptide properties. The amino acid signature of the extract matched that of AMPs that inhibit intracellular targets. Two of the designed PrAMP peptides (OhPrP-3 and OhPrP-5) had high affinity for the ribosome and DnaK. OhPrP-1, 2 and 4 also had favorable interactions with the biomolecular targets investigated. Peptides had bactericidal activity at the minimum inhibitory concentration against Pseudomonas aeruginosa. The designed peptides docked strongly to LasR suggesting possible interference with quorum sensing, and this was corroborated by in vitro data where sub-inhibitory doses of all peptides reduced pyocyanin and pyoverdine expression. The designed peptides can be further studied for the development of new anti-infective agents.
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Affiliation(s)
- Edward Ntim Gasu
- Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Central Laboratory, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - John Kenneth Mensah
- Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Lawrence Sheringham Borquaye
- Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Central Laboratory, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
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9
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Mangano K, Klepacki D, Ohanmu I, Baliga C, Huang W, Brakel A, Krizsan A, Polikanov YS, Hoffmann R, Vázquez-Laslop N, Mankin AS. Inhibition of translation termination by the antimicrobial peptide Drosocin. Nat Chem Biol 2023; 19:1082-1090. [PMID: 36997647 PMCID: PMC10757563 DOI: 10.1038/s41589-023-01300-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 02/24/2023] [Indexed: 04/01/2023]
Abstract
The proline-rich antimicrobial peptide (PrAMP) Drosocin (Dro) from fruit flies shows sequence similarity to other PrAMPs that bind to the ribosome and inhibit protein synthesis by varying mechanisms. The target and mechanism of action of Dro, however, remain unknown. Here we show that Dro arrests ribosomes at stop codons, probably sequestering class 1 release factors associated with the ribosome. This mode of action is comparable to that of apidaecin (Api) from honeybees, making Dro the second member of the type II PrAMP class. Nonetheless, analysis of a comprehensive library of endogenously expressed Dro mutants shows that the interactions of Dro and Api with the target are markedly distinct. While only a few C-terminal amino acids of Api are critical for binding, the interaction of Dro with the ribosome relies on multiple amino acid residues distributed throughout the PrAMP. Single-residue substitutions can substantially enhance the on-target activity of Dro.
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Affiliation(s)
- Kyle Mangano
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Dorota Klepacki
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Irueosa Ohanmu
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Chetana Baliga
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Weiping Huang
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Alexandra Brakel
- Faculty of Chemistry and Mineralogy, Institute of Bioanalytical Chemistry, Leipzig University, Leipzig, Germany
- Center for Biotechnology and Biomedicine (BBZ), Leipzig University, Leipzig, Germany
| | - Andor Krizsan
- Faculty of Chemistry and Mineralogy, Institute of Bioanalytical Chemistry, Leipzig University, Leipzig, Germany
- Center for Biotechnology and Biomedicine (BBZ), Leipzig University, Leipzig, Germany
| | - Yury S Polikanov
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Ralf Hoffmann
- Faculty of Chemistry and Mineralogy, Institute of Bioanalytical Chemistry, Leipzig University, Leipzig, Germany.
- Center for Biotechnology and Biomedicine (BBZ), Leipzig University, Leipzig, Germany.
| | - Nora Vázquez-Laslop
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA.
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA.
| | - Alexander S Mankin
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA.
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA.
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10
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Koller TO, Morici M, Berger M, Safdari HA, Lele DS, Beckert B, Kaur KJ, Wilson DN. Structural basis for translation inhibition by the glycosylated drosocin peptide. Nat Chem Biol 2023; 19:1072-1081. [PMID: 36997646 PMCID: PMC10449632 DOI: 10.1038/s41589-023-01293-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 02/14/2023] [Indexed: 04/07/2023]
Abstract
The proline-rich antimicrobial peptide (PrAMP) drosocin is produced by Drosophila species to combat bacterial infection. Unlike many PrAMPs, drosocin is O-glycosylated at threonine 11, a post-translation modification that enhances its antimicrobial activity. Here we demonstrate that the O-glycosylation not only influences cellular uptake of the peptide but also interacts with its intracellular target, the ribosome. Cryogenic electron microscopy structures of glycosylated drosocin on the ribosome at 2.0-2.8-Å resolution reveal that the peptide interferes with translation termination by binding within the polypeptide exit tunnel and trapping RF1 on the ribosome, reminiscent of that reported for the PrAMP apidaecin. The glycosylation of drosocin enables multiple interactions with U2609 of the 23S rRNA, leading to conformational changes that break the canonical base pair with A752. Collectively, our study reveals novel molecular insights into the interaction of O-glycosylated drosocin with the ribosome, which provide a structural basis for future development of this class of antimicrobials.
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Affiliation(s)
- Timm O Koller
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Martino Morici
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Max Berger
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Haaris A Safdari
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Deepti S Lele
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India
| | - Bertrand Beckert
- Dubochet Center for Imaging (DCI) at EPFL, EPFL SB IPHYS DCI, Lausanne, Switzerland
| | - Kanwal J Kaur
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India
| | - Daniel N Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany.
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11
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Dho M, Candian V, Tedeschi R. Insect Antimicrobial Peptides: Advancements, Enhancements and New Challenges. Antibiotics (Basel) 2023; 12:952. [PMID: 37370271 DOI: 10.3390/antibiotics12060952] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/21/2023] [Accepted: 05/21/2023] [Indexed: 06/29/2023] Open
Abstract
Several insects are known as vectors of a wide range of animal and human pathogens causing various diseases. However, they are also a source of different substances, such as the Antimicrobial Peptides (AMPs), which can be employed in the development of natural bioactive compounds for medical, veterinary and agricultural applications. It is well known that AMP activity, in contrast to most classical antibiotics, does not lead to the development of natural bacterial resistance, or at least the frequency of resistance is considered to be low. Therefore, there is a strong interest in assessing the efficacy of the various peptides known to date, identifying new compounds and evaluating possible solutions in order to increase their production. Moreover, implementing AMP modulation in insect rearing could preserve insect health in large-scale production. This review describes the current knowledge on insect AMPs, presenting the validated ones for the different insect orders. A brief description of their mechanism of action is reported with focus on proposed applications. The possible effects of insect diet on AMP translation and synthesis have been discussed.
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Affiliation(s)
- Matteo Dho
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), University of Torino, Largo P. Braccini 2, 10095 Grugliasco, Italy
| | - Valentina Candian
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), University of Torino, Largo P. Braccini 2, 10095 Grugliasco, Italy
| | - Rosemarie Tedeschi
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), University of Torino, Largo P. Braccini 2, 10095 Grugliasco, Italy
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12
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Lomakin IB, Devarkar SC, Patel S, Grada A, Bunick C. Sarecycline inhibits protein translation in Cutibacterium acnes 70S ribosome using a two-site mechanism. Nucleic Acids Res 2023; 51:2915-2930. [PMID: 36864821 PMCID: PMC10085706 DOI: 10.1093/nar/gkad103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 02/01/2023] [Accepted: 02/07/2023] [Indexed: 03/04/2023] Open
Abstract
Acne vulgaris is a chronic disfiguring skin disease affecting ∼1 billion people worldwide, often having persistent negative effects on physical and mental health. The Gram-positive anaerobe, Cutibacterium acnes is implicated in acne pathogenesis and is, therefore, a main target for antibiotic-based acne therapy. We determined a 2.8-Å resolution structure of the 70S ribosome of Cutibacterium acnes by cryogenic electron microscopy and discovered that sarecycline, a narrow-spectrum antibiotic against Cutibacterium acnes, may inhibit two active sites of this bacterium's ribosome in contrast to the one site detected previously on the model ribosome of Thermus thermophilus. Apart from the canonical binding site at the mRNA decoding center, the second binding site for sarecycline exists at the nascent peptide exit tunnel, reminiscent of the macrolides class of antibiotics. The structure also revealed Cutibacterium acnes-specific features of the ribosomal RNA and proteins. Unlike the ribosome of the Gram-negative bacterium Escherichia coli, Cutibacterium acnes ribosome has two additional proteins, bS22 and bL37, which are also present in the ribosomes of Mycobacterium smegmatis and Mycobacterium tuberculosis. We show that bS22 and bL37 have antimicrobial properties and may be involved in maintaining the healthy homeostasis of the human skin microbiome.
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Affiliation(s)
- Ivan B Lomakin
- Department of Dermatology, Yale University School of Medicine, New Haven, CT06520, USA
| | - Swapnil C Devarkar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06520, USA
| | - Shivali Patel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06520, USA
| | - Ayman Grada
- Department of Dermatology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Christopher G Bunick
- Department of Dermatology, Yale University School of Medicine, New Haven, CT06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06520, USA
- Program in Translational Biomedicine, Yale University School of Medicine, New Haven, CT 06520, USA
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13
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Cui Q, Yu HD, Xu QJ, Liu Y, Wang YT, Li PH, Kong LC, Zhang HP, Jiang XY, Giuliodori AM, Fabbretti A, He CG, Ma HX. Antibiotic synergist OM19r reverses aminoglycoside resistance in multidrug-resistant Escherichia coli. Front Microbiol 2023; 14:1144946. [PMID: 37143537 PMCID: PMC10151501 DOI: 10.3389/fmicb.2023.1144946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 03/24/2023] [Indexed: 05/06/2023] Open
Abstract
Introduction The continued emergence and spread of multidrug-resistant (MDR) bacterial pathogens require a new strategy to improve the efficacy of existing antibiotics. Proline-rich antimicrobial peptides (PrAMPs) could also be used as antibacterial synergists due to their unique mechanism of action. Methods Utilizing a series of experiments on membrane permeability, In vitro protein synthesis, In vitro transcription and mRNA translation, to further elucidate the synergistic mechanism of OM19r combined with gentamicin. Results A proline-rich antimicrobial peptide OM19r was identified in this study and its efficacy against Escherichia coli B2 (E. coli B2) was evaluated on multiple aspects. OM19r increased antibacterial activity of gentamicin against multidrug-resistance E. coli B2 by 64 folds, when used in combination with aminoglycoside antibiotics. Mechanistically, OM19r induced change of inner membrane permeability and inhibited translational elongation of protein synthesis by entering to E. coli B2 via intimal transporter SbmA. OM19r also facilitated the accumulation of intracellular reactive oxygen species (ROS). In animal models, OM19r significantly improved the efficacy of gentamicin against E. coli B2. Discussion Our study reveals that OM19r combined with GEN had a strong synergistic inhibitory effect against multi-drug resistant E. coli B2. OM19r and GEN inhibited translation elongation and initiation, respectively, and ultimately affected the normal protein synthesis of bacteria. These findings provide a potential therapeutic option against multidrug-resistant E. coli.
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Affiliation(s)
- Qi Cui
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Han-Dong Yu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Qi-Jun Xu
- Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, College of Life Sciences, Jilin Agricultural University, Changchun, China
| | - Yue Liu
- Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, College of Life Sciences, Jilin Agricultural University, Changchun, China
| | - Yu-Ting Wang
- Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, College of Life Sciences, Jilin Agricultural University, Changchun, China
| | - Peng-Hui Li
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Ling-Cong Kong
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Hai-Peng Zhang
- Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, College of Life Sciences, Jilin Agricultural University, Changchun, China
| | - Xiu-Yun Jiang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Anna Maria Giuliodori
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Attilio Fabbretti
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Cheng-Guang He
- Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, College of Life Sciences, Jilin Agricultural University, Changchun, China
- Cheng-Guang He,
| | - Hong-Xia Ma
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
- Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, College of Life Sciences, Jilin Agricultural University, Changchun, China
- *Correspondence: Hong-Xia Ma,
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14
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Zhao G, Jia C, Zhu C, Fang M, Li C, Chen Y, He Y, Han S, He Y, Gao J, Wang T, Wang C, Wang J. γ-Core Guided Antibiotic Design Based on Human Enteric Defensin 5. MEMBRANES 2022; 13:51. [PMID: 36676858 PMCID: PMC9862697 DOI: 10.3390/membranes13010051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/22/2022] [Accepted: 12/28/2022] [Indexed: 06/17/2023]
Abstract
An increase in the number of infections caused by resistant bacteria worldwide necessitates the development of alternatives to antibiotics. Human defensin (HD) 5 is an innate immune peptide with broad-spectrum antibacterial activity, but its complicated structure makes its preparation difficult. Herein, we truncated the HD5 structure by extracting the highly conserved γ-core motif. A structure-activity study showed that this motif was ineffective in killing bacteria in the absence of specific spatial conformation. Notably, after the introduction of two intramolecular disulfide bonds, its antibacterial activity was markedly improved. Glu and Ser residues were then replaced with Arg to create the derivative RC18, which exhibited stronger potency than HD5, particularly against methicillin-resistant S. aureus (MRSA). Mechanistically, RC18 bound to lipid A and lipoteichoic acid at higher affinities than HD5. Furthermore, RC18 was more efficient than HD5 in penetrating the bacterial membranes. Molecular dynamics simulation revealed that five Arg residues, Arg1, Arg7, Arg9, Arg15, and Arg18, mediated most of the polar interactions of RC18 with the phospholipid head groups during membrane penetration. In vivo experiments indicated that RC18 decreased MRSA colonization and dramatically improved the survival of infected mice, thus demonstrating that RC18 is a promising drug candidate to treat MRSA infections.
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Affiliation(s)
- Gaomei Zhao
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Combined Injury of PLA, Chongqing Engineering Research Center for Nanomedicine, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, China
| | - Changsheng Jia
- Department of Pharmacy, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
| | - Cheng Zhu
- Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Minchao Fang
- Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Chenwenya Li
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Combined Injury of PLA, Chongqing Engineering Research Center for Nanomedicine, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, China
| | - Yin Chen
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Combined Injury of PLA, Chongqing Engineering Research Center for Nanomedicine, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, China
| | - Yingjuan He
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Combined Injury of PLA, Chongqing Engineering Research Center for Nanomedicine, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, China
| | - Songling Han
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Combined Injury of PLA, Chongqing Engineering Research Center for Nanomedicine, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, China
| | - Yongwu He
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Combined Injury of PLA, Chongqing Engineering Research Center for Nanomedicine, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, China
| | - Jining Gao
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Combined Injury of PLA, Chongqing Engineering Research Center for Nanomedicine, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, China
| | - Tao Wang
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Combined Injury of PLA, Chongqing Engineering Research Center for Nanomedicine, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, China
| | - Cheng Wang
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Combined Injury of PLA, Chongqing Engineering Research Center for Nanomedicine, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, China
| | - Junping Wang
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Combined Injury of PLA, Chongqing Engineering Research Center for Nanomedicine, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, China
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15
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Borovsky D, Rougé P, Shatters RG. Bactericidal Properties of Proline-Rich Aedes aegypti Trypsin Modulating Oostatic Factor ( AeaTMOF). LIFE (BASEL, SWITZERLAND) 2022; 13:life13010019. [PMID: 36675967 PMCID: PMC9862690 DOI: 10.3390/life13010019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/16/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
The antimicrobial properties of proline-rich Aedes aegypti decapeptide TMOF (AeaTMOF) and oncocin112 (1-13) were compared. Incubations with multidrug-resistant Escherichia coli cells showed that AeaTMOF (5 mM) was able to completely inhibit bacterial cell growth, whereas oncocin112 (1-13) (20 mM) partially inhibited bacterial growth as compared with bacterial cells that were not multidrug-resistant cells. AeaTMOF (5 mM) was very effective against Acinetobacter baumannii and Pseudomonas aeruginosa, completely inhibiting cell growth during 15 h incubations. AeaTMOF (5 mM) completely inhibited the Gram-positive bacteria Staphylococcus aureus and Bacillus thurengiensis sups. Israelensis cell growth, whereas oncocin112 (1-13) (10 and 20 mM) failed to affect bacterial cell growth. E. coli cells that lack the SbmA transporter were inhibited by AeaTMOF (5 mM) and not by oncocin112 (1-13) (10 to 20 mM), indicating that AeaTMOF can use other bacterial transporters than SbmA that is mainly used by proline-rich antimicrobial peptides. Incubation of E. coli cells with NaAzide showed that AeaTMOF does not use ABC-like transporters that use ATP hydrolysis to import molecules into bacterial cells. Three-dimensional modeling and docking of AeaTMOF to SbmA and MdtM transporters showed that AeaTMOF can bind these proteins, and the binding location of AeaTMOF inside these protein transporters allows AeaTMOF to be transported into the bacterial cytosol. These results show that AeaTMOF can be used as a future antibacterial agent against both multidrug-resistant Gram-positive and -negative bacteria.
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Affiliation(s)
- Dov Borovsky
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Correspondence:
| | - Pierre Rougé
- Faculte des Sciences Pharmaceutiques, 3106 Toulouse, France
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16
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Yamauchi R, Kawano K, Yamaoka Y, Taniguchi A, Yano Y, Takasu K, Matsuzaki K. Development of Antimicrobial Peptide-Antibiotic Conjugates to Improve the Outer Membrane Permeability of Antibiotics Against Gram-Negative Bacteria. ACS Infect Dis 2022; 8:2339-2347. [PMID: 36255133 DOI: 10.1021/acsinfecdis.2c00406] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Antibiotics have been widely used in the medical field as a treatment for infectious diseases, but they are not effective against all Gram-negative bacteria because of their low permeability to the outer membrane. One of the strategies to improve the antibacterial activity of antibiotics is the coadministration of antibiotics and membrane-perturbing antimicrobial peptides for their synergistic effects. However, because of their different pharmacokinetics, their coadministration may not exert expected effects in the clinical stage. Here, we designed various antimicrobial peptide-antibiotic conjugates as a novel approach to improve the antimicrobial activity of antibiotics. Ampicillin was chosen as a model antibiotic with poor outer membrane permeability, and the effects of the chemistry and position of conjugation and the choice of antimicrobial peptides were examined. One of the ampicillin conjugates exhibited significantly improved antimicrobial activity against ampicillin-resistant Gram-negative bacteria without exerting cytotoxicity against human cultured cells, demonstrating that our novel approach is an effective strategy to improve the antimicrobial activity of antibiotics with low outer membrane permeability.
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Affiliation(s)
- Ruka Yamauchi
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kenichi Kawano
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yousuke Yamaoka
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Aoi Taniguchi
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yoshiaki Yano
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan.,School of Pharmacy and Pharmaceutical Sciences, Mukogawa Women's University, 11-68 Koshien Kyuban-cho, Nishinomiya 663-8179, Hyogo, Japan
| | - Kiyosei Takasu
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Katsumi Matsuzaki
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
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17
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Ghalamara S, Coscueta ER, Silva S, Brazinha C, Pereira CD, Pintado ME. Integrated ultrafiltration, nanofiltration, and reverse osmosis pilot process to produce bioactive protein/peptide fractions from sardine cooking effluent. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 317:115344. [PMID: 35642813 DOI: 10.1016/j.jenvman.2022.115344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 05/06/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
Sardine cooking effluents contain a high level of organic matter, such as proteins and lipids, which allows them to be forward into a chain exploiting high added-value compounds attained from these effluents, increasing their economic value while reducing their environmental effect. Thus, the purpose of this work was to develop an innovative pilot-scale integrated membrane process, with or without enzymatic hydrolysis, to obtain fractions with high protein/peptide and low NaCl contents, as well as optimized bioactive properties. The research strategy followed involved the use of ultrafiltration (UF) and nanofiltration (NF) technologies of the pretreated sardine cooking effluent followed by reverse osmosis (RO) at a pilot scale levels. Moreover, it allowed for the attainment of fractions rich in protein/peptides that might be used in the food, pharmaceutical, or cosmetic industries, particularly after RO, as they present a lower NaCl content. The RO retentate (hydrolyzed sample) coupled with UF and NF resulted in the fractions with the best bioactive properties (higher antioxidant capacity and antimicrobial activity) of all the analyzed samples. Overall, the current work demonstrated the feasibility of exploiting liquid by-products as a source of functional components as well as reinforcing this strategy's potential relevance in future effective management strategies for this type of effluents.
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Affiliation(s)
- Soudabeh Ghalamara
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal
| | - Ezequiel R Coscueta
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal
| | - Sara Silva
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal
| | - Carla Brazinha
- LAQV/Requimte, Department of Chemistry, NOVA School of Science and Technology, FCT NOVA, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
| | - Carlos D Pereira
- Instituto Politécnico de Coimbra - Escola Superior Agraria (IPC/ESAC), Bencanta, 3045-601, Coimbra, Portugal
| | - Manuela E Pintado
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal.
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18
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Khairullina ZZ, Makarov GI, Tereshchenkov AG, Buev VS, Lukianov DA, Polshakov VI, Tashlitsky VN, Osterman IA, Sumbatyan NV. Conjugates of Desmycosin with Fragments of Antimicrobial Peptide Oncocin: Synthesis, Antibacterial Activity, Interaction with Ribosome. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:871-889. [PMID: 36180983 DOI: 10.1134/s0006297922090024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/17/2022] [Accepted: 06/18/2022] [Indexed: 06/16/2023]
Abstract
Design and synthesis of conjugates consisting of the macrolide antibiotic desmycosin and fragments of the antibacterial peptide oncocin were performed in attempt to develop new antimicrobial compounds. New compounds were shown to bind to the E. coli 70S ribosomes, to inhibit bacterial protein synthesis in vitro, as well as to suppress bacterial growth. The conjugates of N-terminal hexa- and tripeptide fragments of oncocin and 3,2',4''-triacetyldesmycosin were found to be active against some strains of macrolide-resistant bacteria. By simulating molecular dynamics of the complexes of these compounds with the wild-type bacterial ribosomes and with ribosomes, containing A2059G 23S RNA mutation, the specific structural features of their interactions were revealed.
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Affiliation(s)
| | | | - Andrey G Tereshchenkov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Vitaly S Buev
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Dmitrii A Lukianov
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, 143025, Russia
| | - Vladimir I Polshakov
- Faculty of Fundamental Medicine, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Vadim N Tashlitsky
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Ilya A Osterman
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, 143025, Russia
| | - Natalia V Sumbatyan
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.
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19
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Fikri F, Wardhana DK, Purnomo A, Khairani S, Chhetri S, Purnama MTE. Aerolysin gene characterization and antimicrobial resistance profile of Aeromonas hydrophila isolated from milkfish (Chanos chanos) in Gresik, Indonesia. Vet World 2022; 15:1759-1764. [PMID: 36185507 PMCID: PMC9394137 DOI: 10.14202/vetworld.2022.1759-1764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 05/31/2022] [Indexed: 11/16/2022] Open
Abstract
Background and Aim: Motile Aeromonas septicemia is a crucial disease in freshwater fish. Aeromonas hydrophila is a disease agent associated with sporadic fish mortality, food safety, and public health. This study aimed to estimate the prevalence and the presence of the aerolysin gene and antimicrobial resistance profile of A. hydrophila isolated from milkfish in Gresik, Indonesia.
Materials and Methods: A total of 153 milkfish gill samples were collected from 16 locations in Gresik and then cultured and identified using biochemical tests. The aerolysin gene was investigated using a polymerase chain reaction, and antimicrobial resistance profiles of the recovered isolates were investigated.
Results: Of the 153 examined samples, 35 (22.9%) were confirmed positive for A. hydrophila and 22 (62.9%) presented the aerolysin gene. The recovered isolates were resistant to the following antibiotics: Amoxicillin (62.9%), tetracycline (60%), streptomycin (54.3%), cefotaxime (51.4%), gentamycin (31.4%), kanamycin (28.6%), erythromycin (25.7%), chloramphenicol (20%), and trimethoprim (14.3%). Meanwhile, only ciprofloxacin, nalidixic acid, and imipenem were indicated as susceptible.
Conclusion: The presence of the aerolysin gene is vital in determining the virulence of A. hydrophila. The study results indicated a high aerolysin gene prevalence. In addition, this study emphasized antibiotic use monitoring, food safety improvement, and negative impact reduction on human health and the environment.
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Affiliation(s)
- Faisal Fikri
- Department of Veterinary Science, Division of Veterinary Clinical Pathology and Physiology, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, Indonesia; Department of Veterinary Science, School of Health and Life Sciences, Universitas Airlangga, Surabaya, Indonesia
| | - Dhandy Koesoemo Wardhana
- Department of Veterinary Science, Division of Veterinary Public Health, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, Indonesia
| | - Agus Purnomo
- Department of Veterinary Surgery and Radiology, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Shafia Khairani
- Department of Biomedical Science, Faculty of Medicine, Universitas Padjajaran, Bandung, Indonesia
| | - Shekhar Chhetri
- Department of Animal Science, College of Natural Resources, Royal University of Bhutan, Lobesa, Punakha, Bhutan
| | - Muhammad Thohawi Elziyad Purnama
- Department of Veterinary Science, School of Health and Life Sciences, Universitas Airlangga, Surabaya, Indonesia; Department of Veterinary Science, Division of Veterinary Anatomy, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, Indonesia
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20
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Antibacterial Peptide NP-6 Affects Staphylococcus aureus by Multiple Modes of Action. Int J Mol Sci 2022; 23:ijms23147812. [PMID: 35887160 PMCID: PMC9319634 DOI: 10.3390/ijms23147812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/30/2022] [Accepted: 07/13/2022] [Indexed: 02/01/2023] Open
Abstract
Our previous study extracted and identified an antibacterial peptide that was named NP-6. Herein, we investigated the physicochemical properties of NP-6, and elucidated the mechanisms underlying its antimicrobial activity against Staphylococcus aureus. The results showed that the hemolysis activity of NP-6 was 2.39 ± 0.13%, lower than Nisin A (3.91 ± 0.43%) at the same concentration (512 µg/mL). Negligible cytotoxicity towards RAW264.7 cells was found when the concentration of NP-6 was lower than 512 µg/mL. In addition, it could keep most of its activity in fetal bovine serum. Moreover, transmission electron microscopy, confocal laser scanning microscopy, and flow cytometry results showed that NP-6 can destroy the integrity of the bacterial cell membrane and increase the membrane permeability. Meanwhile, NP-6 had binding activity with bacterial DNA and RNA in vitro and strongly inhibited the intracellular β-galactosidase activity of S. aureus. Our findings suggest that NP-6 could be a promising candidate against S. aureus.
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21
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22
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Li X, Zuo S, Wang B, Zhang K, Wang Y. Antimicrobial Mechanisms and Clinical Application Prospects of Antimicrobial Peptides. Molecules 2022; 27:2675. [PMID: 35566025 PMCID: PMC9104849 DOI: 10.3390/molecules27092675] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/14/2022] [Accepted: 04/19/2022] [Indexed: 12/16/2022] Open
Abstract
Antimicrobial peptides are a type of small-molecule peptide that widely exist in nature and are components of the innate immunity of almost all living things. They play an important role in resisting foreign invading microorganisms. Antimicrobial peptides have a wide range of antibacterial activities against bacteria, fungi, viruses and other microorganisms. They are active against traditional antibiotic-resistant strains and do not easily induce the development of drug resistance. Therefore, they have become a hot spot of medical research and are expected to become a new substitute for fighting microbial infection and represent a new method for treating drug-resistant bacteria. This review briefly introduces the source and structural characteristics of antimicrobial peptides and describes those that have been used against common clinical microorganisms (bacteria, fungi, viruses, and especially coronaviruses), focusing on their antimicrobial mechanism of action and clinical application prospects.
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Affiliation(s)
- Xin Li
- Department of Infectious Diseases, First Hospital of Jilin University, Changchun 130021, China; (X.L.); (B.W.)
| | - Siyao Zuo
- Department of Dermatology and Venereology, First Hospital of Jilin University, Changchun 130021, China;
| | - Bin Wang
- Department of Infectious Diseases, First Hospital of Jilin University, Changchun 130021, China; (X.L.); (B.W.)
| | - Kaiyu Zhang
- Department of Infectious Diseases, First Hospital of Jilin University, Changchun 130021, China; (X.L.); (B.W.)
| | - Yang Wang
- Department of Infectious Diseases, First Hospital of Jilin University, Changchun 130021, China; (X.L.); (B.W.)
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23
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Borovsky D, Rougé P, Shatters RG. The Ribosome Is the Ultimate Receptor for Trypsin Modulating Oostatic Factor (TMOF). Biomolecules 2022; 12:biom12040577. [PMID: 35454167 PMCID: PMC9028786 DOI: 10.3390/biom12040577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 02/06/2023] Open
Abstract
Aedes aegypti Trypsin Modulating Oostatic Factor (AeaTMOF). a mosquito decapeptide that controls trypsin biosynthesis in female and larval mosquitoes. enters the gut epithelial cells of female mosquitoes using ABC-tmfA receptor/importer. To study the ultimate targeted receptor after AeaTMOF enters the cell, AeaTMOF was incubated in vitro with either Escherichia coli or Spodoptera frugiperda protein-expressing extracts containing 70S and 80S ribosomes, respectively. The effect of AeaTMOF on luciferase biosynthesis in vitro using 70S ribosomes was compared with that of oncocin112 (1–13), a ribosome-binding antibacterial peptide. The IC50 of 1 μM and 2 μM, respectively, for both peptides was determined. Incubation with a protein-expressing system and S. frugiperda 80S ribosomes determined an IC50 of 1.8 μM for Aedes aegypti larval late trypsin biosynthesis. Incubation of purified E. coli ribosome with increasing concentration of AeaTMOF shows that the binding of AeaTMOF to the bacterial ribosome exhibits a high affinity (KD = 23 ± 3.4 nM, Bmax = 0.553 ± 0.023 pmol/μg ribosome and Kassoc = 4.3 × 107 M−1). Molecular modeling and docking experiments show that AeaTMOF binds bacterial and Drosophila ribosome (50S and 60S, respectively) at the entrance of the ribosome exit tunnel, blocking the tRNA entrance and preventing protein biosynthesis. Recombinant E. coli cells that express only ABC-tmfA importer are inhibited by AeaTMOF but not by oncocin112 (1–13). These results suggest that the ribosome is the ultimate targeted receptor of AeaTMOF.
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Affiliation(s)
- Dov Borovsky
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz, Aurora, CO 80045, USA
- Correspondence:
| | - Pierre Rougé
- UMR 152 Pharma-Dev, Faculté des Sciences Pharmaceutiques, Université Toulouse 3, CEDEX 09, F-31062 Toulouse, France;
| | - Robert G. Shatters
- USDA ARS, U.S. Horticultural Research Laboratory, Subtropical Insects and Horticulture Research Unit, 2001 Rock Road, Fort Pierce, FL 34945, USA;
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24
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Dewangan RP, Verma DP, Verma NK, Gupta A, Pant G, Mitra K, Habib S, Ghosh JK. Spermine-Conjugated Short Proline-Rich Lipopeptides as Broad-Spectrum Intracellular Targeting Antibacterial Agents. J Med Chem 2022; 65:5433-5448. [PMID: 35297625 DOI: 10.1021/acs.jmedchem.1c01809] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Toward the design of new proline-rich peptidomimetics, a short peptide segment, present in several proline-rich antimicrobial peptides (AMPs), was selected. Fatty acids of varying lengths and spermine were conjugated at the N- and C-terminals of the peptide, respectively. Spermine-conjugated lipopeptides, C10-PR-Spn and C12-PR-Spn, exhibited minimum inhibitory concentrations within 1.5-6.2 μM against the tested pathogens including resistant bacteria and insignificant hemolytic activity against human red blood cells up to 100 μM concentrations and demonstrated resistance against trypsin digestion. C10-PR-Spn and C12-PR-Spn showed synergistic antimicrobial activity against multidrug-resistant methicillin-resistant Staphylococcus aureus with several tested antibiotics. These lipopeptides did not permeabilize bacterial membrane-mimetic lipid vesicles or damage the Escherichia coli membrane like the nonmembrane-lytic AMP, buforin-II. The results suggested that C10-PR-Spn and C12-PR-Spn could interact with the 70S ribosome of E. coli and inhibit its protein synthesis. C10-PR-Spn and C12-PR-Spn demonstrated superior clearance of bacteria from the spleen, liver, and kidneys of mice, infected with S. aureus ATCC 25923 compared to levofloxacin.
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Affiliation(s)
- Rikeshwer Prasad Dewangan
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh 226031, India
| | - Devesh Pratap Verma
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh 226031, India
| | - Neeraj Kumar Verma
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh 226031, India
| | - Ankit Gupta
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh 226031, India
| | - Garima Pant
- Electron Microscopy Unit, SAIF Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Kalyan Mitra
- Electron Microscopy Unit, SAIF Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Saman Habib
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh 226031, India
| | - Jimut Kanti Ghosh
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh 226031, India
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25
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Brakel A, Krizsan A, Itzenga R, Kraus CN, Otvos L, Hoffmann R. Influence of Substitutions in the Binding Motif of Proline-Rich Antimicrobial Peptide ARV-1502 on 70S Ribosome Binding and Antimicrobial Activity. Int J Mol Sci 2022; 23:ijms23063150. [PMID: 35328571 PMCID: PMC8950706 DOI: 10.3390/ijms23063150] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/07/2022] [Accepted: 03/11/2022] [Indexed: 01/10/2023] Open
Abstract
Proline-rich antimicrobial peptides (PrAMPs) are promising candidates to treat bacterial infections. The designer peptide ARV-1502 exhibits strong antimicrobial effects against Enterobacteriaceae both in vitro and in vivo. Since the inhibitory effects of ARV-1502 reported for the 70 kDa heat-shock protein DnaK do not fully explain the antimicrobial activity of its 176 substituted analogs, we further studied their effect on the bacterial 70S ribosome of Escherichia coli, a known target of PrAMPs. ARV-1502 analogues, substituted in positions 3, 4, and 8 to 12 (underlined) of the binding motif D3KPRPYLPRP12 with aspartic acid, lysine, serine, phenylalanine or leucine, were tested in a competitive fluorescence polarization (FP) binding screening assay using 5(6)-carboxyfluorescein-labeled (Cf-) ARV-1502 and the 70S ribosome isolated from E. coli BW25113. While their effect on ribosomal protein expression was studied for green fluorescent protein (GFP) in a cell-free expression system (in vitro translation), the importance of known PrAMP transporters SbmA and MdtM was investigated using E. coli BW25113 and the corresponding knockout mutants. The dissociation constant (Kd) of 201 ± 16 nmol/L obtained for Cf-ARV-1502 suggests strong binding to the E. coli 70S ribosome. An inhibitory binding assay indicated that the binding site overlaps with those of other PrAMPs including Onc112 and pyrrhocoricin as well as the non-peptidic antibiotics erythromycin and chloramphenicol. All these drugs and drug candidates bind to the exit-tunnel of the 70S ribosome. Substitutions of the C-terminal fragment of the binding motif YLPRP reduced binding. At the same time, inhibition of GFP expression increased with net peptide charge. Interestingly, the MIC values of wild-type and ΔsbmA and ΔmdtM knockout mutants indicated that substitutions in the ribosomal binding motif altered also the bacterial uptake, which was generally improved by incorporation of hydrophobic residues. In conclusion, most substituted ARV-1502 analogs bound weaker to the 70S ribosome than ARV-1502 underlining the importance of the YLPRP binding motif. The weaker ribosomal binding correlated well with decreased antimicrobial activity in vitro. Substituted ARV-1502 analogs with a higher level of hydrophobicity or positive net charge improved the ribosome binding, inhibition of translation, and bacterial uptake.
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Affiliation(s)
- Alexandra Brakel
- Faculty of Chemistry and Mineralogy, Institute of Bioanalytical Chemistry, Universität Leipzig, 04109 Leipzig, Germany; (A.K.); (R.I.)
- Center for Biotechnology and Biomedicine, Universität Leipzig, 04109 Leipzig, Germany
- Correspondence: (A.B.); (R.H.)
| | - Andor Krizsan
- Faculty of Chemistry and Mineralogy, Institute of Bioanalytical Chemistry, Universität Leipzig, 04109 Leipzig, Germany; (A.K.); (R.I.)
- Center for Biotechnology and Biomedicine, Universität Leipzig, 04109 Leipzig, Germany
| | - Renke Itzenga
- Faculty of Chemistry and Mineralogy, Institute of Bioanalytical Chemistry, Universität Leipzig, 04109 Leipzig, Germany; (A.K.); (R.I.)
- Center for Biotechnology and Biomedicine, Universität Leipzig, 04109 Leipzig, Germany
| | - Carl N. Kraus
- Aceragen Inc., Durham, NC 27709, USA; (C.N.K.); (L.O.J.)
| | - Laszlo Otvos
- Aceragen Inc., Durham, NC 27709, USA; (C.N.K.); (L.O.J.)
- Institute of Medical Microbiology, Semmelweis University, 1085 Budapest, Hungary
| | - Ralf Hoffmann
- Faculty of Chemistry and Mineralogy, Institute of Bioanalytical Chemistry, Universität Leipzig, 04109 Leipzig, Germany; (A.K.); (R.I.)
- Center for Biotechnology and Biomedicine, Universität Leipzig, 04109 Leipzig, Germany
- Correspondence: (A.B.); (R.H.)
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26
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Wei DX, Zhang XW. Biosynthesis, Bioactivity, Biosafety and Applications of Antimicrobial Peptides for Human Health. BIOSAFETY AND HEALTH 2022. [DOI: 10.1016/j.bsheal.2022.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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27
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Barale SS, Ghane SG, Sonawane KD. Purification and characterization of antibacterial surfactin isoforms produced by Bacillus velezensis SK. AMB Express 2022; 12:7. [PMID: 35084596 PMCID: PMC8795249 DOI: 10.1186/s13568-022-01348-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 01/16/2022] [Indexed: 11/10/2022] Open
Abstract
Bacillus velezensis SK having broad-spectrum antimicrobial activity has been isolated from soil. The efficient extraction of antimicrobial compounds produced in various mediums has been done using Diaion HP-20 resin. Further, characterization of an antimicrobial compound by TLC, FTIR, in-situ bioautography analysis revealed the presence of cyclic lipopeptides, which is then purified by the combination of silica gel, size exclusion, dual gradient, and RP-HPLC chromatography techniques. Growth kinetic studies showed that Bacillus velezensis SK produces a mixture of lipopeptides (1.33 gL-1). The lipopeptide exhibits good pH (2-10) and temperature stability up to 80 °C. LC-ESI-MS analysis of partially purified lipopeptide identified variant of surfactin, further analysis of purified chromatographic fractions revealed the occurrence of most abundant C15-surfactin homologues (m/z 1036.72 Da). The isolated surfactin exhibits good antimicrobial activity (1600 AU/ml) against drug-resistant food-born B. cereus and human pathogen Staphylococcus aureus. Hence, identified strain B. velezensis SK and its potent antibacterial surfactin lipopeptide could be used in various food and biomedical applications.
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28
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Vazquez-Laslop N, Sharma CM, Mankin A, Buskirk AR. Identifying Small Open Reading Frames in Prokaryotes with Ribosome Profiling. J Bacteriol 2022; 204:e0029421. [PMID: 34339296 PMCID: PMC8765392 DOI: 10.1128/jb.00294-21] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Small proteins encoded by open reading frames (ORFs) shorter than 50 codons (small ORFs [sORFs]) are often overlooked by annotation engines and are difficult to characterize using traditional biochemical techniques. Ribosome profiling has tremendous potential to empirically improve the annotations of prokaryotic genomes. Recent improvements in ribosome profiling methods for bacterial model organisms have revealed many new sORFs in well-characterized genomes. Antibiotics that trap ribosomes just after initiation have played a key role in these developments by allowing the unambiguous identification of the start codons (and, hence, the reading frame) for novel ORFs. Here, we describe these new methods and highlight critical controls and considerations for adapting ribosome profiling to different prokaryotic species.
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Affiliation(s)
- Nora Vazquez-Laslop
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Cynthia M. Sharma
- Molecular Infection Biology II, Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Alexander Mankin
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Allen R. Buskirk
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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29
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Kolano L, Knappe D, Berg A, Berg T, Hoffmann R. Effect of amino acid substitutions on 70S ribosomal binding, cellular uptake, and antimicrobial activity of oncocin Onc112. Chembiochem 2021; 23:e202100609. [PMID: 34902208 PMCID: PMC9306569 DOI: 10.1002/cbic.202100609] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Indexed: 11/06/2022]
Abstract
Proline‐rich antimicrobial peptides (PrAMPs) are promising candidates for the treatment of infections caused by high‐priority human pathogens. Their mode of action consists of (I) passive diffusion across the outer membrane, (II) active transport through the inner membrane, and (III) inhibition of protein biosynthesis by blocking the exit tunnel of the 70S ribosome. We tested whether in vitro data on ribosomal binding and bacterial uptake could predict the antibacterial activity of PrAMPs against Gram‐negative and Gram‐positive bacteria. Ribosomal binding and bacterial uptake rates were measured for 47 derivatives of PrAMP Onc112 and compared to the minimal inhibitory concentrations (MIC) of each peptide. Ribosomal binding was evaluated for ribosome extracts from four Gram‐negative bacteria. Bacterial uptake was assessed by quantifying each peptide in the supernatants of bacterial cultures. Oncocin analogues with a higher net positive charge appeared to be more active, although their ribosome binding and uptake rates were not necessarily better than for Onc112. The data suggest a complex mode of action influenced by further factors improving or reducing the antibacterial activity, including diffusion through membranes, transport mechanism, secondary targets, off‐target binding, intracellular distribution, and membrane effects. Relying only on in vitro binding and uptake data may not be sufficient for the rational development of more active analogues.
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Affiliation(s)
- Lisa Kolano
- Universität Leipzig Fakultät für Chemie und Mineralogie: Universitat Leipzig Fakultat fur Chemie und Mineralogie, Chemie und Mineralogie, GERMANY
| | - Daniel Knappe
- Universität Leipzig Fakultät für Chemie und Mineralogie: Universitat Leipzig Fakultat fur Chemie und Mineralogie, Chemie und Mineralogie, GERMANY
| | - Angela Berg
- Universität Leipzig Fakultät für Chemie und Mineralogie: Universitat Leipzig Fakultat fur Chemie und Mineralogie, Chemie und Mineralogie, GERMANY
| | - Thorsten Berg
- Universität Leipzig Fakultät für Chemie und Mineralogie: Universitat Leipzig Fakultat fur Chemie und Mineralogie, Chemie und Mineralogie, GERMANY
| | - Ralf Hoffmann
- Institut für Bioanalytische Chemie, Biotechnologisch-Biomedizinisches Zentrum, Deutscher Platz 5, 04103, Leipzig, GERMANY
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30
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Shirokikh NE. Translation complex stabilization on messenger RNA and footprint profiling to study the RNA responses and dynamics of protein biosynthesis in the cells. Crit Rev Biochem Mol Biol 2021; 57:261-304. [PMID: 34852690 DOI: 10.1080/10409238.2021.2006599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
During protein biosynthesis, ribosomes bind to messenger (m)RNA, locate its protein-coding information, and translate the nucleotide triplets sequentially as codons into the corresponding sequence of amino acids, forming proteins. Non-coding mRNA features, such as 5' and 3' untranslated regions (UTRs), start sites or stop codons of different efficiency, stretches of slower or faster code and nascent polypeptide interactions can alter the translation rates transcript-wise. Most of the homeostatic and signal response pathways of the cells converge on individual mRNA control, as well as alter the global translation output. Among the multitude of approaches to study translational control, one of the most powerful is to infer the locations of translational complexes on mRNA based on the mRNA fragments protected by these complexes from endonucleolytic hydrolysis, or footprints. Translation complex profiling by high-throughput sequencing of the footprints allows to quantify the transcript-wise, as well as global, alterations of translation, and uncover the underlying control mechanisms by attributing footprint locations and sizes to different configurations of the translational complexes. The accuracy of all footprint profiling approaches critically depends on the fidelity of footprint generation and many methods have emerged to preserve certain or multiple configurations of the translational complexes, often in challenging biological material. In this review, a systematic summary of approaches to stabilize translational complexes on mRNA for footprinting is presented and major findings are discussed. Future directions of translation footprint profiling are outlined, focusing on the fidelity and accuracy of inference of the native in vivo translation complex distribution on mRNA.
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Affiliation(s)
- Nikolay E Shirokikh
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
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31
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DeJong MP, Ritter SC, Fransen KA, Tresnak DT, Golinski AW, Hackel BJ. A Platform for Deep Sequence-Activity Mapping and Engineering Antimicrobial Peptides. ACS Synth Biol 2021; 10:2689-2704. [PMID: 34506711 DOI: 10.1021/acssynbio.1c00314] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Developing potent antimicrobials, and platforms for their study and engineering, is critical as antibiotic resistance grows. A high-throughput method to quantify antimicrobial peptide and protein (AMP) activity across a broad continuum would be powerful to elucidate sequence-activity landscapes and identify potent mutants. Yet the complexity of antimicrobial activity has largely constrained the scope and mechanistic bandwidth of AMP variant analysis. We developed a platform to efficiently perform sequence-activity mapping of AMPs via depletion (SAMP-Dep): a bacterial host culture is transformed with an AMP mutant library, induced to intracellularly express AMPs, grown under selective pressure, and deep sequenced to quantify mutant depletion. The slope of mutant growth rate versus induction level indicates potency. Using SAMP-Dep, we mapped the sequence-activity landscape of 170 000 mutants of oncocin, a proline-rich AMP, for intracellular activity against Escherichia coli. Clonal validation supported the platform's sensitivity and accuracy. The mapped landscape revealed an extended oncocin pharmacophore contrary to earlier structural studies, clarified the C-terminus role in internalization, identified functional epistasis, and guided focused, successful synthetic peptide library design, yielding a mutant with 2-fold enhancement in both intracellular and extracellular activity. The efficiency of SAMP-Dep poises the platform to transform AMP engineering, characterization, and discovery.
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Affiliation(s)
- Matthew P. DeJong
- Department of Chemical Engineering and Materials Science, University of Minnesota − Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Seth C. Ritter
- Department of Chemical Engineering and Materials Science, University of Minnesota − Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Katharina A. Fransen
- Department of Chemical Engineering and Materials Science, University of Minnesota − Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Daniel T. Tresnak
- Department of Chemical Engineering and Materials Science, University of Minnesota − Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Alexander W. Golinski
- Department of Chemical Engineering and Materials Science, University of Minnesota − Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Benjamin J. Hackel
- Department of Chemical Engineering and Materials Science, University of Minnesota − Twin Cities, Minneapolis, Minnesota 55455, United States
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32
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Zhang QY, Yan ZB, Meng YM, Hong XY, Shao G, Ma JJ, Cheng XR, Liu J, Kang J, Fu CY. Antimicrobial peptides: mechanism of action, activity and clinical potential. Mil Med Res 2021; 8:48. [PMID: 34496967 PMCID: PMC8425997 DOI: 10.1186/s40779-021-00343-2] [Citation(s) in RCA: 206] [Impact Index Per Article: 68.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 08/30/2021] [Indexed: 12/15/2022] Open
Abstract
The management of bacterial infections is becoming a major clinical challenge due to the rapid evolution of antibiotic resistant bacteria. As an excellent candidate to overcome antibiotic resistance, antimicrobial peptides (AMPs) that are produced from the synthetic and natural sources demonstrate a broad-spectrum antimicrobial activity with the high specificity and low toxicity. These peptides possess distinctive structures and functions by employing sophisticated mechanisms of action. This comprehensive review provides a broad overview of AMPs from the origin, structural characteristics, mechanisms of action, biological activities to clinical applications. We finally discuss the strategies to optimize and develop AMP-based treatment as the potential antimicrobial and anticancer therapeutics.
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Affiliation(s)
- Qi-Yu Zhang
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, No. 928, Street 2, Xiasha Higher Education Zone, Hangzhou, 310018, Zhejiang, China
| | - Zhi-Bin Yan
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, No. 928, Street 2, Xiasha Higher Education Zone, Hangzhou, 310018, Zhejiang, China
| | - Yue-Ming Meng
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, No. 928, Street 2, Xiasha Higher Education Zone, Hangzhou, 310018, Zhejiang, China
| | - Xiang-Yu Hong
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, No. 928, Street 2, Xiasha Higher Education Zone, Hangzhou, 310018, Zhejiang, China
| | - Gang Shao
- Department of Oncology, The 903rd Hospital of PLA, Hangzhou, 310013, Zhejiang, China
| | - Jun-Jie Ma
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, No. 928, Street 2, Xiasha Higher Education Zone, Hangzhou, 310018, Zhejiang, China
| | - Xu-Rui Cheng
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, No. 928, Street 2, Xiasha Higher Education Zone, Hangzhou, 310018, Zhejiang, China
| | - Jun Liu
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California San Francisco, 555 Mission Bay Blvd. South, San Francisco, CA, 94158, USA
| | - Jian Kang
- Oncogenic Signaling and Growth Control Program, Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC, 3000, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Cai-Yun Fu
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, No. 928, Street 2, Xiasha Higher Education Zone, Hangzhou, 310018, Zhejiang, China.
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Pacor S, Benincasa M, Musso MV, Krce L, Aviani I, Pallavicini A, Scocchi M, Gerdol M, Mardirossian M. The proline-rich myticalins from Mytilus galloprovincialis display a membrane-permeabilizing antimicrobial mode of action. Peptides 2021; 143:170594. [PMID: 34118363 DOI: 10.1016/j.peptides.2021.170594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/19/2021] [Accepted: 06/03/2021] [Indexed: 12/15/2022]
Abstract
Bivalve mollusks are continuously exposed to potentially pathogenic microorganisms living in the marine environment. Not surprisingly, these filter-feeders developed a robust innate immunity to protect themselves, which includes a broad panel of antimicrobial peptides. Among these, myticalins represent a recently discovered family of linear cationic peptides expressed in the gills of Mytilus galloprovincialis. Even though myticalins and insect and mammalian proline-rich antimicrobial peptides (PrAMPs) share a similar amino acid composition, we here show that none of the tested mussel peptides use a non-lytic mode of action relying on the bacterial transporter SbmA. On the other hand, all the tested myticalins perturbed and permeabilized the membranes of E. coli BW25113, as shown by flow-cytometry and atomic force microscopy. Circular dichroism spectra revealed that most myticalins did not adopt recognizable secondary structures in the presence of amphipathic environments, such as biological membranes. To explore possible uses of myticalins for biotech, we assessed their biocompatibility with a human cell line. Non-negligible cytotoxic effects displayed by myticalins indicate that their optimization would be required before their further use as lead compounds in the development of new antibiotics.
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Affiliation(s)
- Sabrina Pacor
- Department of Life Sciences, Via Licio Giorgieri 5, University of Trieste, 34127 Trieste, Italy.
| | - Monica Benincasa
- Department of Life Sciences, Via Licio Giorgieri 5, University of Trieste, 34127 Trieste, Italy.
| | - Maria Valentina Musso
- Department of Life Sciences, Via Licio Giorgieri 5, University of Trieste, 34127 Trieste, Italy.
| | - Lucija Krce
- Department of Physics, Faculty of Science, University of Split, Soba B3-18, Ruđera Boškovića 33, 21000 Split, Croatia.
| | - Ivica Aviani
- Department of Physics, Faculty of Science, University of Split, Soba B3-18, Ruđera Boškovića 33, 21000 Split, Croatia.
| | - Alberto Pallavicini
- Department of Life Sciences, Via Licio Giorgieri 5, University of Trieste, 34127 Trieste, Italy.
| | - Marco Scocchi
- Department of Life Sciences, Via Licio Giorgieri 5, University of Trieste, 34127 Trieste, Italy.
| | - Marco Gerdol
- Department of Life Sciences, Via Licio Giorgieri 5, University of Trieste, 34127 Trieste, Italy.
| | - Mario Mardirossian
- Department of Medical Sciences, University of Trieste, Laboratorio Clinica Odontostomatologica, Piazza dell'Ospitale 1, 34125 Trieste, Italy.
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34
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Patriarca EJ, Cermola F, D’Aniello C, Fico A, Guardiola O, De Cesare D, Minchiotti G. The Multifaceted Roles of Proline in Cell Behavior. Front Cell Dev Biol 2021; 9:728576. [PMID: 34458276 PMCID: PMC8397452 DOI: 10.3389/fcell.2021.728576] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 07/23/2021] [Indexed: 12/13/2022] Open
Abstract
Herein, we review the multifaceted roles of proline in cell biology. This peculiar cyclic imino acid is: (i) A main precursor of extracellular collagens (the most abundant human proteins), antimicrobial peptides (involved in innate immunity), salivary proteins (astringency, teeth health) and cornifins (skin permeability); (ii) an energy source for pathogenic bacteria, protozoan parasites, and metastatic cancer cells, which engage in extracellular-protein degradation to invade their host; (iii) an antistress molecule (an osmolyte and chemical chaperone) helpful against various potential harms (UV radiation, drought/salinity, heavy metals, reactive oxygen species); (iv) a neural metabotoxin associated with schizophrenia; (v) a modulator of cell signaling pathways such as the amino acid stress response and extracellular signal-related kinase pathway; (vi) an epigenetic modifier able to promote DNA and histone hypermethylation; (vii) an inducer of proliferation of stem and tumor cells; and (viii) a modulator of cell morphology and migration/invasiveness. We highlight how proline metabolism impacts beneficial tissue regeneration, but also contributes to the progression of devastating pathologies such as fibrosis and metastatic cancer.
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Affiliation(s)
| | | | | | | | | | | | - Gabriella Minchiotti
- Stem Cell Fate Laboratory, Institute of Genetics and Biophysics “A. Buzzati Traverso”, Consiglio Nazionale delle Ricerche, Naples, Italy
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35
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Armas F, Di Stasi A, Mardirossian M, Romani AA, Benincasa M, Scocchi M. Effects of Lipidation on a Proline-Rich Antibacterial Peptide. Int J Mol Sci 2021; 22:7959. [PMID: 34360723 PMCID: PMC8347091 DOI: 10.3390/ijms22157959] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/21/2021] [Accepted: 07/22/2021] [Indexed: 01/04/2023] Open
Abstract
The emergence of multidrug-resistant bacteria is a worldwide health problem. Antimicrobial peptides have been recognized as potential alternatives to conventional antibiotics, but still require optimization. The proline-rich antimicrobial peptide Bac7(1-16) is active against only a limited number of Gram-negative bacteria. It kills bacteria by inhibiting protein synthesis after its internalization, which is mainly supported by the bacterial transporter SbmA. In this study, we tested two different lipidated forms of Bac7(1-16) with the aim of extending its activity against those bacterial species that lack SbmA. We linked a C12-alkyl chain or an ultrashort cationic lipopeptide Lp-I to the C-terminus of Bac7(1-16). Both the lipidated Bac-C12 and Bac-Lp-I forms acquired activity at low micromolar MIC values against several Gram-positive and Gram-negative bacteria. Moreover, unlike Bac7(1-16), Bac-C12, and Bac-Lp-I did not select resistant mutants in E. coli after 14 times of exposure to sub-MIC concentrations of the respective peptide. We demonstrated that the extended spectrum of activity and absence of de novo resistance are likely related to the acquired capability of the peptides to permeabilize cell membranes. These results indicate that C-terminal lipidation of a short proline-rich peptide profoundly alters its function and mode of action and provides useful insights into the design of novel broad-spectrum antibacterial agents.
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Affiliation(s)
- Federica Armas
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (F.A.); (A.D.S.); (M.M.); (M.B.)
- Area Science Park, Padriciano, 34149 Trieste, Italy
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore 138602, Singapore
| | - Adriana Di Stasi
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (F.A.); (A.D.S.); (M.M.); (M.B.)
| | - Mario Mardirossian
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (F.A.); (A.D.S.); (M.M.); (M.B.)
- Department of Medical Sciences, University of Trieste, 34129 Trieste, Italy
| | | | - Monica Benincasa
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (F.A.); (A.D.S.); (M.M.); (M.B.)
| | - Marco Scocchi
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (F.A.); (A.D.S.); (M.M.); (M.B.)
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36
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Khairullina ZZ, Tereshchenkov AG, Zavyalova SA, Komarova ES, Lukianov DA, Tashlitsky VN, Osterman IA, Sumbatyan NV. Interaction of Chloramphenicol Cationic Peptide Analogues with the Ribosome. BIOCHEMISTRY (MOSCOW) 2021; 85:1443-1457. [PMID: 33280584 DOI: 10.1134/s0006297920110127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Virtual screening of all possible tripeptide analogues of chloramphenicol was performed using molecular docking to evaluate their affinity to bacterial ribosomes. Chloramphenicol analogues that demonstrated the lowest calculated energy of interaction with ribosomes were synthesized. Chloramphenicol amine (CAM) derivatives, which contained specific peptide fragments from the proline-rich antimicrobial peptides were produced. It was demonstrated using displacement of the fluorescent erythromycin analogue from its complex with ribosomes that the novel peptide analogues of chloramphenicol were able to bind bacterial ribosome; all the designed tripeptide analogues and one of the chloramphenicol amine derivatives containing fragment of the proline-rich antimicrobial peptides exhibited significantly greater affinity to Escherichia coli ribosome than chloramphenicol. Correlation between the calculated and experimentally evaluated levels of the ligand efficiencies was observed. In vitro protein biosynthesis inhibition assay revealed, that the RAW-CAM analogue shows activity at the level of chloramphenicol. These data were confirmed by the chemical probing assay, according to which binding pattern of this analogue in the nascent peptide exit tunnel was similar to chloramphenicol.
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Affiliation(s)
- Z Z Khairullina
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - A G Tereshchenkov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - S A Zavyalova
- Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
| | - E S Komarova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119992, Russia.,Skolkovo Institute of Science and Technology, Moscow, 143025, Russia
| | - D A Lukianov
- Skolkovo Institute of Science and Technology, Moscow, 143025, Russia
| | - V N Tashlitsky
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - I A Osterman
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.,Skolkovo Institute of Science and Technology, Moscow, 143025, Russia
| | - N V Sumbatyan
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.
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37
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Borovsky D, Deckers K, Vanhove AC, Verstraete M, Rougé P, Shatters RG, Powell CA. Cloning and Characterization of Aedes aegypti Trypsin Modulating Oostatic Factor (TMOF) Gut Receptor. Biomolecules 2021; 11:biom11070934. [PMID: 34201823 PMCID: PMC8301768 DOI: 10.3390/biom11070934] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 06/18/2021] [Accepted: 06/20/2021] [Indexed: 12/17/2022] Open
Abstract
Trypsin Modulating Oostatic Factor (TMOF) receptor was solubilized from the guts of female Ae. Aegypti and cross linked to His6-TMOF and purified by Ni affinity chromatography. SDS PAGE identified two protein bands (45 and 61 kDa). The bands were cut digested and analyzed using MS/MS identifying a protein sequence (1306 amino acids) in the genome of Ae. aegypti. The mRNA of the receptor was extracted, the cDNA sequenced and cloned into pTAC-MAT-2. E. coli SbmA− was transformed with the recombinant plasmid and the receptor was expressed in the inner membrane of the bacterial cell. The binding kinetics of TMOF-FITC was then followed showing that the cloned receptor exhibits high affinity to TMOF (KD = 113.7 ± 18 nM ± SEM and Bmax = 28.7 ± 1.8 pmol ± SEM). Incubation of TMOF-FITC with E. coli cells that express the receptor show that the receptor binds TMOF and imports it into the bacterial cells, indicating that in mosquitoes the receptor imports TMOF into the gut epithelial cells. A 3D modeling of the receptor indicates that the receptor has ATP binding sites and TMOF transport into recombinant E. coli cells is inhibited with ATPase inhibitors Na Arsenate and Na Azide.
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Affiliation(s)
- Dov Borovsky
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz School of Medicine, Aurora, CO 80045, USA
- Correspondence:
| | - Kato Deckers
- Zoological Institute, Katholieke Universiteit Leuven, 3000 Leuven, Belgium; (K.D.); (A.C.V.); (M.V.)
| | - Anne Catherine Vanhove
- Zoological Institute, Katholieke Universiteit Leuven, 3000 Leuven, Belgium; (K.D.); (A.C.V.); (M.V.)
| | - Maud Verstraete
- Zoological Institute, Katholieke Universiteit Leuven, 3000 Leuven, Belgium; (K.D.); (A.C.V.); (M.V.)
| | - Pierre Rougé
- UMR 152 Pharma-Dev, Faculté des Sciences Pharmaceutiques, Institut de Recherche et Développement, Université Toulouse 3, F-31062 Toulouse, France;
| | - Robert G. Shatters
- USDA ARS, Subtropical Horticultural Laboratory, 2001 Rock Road, Ft. Pierce, FL 34945, USA;
| | - Charles A. Powell
- UF-IFAS Indian River Research and Education Center, Fort Pierce, FL 34945, USA;
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38
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Khodaparast L, Wu G, Khodaparast L, Schmidt BZ, Rousseau F, Schymkowitz J. Bacterial Protein Homeostasis Disruption as a Therapeutic Intervention. Front Mol Biosci 2021; 8:681855. [PMID: 34150852 PMCID: PMC8206779 DOI: 10.3389/fmolb.2021.681855] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/04/2021] [Indexed: 12/15/2022] Open
Abstract
Cells have evolved a complex molecular network, collectively called the protein homeostasis (proteostasis) network, to produce and maintain proteins in the appropriate conformation, concentration and subcellular localization. Loss of proteostasis leads to a reduction in cell viability, which occurs to some degree during healthy ageing, but is also the root cause of a group of diverse human pathologies. The accumulation of proteins in aberrant conformations and their aggregation into specific beta-rich assemblies are particularly detrimental to cell viability and challenging to the protein homeostasis network. This is especially true for bacteria; it can be argued that the need to adapt to their changing environments and their high protein turnover rates render bacteria particularly vulnerable to the disruption of protein homeostasis in general, as well as protein misfolding and aggregation. Targeting bacterial proteostasis could therefore be an attractive strategy for the development of novel antibacterial therapeutics. This review highlights advances with an antibacterial strategy that is based on deliberately inducing aggregation of target proteins in bacterial cells aiming to induce a lethal collapse of protein homeostasis. The approach exploits the intrinsic aggregation propensity of regions residing in the hydrophobic core regions of the polypeptide sequence of proteins, which are genetically conserved because of their essential role in protein folding and stability. Moreover, the molecules were designed to target multiple proteins, to slow down the build-up of resistance. Although more research is required, results thus far allow the hope that this strategy may one day contribute to the arsenal to combat multidrug-resistant bacterial infections.
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Affiliation(s)
- Laleh Khodaparast
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Guiqin Wu
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Ladan Khodaparast
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Béla Z Schmidt
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Frederic Rousseau
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
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Ebou A, Koua D, Addablah A, Kakou-Ngazoa S, Dutertre S. Combined Proteotranscriptomic-Based Strategy to Discover Novel Antimicrobial Peptides from Cone Snails. Biomedicines 2021; 9:344. [PMID: 33805497 PMCID: PMC8066717 DOI: 10.3390/biomedicines9040344] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 12/21/2022] Open
Abstract
Despite their impressive diversity and already broad therapeutic applications, cone snail venoms have received less attention as a natural source in the investigation of antimicrobial peptides than other venomous animals such as scorpions, spiders, or snakes. Cone snails are among the largest genera (Conus sp.) of marine invertebrates, with more than seven hundred species described to date. These predatory mollusks use their sophisticated venom apparatus to capture prey or defend themselves. In-depth studies of these venoms have unraveled many biologically active peptides with pharmacological properties of interest in the field of pain management, the treatment of epilepsy, neurodegenerative diseases, and cardiac ischemia. Considering sequencing efficiency and affordability, cone snail venom gland transcriptome analyses could allow the discovery of new, promising antimicrobial peptides. We first present here the need for novel compounds like antimicrobial peptides as a viable alternative to conventional antibiotics. Secondly, we review the current knowledge on cone snails as a source of antimicrobial peptides. Then, we present the current state of the art in analytical methods applied to crude or milked venom followed by how antibacterial activity assay can be implemented for fostering cone snail antimicrobial peptides studies. We also propose a new innovative profile Hidden Markov model-based approach to annotate full venom gland transcriptomes and speed up the discovery of potentially active peptides from cone snails.
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Affiliation(s)
- Anicet Ebou
- Bioinformatic Team, Département Agriculture et Ressource Animales, UMRI 28, Institut National Polytechnique Félix Houphouët-Boigny, Yamoussoukro BP 1093, Ivory Coast;
| | - Dominique Koua
- Bioinformatic Team, Département Agriculture et Ressource Animales, UMRI 28, Institut National Polytechnique Félix Houphouët-Boigny, Yamoussoukro BP 1093, Ivory Coast;
| | - Audrey Addablah
- Plateforme de Biologie Moléculaire, Institut Pasteur de Côte d’Ivoire, Abidjan BP 490, Ivory Coast; (A.A.); (S.K.-N.)
| | - Solange Kakou-Ngazoa
- Plateforme de Biologie Moléculaire, Institut Pasteur de Côte d’Ivoire, Abidjan BP 490, Ivory Coast; (A.A.); (S.K.-N.)
| | - Sébastien Dutertre
- Institut des Biomolécules Max Mousseron, UMR 5247, Université de Montpellier, CNRS, ENSCM, 34095 Montpellier, France
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40
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Upert G, Luther A, Obrecht D, Ermert P. Emerging peptide antibiotics with therapeutic potential. MEDICINE IN DRUG DISCOVERY 2021; 9:100078. [PMID: 33398258 PMCID: PMC7773004 DOI: 10.1016/j.medidd.2020.100078] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/15/2020] [Accepted: 12/27/2020] [Indexed: 02/09/2023] Open
Abstract
This review covers some of the recent progress in the field of peptide antibiotics with a focus on compounds with novel or established mode of action and with demonstrated efficacy in animal infection models. Novel drug discovery approaches, linear and macrocyclic peptide antibiotics, lipopeptides like the polymyxins as well as peptides addressing targets located in the plasma membrane or in the outer membrane of bacterial cells are discussed.
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Key Words
- ADMET, absorption, distribution, metabolism and excretion – toxicity in pharmacokinetics
- AMP, antimicrobial peptide
- AMR, antimicrobial resistance
- ATCC, ATCC cell collection
- Antibiotic
- BAM, β-barrel assembly machinery
- CC50, cytotoxic concentration to kill 50% of cells
- CD, circular dichroism
- CFU, colony forming unit
- CLSI, clinical and laboratory standards institute
- CMS, colistin methane sulfonate
- DMPC, 1,2-dimyristoyl-sn-glycero-3-phosphocholine
- ESKAPE, acronym encompassing six bacterial pathogens (often carrying antibiotic resistance): Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumonia, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp
- FDA, U. S. Food and Drug Administration
- HABP, hospital acquired bacterial pneumonia
- HDP, host-defense peptide
- HEK293, human embryonic kidney 293 cells
- HK-2, human kidney 2 cells (proximal tubular cell line)
- HepG2, human hepatocellular carcinoma cell line
- Hpg, 4-hydroxy-phenyl glycine
- ITC, isothermal titration calorimetry
- KPC, Klebsiella pneumoniae metallo-β-lactamase C resistant
- LPS, lipopolysaccharide
- LptA, lipopolysaccharide transport protein A
- LptC, lipopolysaccharide transport protein C
- LptD, lipopolysaccharide transport protein D
- MDR, multidrug-resistant
- MH-I, Müller-Hinton broth I
- MH-II, Müller-Hinton broth II (cation adjusted)
- MIC, minimal inhibitory concentration
- MRSA, methicilline-resistant S. aureus
- MSSA, methicilline-sensitive S. aureus
- MoA, mechanism (mode) of action
- NDM-1, New Delhi metallo-β-lactamase resistant
- NOAEL, no adverse effect level
- ODL, odilorhabdin
- OMPTA (outer membrane targeting antibiotic)
- OMPTA, outer membrane targeting antibiotic
- Omp, outer membrane protein
- PBMC, peripheral mononuclear blood cell
- PBP, penicillin-binding protein
- PBS, phosphate-buffered saline
- PK, pharmacokinetics
- POPC, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
- POPG, 2-oleoyl-1-palmitoyl-sn-glycero-3-phospho-(1-glycerol)
- PrAMPs, polyproline antimicrobial peptides
- RBC, red blood cell
- SAR, structure-activity relationship
- SPR, surface plasmon resonance
- SPase I, signal peptidase I
- VABP, ventilator associated bacterial pneumonia
- VIM-1, beta-lactamase 2 (K. pneumoniae)
- VISA, vancomycin-intermediate S. aureus
- VRE, vancomycin-resistant enterococcus
- WHO, World Health Organization
- WT, wild type
- WTA, wall teichoic acid
- XDR, extremely drug-resistant
- antimicrobial peptide
- antimicrobial resistance
- bid, bis in die (two times a day)
- i.p., intraperitoneal
- i.v., intravenous
- lipopeptide
- mITT population, minimal intend-to-treat population
- peptide antibiotic
- s.c., subcutaneous
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Affiliation(s)
- Gregory Upert
- Polyphor Ltd, Hegenheimermattweg 125, 4123 Allschwil, Switzerland
| | - Anatol Luther
- Bachem AG, Hauptstrasse 114, 4416 Bubendorf, Switzerland
| | - Daniel Obrecht
- Polyphor Ltd, Hegenheimermattweg 125, 4123 Allschwil, Switzerland
| | - Philipp Ermert
- Polyphor Ltd, Hegenheimermattweg 125, 4123 Allschwil, Switzerland
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41
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Zhang L, He J, Bai L, Ruan S, Yang T, Luo Y. Ribosome-targeting antibacterial agents: Advances, challenges, and opportunities. Med Res Rev 2021; 41:1855-1889. [PMID: 33501747 DOI: 10.1002/med.21780] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/08/2020] [Accepted: 12/19/2020] [Indexed: 02/05/2023]
Abstract
Ribosomes, which synthesize proteins, are critical organelles for the survival and growth of bacteria. About 60% of approved antibiotics discovered so far combat pathogenic bacteria by targeting ribosomes. However, several issues, such as drug resistance and toxicity, have impeded the clinical use of ribosome-targeting antibiotics. Moreover, the complexity of the bacteria ribosome structure has retarded the discovery of new ribosome-targeting agents that are considered as the key to the drug-resistance and toxicity. To deal with these challenges, efforts such as medicinal chemistry optimization, combination treatment, and new drug delivery system have been developed. But not enough, the development of structural biology and new screening methods bring powerful tools, such as cryo-electron microscopy technology, advanced computer-aided drug design, and cell-free in vitro transcription/translation systems, for the discovery of novel ribosome-targeting antibiotics. Thus, in this paper, we overview the research on different aspects of bacterial ribosomes, especially focus on discussing the challenges in the discovery of ribosome-targeting antibacterial drugs and advances made to address issues such as drug-resistance and selectivity, which, we believe, provide perspectives for the discovery of novel antibiotics.
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Affiliation(s)
- Laiying Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Jun He
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Lang Bai
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Shihua Ruan
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Tao Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China.,Laboratory of Human Diseases and Immunotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China.,Institute of Immunology and Inflammation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Youfu Luo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
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42
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Proline-rich antimicrobial peptide Api137 is bactericidal in porcine blood infected ex vivo with a porcine or human Klebsiella pneumoniae strain. J Glob Antimicrob Resist 2020; 24:127-135. [PMID: 33373733 DOI: 10.1016/j.jgar.2020.12.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 12/04/2020] [Accepted: 12/18/2020] [Indexed: 11/20/2022] Open
Abstract
OBJECTIVES Klebsiella pneumoniae is an emerging invasive pathogen in humans and pigs. Resistance against multiple antibiotics in this species is a major health concern and the development of new antibiotics is urgently needed. The objective of this study was to investigate the effects of proline-rich antimicrobial peptides (PrAMPs) on the survival of K. pneumoniae strains in porcine blood. METHODS We established a bactericidal assay with K. pneumoniae in fresh blood drawn from 4-week-old piglets. PrAMPs, namely the apidaecins Api137 and Api802 as well as the oncocin Onc112, were added to ex vivo-infected whole blood samples in order to study their bactericidal effects and, in the case of Api137, also immune responses. RESULTS A porcine invasive and a human iucA+rmpA+ K. pneumoniae strain showed prominent proliferation in porcine blood. Application of Api137 resulted in a dose-dependent prominent bactericidal effect killing the invasive porcine K. pneumoniae strain. Addition of 8 μg/mL Api137 also resulted in complete killing of the human iucA+rmpA+ strain. Cytotoxicity, haemolysis and induction of the pro-inflammatory cytokine tumour necrosis factor-alpha (TNFα) in K. pneumoniae-infected porcine blood treated with Api137 was comparable with values obtained after application of 10 μg/mL cefquinome. CONCLUSION We describe a new non-rodent model for invasive K. pneumoniae bacteraemia and present promising data for the PrAMP Api137 for the control of infection with hypervirulent K. pneumoniae strains.
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43
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Kopeikin PM, Zharkova MS, Kolobov AA, Smirnova MP, Sukhareva MS, Umnyakova ES, Kokryakov VN, Orlov DS, Milman BL, Balandin SV, Panteleev PV, Ovchinnikova TV, Komlev AS, Tossi A, Shamova OV. Caprine Bactenecins as Promising Tools for Developing New Antimicrobial and Antitumor Drugs. Front Cell Infect Microbiol 2020; 10:552905. [PMID: 33194795 PMCID: PMC7604311 DOI: 10.3389/fcimb.2020.552905] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 09/28/2020] [Indexed: 02/01/2023] Open
Abstract
Proline-rich antimicrobial peptides (PR-AMPs) having a potent antimicrobial activity predominantly toward Gram-negative bacteria and negligible toxicity toward host cells, are attracting attention as new templates for developing antibiotic drugs. We have previously isolated and characterized several bactenecins that are promising in this respect, from the leukocytes of the domestic goat Capra hircus: ChBac5, miniChBac7.5N-α, and -β, as well as ChBac3.4. Unlike the others, ChBac3.4 shows a somewhat unusual pattern of activities for a mammalian PR-AMP: it is more active against bacterial membranes as well as tumor and, to the lesser extent, normal cells. Here we describe a SAR study of ChBac3.4 (RFRLPFRRPPIRIHPPPFYPPFRRFL-NH2) which elucidates its peculiarities and evaluates its potential as a lead for antimicrobial or anticancer drugs based on this peptide. A set of designed structural analogues of ChBac3.4 was explored for antibacterial activity toward drug-resistant clinical isolates and antitumor properties. The N-terminal region was found to be important for the antimicrobial action, but not responsible for the toxicity toward mammalian cells. A shortened variant with the best selectivity index toward bacteria demonstrated a pronounced synergy in combination with antibiotics against Gram-negative strains, albeit with a somewhat reduced ability to inhibit biofilm formation compared to native peptide. C-terminal amidation was examined for some analogues, which did not affect antimicrobial activity, but somewhat altered the cytotoxicity toward host cells. Interestingly, non-amidated peptides showed a slight delay in their impact on bacterial membrane integrity. Peptides with enhanced hydrophobicity showed increased toxicity, but in most cases their selectivity toward tumor cells also improved. While most analogues lacked hemolytic properties, a ChBac3.4 variant with two additional tryptophan residues demonstrated an appreciable activity toward human erythrocytes. The variant demonstrating the best tumor/nontumor cell selectivity was found to more actively initiate apoptosis in target cells, though its action was slower than that of the native ChBac3.4. Its antitumor effectiveness was successfully verified in vivo in a murine Ehrlich ascites carcinoma model. The obtained results demonstrate the potential of structural modification to manage caprine bactenecins’ selectivity and activity spectrum and confirm that they are promising prototypes for antimicrobial and anticancer drugs design.
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Affiliation(s)
- Pavel M Kopeikin
- Laboratory of Design and Synthesis of Biologically Active Peptides, Department of General Pathology and Pathophysiology, FSBSI Institute of Experimental Medicine, Saint Petersburg, Russia
| | - Maria S Zharkova
- Laboratory of Design and Synthesis of Biologically Active Peptides, Department of General Pathology and Pathophysiology, FSBSI Institute of Experimental Medicine, Saint Petersburg, Russia
| | - Alexander A Kolobov
- Laboratory of Peptide Chemistry, State Research Institute of Highly Pure Biopreparations, Saint Petersburg, Russia
| | - Maria P Smirnova
- Laboratory of Peptide Chemistry, State Research Institute of Highly Pure Biopreparations, Saint Petersburg, Russia
| | - Maria S Sukhareva
- Laboratory of Design and Synthesis of Biologically Active Peptides, Department of General Pathology and Pathophysiology, FSBSI Institute of Experimental Medicine, Saint Petersburg, Russia
| | - Ekaterina S Umnyakova
- Laboratory of Design and Synthesis of Biologically Active Peptides, Department of General Pathology and Pathophysiology, FSBSI Institute of Experimental Medicine, Saint Petersburg, Russia
| | - Vladimir N Kokryakov
- Laboratory of Design and Synthesis of Biologically Active Peptides, Department of General Pathology and Pathophysiology, FSBSI Institute of Experimental Medicine, Saint Petersburg, Russia
| | - Dmitriy S Orlov
- Laboratory of Design and Synthesis of Biologically Active Peptides, Department of General Pathology and Pathophysiology, FSBSI Institute of Experimental Medicine, Saint Petersburg, Russia
| | - Boris L Milman
- Laboratory of Design and Synthesis of Biologically Active Peptides, Department of General Pathology and Pathophysiology, FSBSI Institute of Experimental Medicine, Saint Petersburg, Russia
| | - Sergey V Balandin
- Science-Educational Center, M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, The Russian Academy of Sciences, Moscow, Russia
| | - Pavel V Panteleev
- Science-Educational Center, M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, The Russian Academy of Sciences, Moscow, Russia
| | - Tatiana V Ovchinnikova
- Science-Educational Center, M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, The Russian Academy of Sciences, Moscow, Russia.,Department of Biotechnology, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Aleksey S Komlev
- Laboratory of Design and Synthesis of Biologically Active Peptides, Department of General Pathology and Pathophysiology, FSBSI Institute of Experimental Medicine, Saint Petersburg, Russia
| | - Alessandro Tossi
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Olga V Shamova
- Laboratory of Design and Synthesis of Biologically Active Peptides, Department of General Pathology and Pathophysiology, FSBSI Institute of Experimental Medicine, Saint Petersburg, Russia
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44
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Sancho-Vaello E, Gil-Carton D, François P, Bonetti EJ, Kreir M, Pothula KR, Kleinekathöfer U, Zeth K. The structure of the antimicrobial human cathelicidin LL-37 shows oligomerization and channel formation in the presence of membrane mimics. Sci Rep 2020; 10:17356. [PMID: 33060695 PMCID: PMC7562864 DOI: 10.1038/s41598-020-74401-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 09/26/2020] [Indexed: 12/22/2022] Open
Abstract
The human cathelicidin LL-37 serves a critical role in the innate immune system defending bacterial infections. LL-37 can interact with molecules of the cell wall and perforate cytoplasmic membranes resulting in bacterial cell death. To test the interactions of LL-37 and bacterial cell wall components we crystallized LL-37 in the presence of detergents and obtained the structure of a narrow tetrameric channel with a strongly charged core. The formation of a tetramer was further studied by cross-linking in the presence of detergents and lipids. Using planar lipid membranes a small but defined conductivity of this channel could be demonstrated. Molecular dynamic simulations underline the stability of this channel in membranes and demonstrate pathways for the passage of water molecules. Time lapse studies of E. coli cells treated with LL-37 show membrane discontinuities in the outer membrane followed by cell wall damage and cell death. Collectively, our results open a venue to the understanding of a novel AMP killing mechanism and allows the rational design of LL-37 derivatives with enhanced bactericidal activity.
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Affiliation(s)
- Enea Sancho-Vaello
- Unidad de Biofisica, Centro Mixto Consejo Superior de Investigaciones Cientificas-Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC, UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia, Spain.,Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - David Gil-Carton
- Structural Biology Unit, CIC bioGUNE, Parque Tecnológico de Bizkaia Edificio 800, 48160, Derio, Spain
| | - Patrice François
- Genomic Research Laboratory, Department of Medical Specialities, Geneva University Hospitals, University of Geneva, Genève, Switzerland
| | - Eve-Julie Bonetti
- Genomic Research Laboratory, Department of Medical Specialities, Geneva University Hospitals, University of Geneva, Genève, Switzerland
| | - Mohamed Kreir
- Nanion Technologies GmbH, Gabrielenstraße 9, 80636, Munich, Germany.,Janssen Pharmaceutica NV, Janssen R&D, Nonclinical Safety, Beerse, Belgium
| | - Karunakar Reddy Pothula
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759, Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759, Bremen, Germany
| | - Kornelius Zeth
- Department of Science and Environment, Roskilde University, Universitetsvej 1, 4000, Roskilde, Denmark.
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45
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Mangano K, Florin T, Shao X, Klepacki D, Chelysheva I, Ignatova Z, Gao Y, Mankin AS, Vázquez-Laslop N. Genome-wide effects of the antimicrobial peptide apidaecin on translation termination in bacteria. eLife 2020; 9:e62655. [PMID: 33031031 PMCID: PMC7544508 DOI: 10.7554/elife.62655] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 09/20/2020] [Indexed: 12/16/2022] Open
Abstract
Biochemical studies suggested that the antimicrobial peptide apidaecin (Api) inhibits protein synthesis by binding in the nascent peptide exit tunnel and trapping the release factor associated with a terminating ribosome. The mode of Api action in bacterial cells had remained unknown. Here genome-wide analysis reveals that in bacteria, Api arrests translating ribosomes at stop codons and causes pronounced queuing of the trailing ribosomes. By sequestering the available release factors, Api promotes pervasive stop codon bypass, leading to the expression of proteins with C-terminal extensions. Api-mediated translation arrest leads to the futile activation of the ribosome rescue systems. Understanding the unique mechanism of Api action in living cells may facilitate the development of new medicines and research tools for genome exploration.
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Affiliation(s)
- Kyle Mangano
- Center for Biomolecular Sciences, University of Illinois at ChicagoChicagoUnited States
- Department of Pharmaceutical Sciences, University of Illinois at ChicagoChicagoUnited States
| | - Tanja Florin
- Center for Biomolecular Sciences, University of Illinois at ChicagoChicagoUnited States
| | - Xinhao Shao
- Department of Pharmaceutical Sciences, University of Illinois at ChicagoChicagoUnited States
| | - Dorota Klepacki
- Center for Biomolecular Sciences, University of Illinois at ChicagoChicagoUnited States
| | - Irina Chelysheva
- Institute of Biochemistry and Molecular Biology, University of HamburgHamburgGermany
| | - Zoya Ignatova
- Institute of Biochemistry and Molecular Biology, University of HamburgHamburgGermany
| | - Yu Gao
- Department of Pharmaceutical Sciences, University of Illinois at ChicagoChicagoUnited States
| | - Alexander S Mankin
- Center for Biomolecular Sciences, University of Illinois at ChicagoChicagoUnited States
- Department of Pharmaceutical Sciences, University of Illinois at ChicagoChicagoUnited States
| | - Nora Vázquez-Laslop
- Center for Biomolecular Sciences, University of Illinois at ChicagoChicagoUnited States
- Department of Pharmaceutical Sciences, University of Illinois at ChicagoChicagoUnited States
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46
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Sola R, Mardirossian M, Beckert B, Sanghez De Luna L, Prickett D, Tossi A, Wilson DN, Scocchi M. Characterization of Cetacean Proline-Rich Antimicrobial Peptides Displaying Activity against ESKAPE Pathogens. Int J Mol Sci 2020; 21:E7367. [PMID: 33036159 PMCID: PMC7582929 DOI: 10.3390/ijms21197367] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 09/28/2020] [Accepted: 09/29/2020] [Indexed: 12/27/2022] Open
Abstract
Proline-rich antimicrobial peptides (PrAMPs) may be a valuable weapon against multi-drug resistant pathogens, combining potent antimicrobial activity with low cytotoxicity. We have identified novel PrAMPs from five cetacean species (cePrAMPs), and characterized their potency, mechanism of action and in vitro cytotoxicity. Despite the homology between the N-terminal of cePrAMPs and the bovine PrAMP Bac7, some differences emerged in their sequence, activity spectrum and mode of action. CePrAMPs with the highest similarity with the Bac7(1-35) fragment inhibited bacterial protein synthesis without membrane permeabilization, while a second subgroup of cePrAMPs was more membrane-active but less efficient at inhibiting bacterial translation. Such differences may be ascribable to differences in presence and positioning of Trp residues and of a conserved motif seemingly required for translation inhibition. Unlike Bac7(1-35), which requires the peptide transporter SbmA for its uptake, the activity of cePrAMPs was mostly independent of SbmA, regardless of their mechanism of action. Two peptides displayed a promisingly broad spectrum of activity, with minimal inhibiting concentration MIC ≤ 4 µM against several bacteria of the ESKAPE group, including Pseudomonas aeruginosa and Enterococcus faecium. Our approach has led us to discover several new peptides; correlating their sequences and mechanism of action will provide useful insights for designing optimized future peptide-based antibiotics.
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Affiliation(s)
- Riccardo Sola
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (R.S.); (L.S.D.L.); (D.P.); (A.T.); mscocchi.units.it (M.S.)
| | - Mario Mardirossian
- Department of Medical Sciences, University of Trieste, 34125 Trieste, Italy;
| | - Bertrand Beckert
- Institute for Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany; (B.B.); (D.N.W.)
| | - Laura Sanghez De Luna
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (R.S.); (L.S.D.L.); (D.P.); (A.T.); mscocchi.units.it (M.S.)
| | - Dennis Prickett
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (R.S.); (L.S.D.L.); (D.P.); (A.T.); mscocchi.units.it (M.S.)
| | - Alessandro Tossi
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (R.S.); (L.S.D.L.); (D.P.); (A.T.); mscocchi.units.it (M.S.)
| | - Daniel N. Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany; (B.B.); (D.N.W.)
| | - Marco Scocchi
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (R.S.); (L.S.D.L.); (D.P.); (A.T.); mscocchi.units.it (M.S.)
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47
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Arbour CA, Mendoza LG, Stockdill JL. Recent advances in the synthesis of C-terminally modified peptides. Org Biomol Chem 2020; 18:7253-7272. [PMID: 32914156 PMCID: PMC9508648 DOI: 10.1039/d0ob01417f] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
C-Terminally modified peptides are important for the development and delivery of peptide-based pharmaceuticals because they impact peptide activity, stability, hydrophobicity, and membrane permeability. Additionally, the vulnerability of C-terminal esters to cleavage by endogenous esterases makes them excellent pro-drugs. Methods for post-SPPS C-terminal functionalization potentially enable access to libraries of modified peptides, facilitating tailoring of their solubility, potency, toxicity, and uptake pathway. Apparently minor structural changes can significantly impact the binding, folding, and pharmacokinetics of the peptide. This review summarizes developments in chemical methods for C-terminal modification of peptides published since the last review on this topic in 2003.
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Affiliation(s)
- Christine A Arbour
- Wayne State University, Department of Chemistry, Detroit, Michigan, USA.
| | - Lawrence G Mendoza
- Wayne State University, Department of Chemistry, Detroit, Michigan, USA.
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48
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Muthunayake NS, Islam R, Inutan ED, Colangelo W, Trimpin S, Cunningham PR, Chow CS. Expression and In Vivo Characterization of the Antimicrobial Peptide Oncocin and Variants Binding to Ribosomes. Biochemistry 2020; 59:3380-3391. [PMID: 32840100 DOI: 10.1021/acs.biochem.0c00600] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Peptides have important biomedical applications, but poor correlation between in vitro and in vivo activities can limit their development for clinical use. The ability to generate peptides and monitor their expression with new mass spectrometric methods and biological activities in vivo would be an advantage for the discovery and improvement of peptide-based drugs. In this study, a plasmid-based system was used to express the ribosome-targeting peptide oncocin (19 amino acids, VDKPPYLPRPRPPRRIYNR) and to determine its direct antibacterial effects on Escherichia coli. Previous biochemical and structure studies showed that oncocin targets the bacterial ribosome. The oncocin peptide generated in vivo strongly inhibits bacterial growth. In vivo dimethyl sulfate footprinting of oncocin on the rRNA gives results that are consistent with those of in vitro studies but reveals additional binding interactions with E. coli ribosomes. Furthermore, expression of truncated or mutated peptides reveals which amino acids are important for antimicrobial activity. Overall, the in vivo peptide expression system can be used to investigate biological activities and interactions of peptides with their targets within the cellular environment and to separate contributions of the sequence to cellular transport. This strategy has future applications for improving the effectiveness of existing peptides and developing new peptide-based drugs.
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Affiliation(s)
- Nisansala S Muthunayake
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States.,Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202, United States
| | - Rabiul Islam
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Ellen D Inutan
- Department of Chemistry, Mindanao State University-Iligan Institute of Technology, Iligan 9200, Philippines
| | - Wesley Colangelo
- Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202, United States
| | - Sarah Trimpin
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Philip R Cunningham
- Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202, United States
| | - Christine S Chow
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
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49
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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] [MESH Headings] [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 MineralogyInstitute of Bioanalytical ChemistryDeutscher Platz 504103LeipzigGermany
- Center for Biotechnology and Biomedicine (BBZ)Deutscher Platz 504103LeipzigGermany
| | - Daniel Knappe
- Faculty of Chemistry and MineralogyInstitute of Bioanalytical ChemistryDeutscher Platz 504103LeipzigGermany
- Center for Biotechnology and Biomedicine (BBZ)Deutscher Platz 504103LeipzigGermany
- EnBiotix GmbHLeipzigDeutscher Platz 5E04103LeipzigGermany
| | - Daniela Volke
- Faculty of Chemistry and MineralogyInstitute of Bioanalytical ChemistryDeutscher Platz 504103LeipzigGermany
- Center for Biotechnology and Biomedicine (BBZ)Deutscher Platz 504103LeipzigGermany
| | - Norbert Sträter
- Faculty of Chemistry and MineralogyInstitute of Bioanalytical ChemistryDeutscher Platz 504103LeipzigGermany
- Center for Biotechnology and Biomedicine (BBZ)Deutscher Platz 504103LeipzigGermany
| | - Ralf Hoffmann
- Faculty of Chemistry and MineralogyInstitute of Bioanalytical ChemistryDeutscher Platz 504103LeipzigGermany
- Center for Biotechnology and Biomedicine (BBZ)Deutscher Platz 504103LeipzigGermany
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50
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Mardirossian M, Sola R, Beckert B, Valencic E, Collis DWP, Borišek J, Armas F, Di Stasi A, Buchmann J, Syroegin EA, Polikanov YS, Magistrato A, Hilpert K, Wilson DN, Scocchi M. Peptide Inhibitors of Bacterial Protein Synthesis with Broad Spectrum and SbmA-Independent Bactericidal Activity against Clinical Pathogens. J Med Chem 2020; 63:9590-9602. [PMID: 32787108 DOI: 10.1021/acs.jmedchem.0c00665] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Proline-rich antimicrobial peptides (PrAMPs) are promising lead compounds for developing new antimicrobials; however, their narrow spectrum of action is limiting. PrAMPs kill bacteria binding to their ribosomes and inhibiting protein synthesis. In this study, 133 derivatives of the PrAMP Bac7(1-16) were synthesized to identify the crucial residues for ribosome inactivation and antimicrobial activity. Then, five new Bac7(1-16) derivatives were conceived and characterized by antibacterial and membrane permeabilization assays, X-ray crystallography, and molecular dynamics simulations. Some derivatives displayed broad spectrum activity, encompassing Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumanii, Pseudomonas aeruginosa, and Staphylococcus aureus. Two peptides out of five acquired a weak membrane-perturbing activity while maintaining the ability to inhibit protein synthesis. These derivatives became independent of the SbmA transporter, commonly used by native PrAMPs, suggesting that they obtained a novel route to enter bacterial cells. PrAMP-derived compounds could become new-generation antimicrobials to combat antibiotic-resistant pathogens.
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Affiliation(s)
- Mario Mardirossian
- Department of Medical Sciences, University of Trieste, 34125 Trieste, Italy
| | - Riccardo Sola
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Bertrand Beckert
- Institut für Biochemie und Molekularbiologie, University of Hamburg, 20146 Hamburg, Germany
| | - Erica Valencic
- Institute for Maternal and Child Health-IRCCS "Burlo Garofolo", 30137 Trieste, Italy
| | | | | | - Federica Armas
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Adriana Di Stasi
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Jan Buchmann
- Institut für Biochemie und Molekularbiologie, University of Hamburg, 20146 Hamburg, Germany.,Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Egor A Syroegin
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Yury S Polikanov
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois 60607, United States.,Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | | | - Kai Hilpert
- Institute of Infection and Immunology, St. George's, University of London, SW 17 0RE London, U.K
| | - Daniel N Wilson
- Institut für Biochemie und Molekularbiologie, University of Hamburg, 20146 Hamburg, Germany
| | - Marco Scocchi
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
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