1
|
Corman HN, Ross JN, Fields FR, Shoue DA, McDowell MA, Lee SW. Rationally Designed Minimal Bioactive Domains of AS-48 Bacteriocin Homologs Possess Potent Antileishmanial Properties. Microbiol Spectr 2022; 10:e0265822. [PMID: 36342284 PMCID: PMC9769502 DOI: 10.1128/spectrum.02658-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/04/2022] [Indexed: 11/09/2022] Open
Abstract
Leishmaniasis, a category I neglected tropical disease, is a group of diseases caused by the protozoan parasite Leishmania species with a wide range of clinical manifestations. Current treatment options can be highly toxic and expensive, with drug relapse and the emergence of resistance. Bacteriocins, antimicrobial peptides ribosomally produced by bacteria, are a relatively new avenue for potential antiprotozoal drugs. Particular interest has been focused on enterocin AS-48, with previously proven efficacy against protozoan species, including Leishmania spp. Sequential characterization of enterocin AS-48 has illustrated that antibacterial bioactivity is preserved in linearized, truncated forms; however, minimal domains of AS-48 bacteriocins have not yet been explored against protozoans. Using rational design techniques to improve membrane penetration activity, we designed peptide libraries using the minimal bioactive domain of AS-48 homologs. Stepwise changes to the charge (z), hydrophobicity (H), and hydrophobic dipole moment (μH) were achieved through lysine and tryptophan substitutions and the inversion of residues within the helical wheel, respectively. A total of 480 synthetic peptide variants were assessed for antileishmanial activity against Leishmania donovani. One hundred seventy-two peptide variants exhibited 50% inhibitory concentration (IC50) values below 20 μM against axenic amastigotes, with 60 peptide variants in the nanomolar range. Nine peptide variants exhibited potent activity against intracellular amastigotes with observed IC50 values of <4 μM and limited in vitro host cell toxicity, making them worthy of further drug development. Our work demonstrates that minimal bioactive domains of naturally existing bacteriocins can be synthetically engineered to increase membrane penetration against Leishmania spp. with minimal host cytotoxicity, holding the promise of novel, potent antileishmanial therapies. IMPORTANCE Leishmaniasis is a neglected tropical disease caused by protozoan parasites of the genus Leishmania. There are three primary clinical forms, cutaneous, mucocutaneous, and visceral, with visceral leishmaniasis being fatal if left untreated. Current drug treatments are less than ideal, especially in resource-limited areas, due to the difficult administration and treatment regimens as well as the high cost and the emergence of drug resistance. Identifying potent antileishmanial agents is of the utmost importance. We utilized rational design techniques to synthesize enterocin AS-48 and AS-48-like bacteriocin-based peptides and screened these peptides against L. donovani using a fluorescence-based phenotypic assay. Our results suggest that bacteriocins, specifically these rationally designed AS-48-like peptides, are promising leads for further development as antileishmanial drugs.
Collapse
Affiliation(s)
- Hannah N. Corman
- University of Notre Dame, Department of Biological Sciences, Notre Dame, Indiana, USA
- University of Notre Dame, Eck Institute for Global Health, Notre Dame, Indiana, USA
| | - Jessica N. Ross
- University of Notre Dame, Department of Biological Sciences, Notre Dame, Indiana, USA
- University of Notre Dame, Eck Institute for Global Health, Notre Dame, Indiana, USA
| | | | - Douglas A. Shoue
- University of Notre Dame, Department of Biological Sciences, Notre Dame, Indiana, USA
- University of Notre Dame, Eck Institute for Global Health, Notre Dame, Indiana, USA
| | - Mary Ann McDowell
- University of Notre Dame, Department of Biological Sciences, Notre Dame, Indiana, USA
- University of Notre Dame, Eck Institute for Global Health, Notre Dame, Indiana, USA
| | - Shaun W. Lee
- University of Notre Dame, Department of Biological Sciences, Notre Dame, Indiana, USA
- University of Notre Dame, Eck Institute for Global Health, Notre Dame, Indiana, USA
| |
Collapse
|
2
|
Lee S. Meet the Editorial Board Member. Curr Drug Targets 2022. [DOI: 10.2174/138945012307220430173248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- S. Lee
- University of Notre Dame Notre Dame, IN USA
| |
Collapse
|
3
|
Romero-Severson J, Moran TE, Shrader DG, Fields FR, Pandey-Joshi S, Thomas CL, Palmer EC, Shrout JD, Pfrender ME, Lee SW. A Seed-Endophytic Bacillus safensis Strain With Antimicrobial Activity Has Genes for Novel Bacteriocin-Like Antimicrobial Peptides. Front Microbiol 2021; 12:734216. [PMID: 34646254 PMCID: PMC8503640 DOI: 10.3389/fmicb.2021.734216] [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: 06/30/2021] [Accepted: 08/20/2021] [Indexed: 12/04/2022] Open
Abstract
Bacteriocins are a highly diverse group of antimicrobial peptides that have been identified in a wide range of commensal and probiotic organisms, especially those resident in host microbiomes. Rising antibiotic resistance have fueled renewed research into new drug scaffolds such as antimicrobial peptides for use in therapeutics. In this investigation, we examined mung bean seeds for endophytes possessing activity against human and plant pathogens. We isolated a novel strain of Bacillus safensis, from the contents of surface-sterilized mung bean seed, which we termed B. safensis C3. Genome sequencing of C3 identified three distinct biosynthetic systems that produce bacteriocin-based peptides. C3 exhibited antibacterial activity against Escherichia coli, Xanthomonas axonopodis, and Pseudomonas syringae. Robust antimicrobial activity of B. safensis C3 was observed when C3 was co-cultured with Bacillus subtilis. Using the cell-free supernatant of C3 and cation exchange chromatography, we enriched a product that retained antimicrobial activity against B. subtilis. The peptide was found to be approximately 3.3 kDa in size by mass spectrometry, and resistant to proteolysis by Carboxypeptidase Y and Endoproteinase GluC, suggesting that it is a modified variant of an AS-48 like bacteriocin. Our findings open new avenues into further development of novel bacteriocin-based scaffolds for therapeutic development, as well as further investigations into how our discoveries of bacteriocin-producing plant commensal microorganisms may have the potential for an immediate impact on the safety of food supplies.
Collapse
Affiliation(s)
- Jeanne Romero-Severson
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
| | - Thomas E Moran
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
| | - Donna G Shrader
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
| | - Francisco R Fields
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
| | - Susan Pandey-Joshi
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
| | - Clayton L Thomas
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
| | - Emily C Palmer
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States.,Department of Civil and Environmental Engineering, University of Notre Dame, Notre Dame, IN, United States
| | - Joshua D Shrout
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States.,Department of Civil and Environmental Engineering, University of Notre Dame, Notre Dame, IN, United States
| | - Michael E Pfrender
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
| | - Shaun W Lee
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
| |
Collapse
|
4
|
Rodríguez AA, Otero-González A, Ghattas M, Ständker L. Discovery, Optimization, and Clinical Application of Natural Antimicrobial Peptides. Biomedicines 2021; 9:1381. [PMID: 34680498 PMCID: PMC8533436 DOI: 10.3390/biomedicines9101381] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 09/28/2021] [Indexed: 12/12/2022] Open
Abstract
Antimicrobial peptides (AMPs) are widespread in multicellular organisms. These structurally diverse molecules are produced as the first line of defense against pathogens such as bacteria, viruses, fungi, and parasites. Also known as host defense peptides in higher eukaryotic organisms, AMPs display immunomodulatory and anticancer activities. During the last 30 years, technological advances have boosted the research on antimicrobial peptides, which have also attracted great interest as an alternative to tackling the antimicrobial resistance scenario mainly provoked by some bacterial and fungal pathogens. However, the introduction of natural AMPs in clinical trials faces challenges such as proteolytic digestion, short half-lives, and cytotoxicity upon systemic and oral application. Therefore, some strategies have been implemented to improve the properties of AMPs aiming to be used as effective therapeutic agents. In the present review, we summarize the discovery path of AMPs, focusing on preclinical development, recent advances in chemical optimization and peptide delivery systems, and their introduction into the market.
Collapse
Affiliation(s)
- Armando A. Rodríguez
- Core Facility for Functional Peptidomics, Ulm University Medical Center, 89081 Ulm, Germany
- Core Unit of Mass Spectrometry and Proteomics, Ulm University Medical Center, 89081 Ulm, Germany
| | | | - Maretchia Ghattas
- Faculty of Pharmacy and Biotechnology, German University in Cairo (GUC), Cairo 11511, Egypt;
| | - Ludger Ständker
- Core Facility for Functional Peptidomics, Ulm University Medical Center, 89081 Ulm, Germany
| |
Collapse
|
5
|
Vaca J, Ortiz A, Sansinenea E. Bacillus sp. Bacteriocins: Natural Weapons against Bacterial Enemies. Curr Med Chem 2021; 29:2093-2108. [PMID: 34047258 DOI: 10.2174/0929867328666210527093041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/08/2021] [Accepted: 04/13/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Currently, antibiotic-resistant pathogenic bacteria are emerging as an important health problem worldwide. The search for new compounds with antibiotic characteristics is the most promising alternative. Bacteriocins are natural compounds that are inhibitory against pathogens, and Bacillus species are the major producers of these compounds, which have shown antimicrobial activity against clinically important bacteria. These peptides not only have potential in the pharmaceutical industry but also in food and agricultural sectors. OBJECTIVE We provide an overview of the recent bacteriocins isolated from different species of Bacillus including their applications and the older bacteriocins. RESULTS In this review, we have revised some works about the improvements carried out in the production of bacteriocins. CONCLUSION These applications make bacteriocins very promising compounds that need to study for industrial production.
Collapse
Affiliation(s)
- Jessica Vaca
- Facultad De Ciencias Químicas, Benemérita Universidad Autónoma De Puebla, 72590 Puebla; Pue, Mexico
| | - Aurelio Ortiz
- Facultad De Ciencias Químicas, Benemérita Universidad Autónoma De Puebla, 72590 Puebla; Pue, Mexico
| | - Estibaliz Sansinenea
- Facultad De Ciencias Químicas, Benemérita Universidad Autónoma De Puebla, 72590 Puebla; Pue, Mexico
| |
Collapse
|
6
|
Lee S. Meet Our Editorial Board Member. Curr Drug Targets 2021. [DOI: 10.2174/138945012207210316111310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- S. Lee
- University of Notre Dame Notre Dame, IN,United States
| |
Collapse
|
7
|
Ross JN, Fields FR, Kalwajtys VR, Gonzalez AJ, O’Connor S, Zhang A, Moran TE, Hammers DE, Carothers KE, Lee SW. Synthetic Peptide Libraries Designed From a Minimal Alpha-Helical Domain of AS-48-Bacteriocin Homologs Exhibit Potent Antibacterial Activity. Front Microbiol 2020; 11:589666. [PMID: 33281785 PMCID: PMC7689250 DOI: 10.3389/fmicb.2020.589666] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/08/2020] [Indexed: 12/28/2022] Open
Abstract
The circularized bacteriocin enterocin AS-48 produced by Enterococcus sp. exhibits antibacterial activity through membrane disruption. The membrane-penetrating activity of enterocin AS-48 has been attributed to a specific alpha-helical region on the circular peptide. Truncated, linearized forms containing these domains have been shown to preserve limited bactericidal activity. We utilized the amino acid sequence of the active helical domain of enterocin AS-48 to perform a homology-based search of similar sequences in other bacterial genomes. We identified similar domains in three previously uncharacterized AS-48-like bacteriocin genes in Clostridium sordellii, Paenibacillus larvae, and Bacillus xiamenensis. Enterocin AS-48 and homologs from these bacterial species were used as scaffolds for the design of a minimal peptide library based on the active helical domain of each bacteriocin sequence. 95 synthetic peptide variants of each scaffold peptide, designated Syn-enterocin, Syn-sordellicin, Syn-larvacin, and Syn-xiamensin, were designed and synthesized from each scaffold sequence based on defined biophysical parameters. A total of 384 total peptides were assessed for antibacterial activity against Gram-negative and Gram-positive bacteria. Minimal Inhibitory Concentrations (MICs) as low as 15.6 nM could be observed for the most potent peptide candidate tested, with no significant cytotoxicity to eukaryotic cells. Our work demonstrates for the first time a general workflow of using minimal domains of natural bacteriocin sequences as scaffolds to design and rapidly synthesize a library of bacteriocin-based antimicrobial peptide variants for evaluation.
Collapse
Affiliation(s)
- Jessica N. Ross
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
| | - Francisco R. Fields
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
| | - Veronica R. Kalwajtys
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
| | - Alejandro J. Gonzalez
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
| | - Samantha O’Connor
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States
| | - Angela Zhang
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
| | - Thomas E. Moran
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
| | - Daniel E. Hammers
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, United States
| | - Katelyn E. Carothers
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, United States
| | - Shaun W. Lee
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, United States
| |
Collapse
|
8
|
LHH1, a novel antimicrobial peptide with anti-cancer cell activity identified from Lactobacillus casei HZ1. AMB Express 2020; 10:204. [PMID: 33175275 PMCID: PMC7658291 DOI: 10.1186/s13568-020-01139-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 10/27/2020] [Indexed: 12/18/2022] Open
Abstract
Antimicrobial peptides have been attracting increasing attention for their multiple beneficial effects. In present study, a novel AMP with a molecular weight of 1875.5 Da, was identified from the genome of Lactobacillus casei HZ1. The peptide, which was named as LHH1 was comprised of 16 amino acid residues, and its α-helix content was 95.34% when dissolved in 30 mM SDS. LHH1 exhibited a broad range of antimicrobial activities against Gram-positive bacteria and fungus. It could effectively inhibit Staphylococcus aureus with a minimum inhibitory concentration of 3.5 μM and showed a low hemolytic activity. The scanning electron microscope, confocal laser scanning microscope and flow cytometry results showed that LHH1 exerted its antibacterial activity by damaging the cell membrane of Staphylococcus aureus. Meanwhile, LHH1 also exhibited anti-cancer cell activities against several cancer cells via breaking the cell membrane of MGC803, HCT116 and C666-1 cancer cells.
Collapse
|
9
|
Browne K, Chakraborty S, Chen R, Willcox MDP, Black DS, Walsh WR, Kumar N. A New Era of Antibiotics: The Clinical Potential of Antimicrobial Peptides. Int J Mol Sci 2020; 21:E7047. [PMID: 32987946 PMCID: PMC7582481 DOI: 10.3390/ijms21197047] [Citation(s) in RCA: 207] [Impact Index Per Article: 51.8] [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: 09/22/2020] [Accepted: 09/22/2020] [Indexed: 12/13/2022] Open
Abstract
Antimicrobial resistance is a multifaceted crisis, imposing a serious threat to global health. The traditional antibiotic pipeline has been exhausted, prompting research into alternate antimicrobial strategies. Inspired by nature, antimicrobial peptides are rapidly gaining attention for their clinical potential as they present distinct advantages over traditional antibiotics. Antimicrobial peptides are found in all forms of life and demonstrate a pivotal role in the innate immune system. Many antimicrobial peptides are evolutionarily conserved, with limited propensity for resistance. Additionally, chemical modifications to the peptide backbone can be used to improve biological activity and stability and reduce toxicity. This review details the therapeutic potential of peptide-based antimicrobials, as well as the challenges needed to overcome in order for clinical translation. We explore the proposed mechanisms of activity, design of synthetic biomimics, and how this novel class of antimicrobial compound may address the need for effective antibiotics. Finally, we discuss commercially available peptide-based antimicrobials and antimicrobial peptides in clinical trials.
Collapse
Affiliation(s)
- Katrina Browne
- School of Chemistry, University of New South Wales (UNSW) Sydney, Sydney 2052, Australia; (K.B.); (S.C.); (R.C.)
| | - Sudip Chakraborty
- School of Chemistry, University of New South Wales (UNSW) Sydney, Sydney 2052, Australia; (K.B.); (S.C.); (R.C.)
| | - Renxun Chen
- School of Chemistry, University of New South Wales (UNSW) Sydney, Sydney 2052, Australia; (K.B.); (S.C.); (R.C.)
| | - Mark DP Willcox
- School of Optometry and Vision Science, University of New South Wales (UNSW) Sydney, Sydney 2052, Australia;
| | - David StClair Black
- School of Chemistry, University of New South Wales (UNSW) Sydney, Sydney 2052, Australia; (K.B.); (S.C.); (R.C.)
| | - William R Walsh
- Surgical and Orthopaedic Research Laboratories (SORL), Prince of Wales Clinical School, Prince of Wales Hospital, University of New South Wales (UNSW), Randwick 2031, Australia;
| | - Naresh Kumar
- School of Chemistry, University of New South Wales (UNSW) Sydney, Sydney 2052, Australia; (K.B.); (S.C.); (R.C.)
| |
Collapse
|
10
|
Toushik SH, Mizan MFR, Hossain MI, Ha SD. Fighting with old foes: The pledge of microbe-derived biological agents to defeat mono- and mixed-bacterial biofilms concerning food industries. Trends Food Sci Technol 2020. [DOI: 10.1016/j.tifs.2020.03.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
11
|
Fields FR, Manzo G, Hind CK, Janardhanan J, Foik IP, Carmo Silva PD, Balsara RD, Clifford M, Vu HM, Ross JN, Kalwajtys VR, Gonzalez AJ, Bui TT, Ploplis VA, Castellino FJ, Siryaporn A, Chang M, Sutton JM, Mason AJ, Lee S. Synthetic Antimicrobial Peptide Tuning Permits Membrane Disruption and Interpeptide Synergy. ACS Pharmacol Transl Sci 2020; 3:418-424. [PMID: 32566907 DOI: 10.1021/acsptsci.0c00001] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Indexed: 12/19/2022]
Abstract
The ribosomally produced antimicrobial peptides of bacteria (bacteriocins) represent an unexplored source of membrane-active antibiotics. We designed a library of linear peptides from a circular bacteriocin and show that pore-formation dynamics in bacterial membranes are tunable via selective amino acid substitution. We observed antibacterial interpeptide synergy indicating that fundamentally altering interactions with the membrane enables synergy. Our findings suggest an approach for engineering pore-formation through rational peptide design and increasing the utility of novel antimicrobial peptides by exploiting synergy.
Collapse
Affiliation(s)
- Francisco R Fields
- Department of Biology, University of Notre Dame, Notre Dame, Indiana 46556, United States.,Eck Institute of Global Health, University of Notre Dame, Notre Dame, Indiana 46556, United States.,Chemistry Biology Biochemistry Interface, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Giorgia Manzo
- Institue of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
| | - Charlotte K Hind
- Technology Development Group, National Infection Service, Public Health England, Salisbury SP4 0JG, U.K
| | - Jeshina Janardhanan
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Ilona P Foik
- Department of Physics and Astronomy, University of California Irvine, Irvine, California 92697, United States
| | - Phoebe Do Carmo Silva
- Technology Development Group, National Infection Service, Public Health England, Salisbury SP4 0JG, U.K
| | - Rashna D Balsara
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States.,W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Melanie Clifford
- Technology Development Group, National Infection Service, Public Health England, Salisbury SP4 0JG, U.K
| | - Henry M Vu
- Department of Biology, University of Notre Dame, Notre Dame, Indiana 46556, United States.,W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Jessica N Ross
- Department of Biology, University of Notre Dame, Notre Dame, Indiana 46556, United States.,Eck Institute of Global Health, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Veronica R Kalwajtys
- Department of Biology, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Alejandro J Gonzalez
- Department of Biology, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Tam T Bui
- Centre for Biomolecular Spectroscopy and Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, London SE1 1UL, United Kingdom
| | - Victoria A Ploplis
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States.,W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Francis J Castellino
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States.,W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Albert Siryaporn
- Department of Physics and Astronomy, University of California Irvine, Irvine, California 92697, United States.,Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, California 92697, United States
| | - Mayland Chang
- Chemistry Biology Biochemistry Interface, University of Notre Dame, Notre Dame, Indiana 46556, United States.,Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - J Mark Sutton
- Technology Development Group, National Infection Service, Public Health England, Salisbury SP4 0JG, U.K
| | - A James Mason
- Institue of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
| | - Shaun Lee
- Department of Biology, University of Notre Dame, Notre Dame, Indiana 46556, United States.,Eck Institute of Global Health, University of Notre Dame, Notre Dame, Indiana 46556, United States.,Chemistry Biology Biochemistry Interface, University of Notre Dame, Notre Dame, Indiana 46556, United States
| |
Collapse
|
12
|
Ying Y, Wang H, Xi X, Ma C, Liu Y, Zhou M, Du Q, Burrows JF, Wei M, Chen T, Wang L. Design of N-Terminal Derivatives from a Novel Dermaseptin Exhibiting Broad-Spectrum Antimicrobial Activity against Isolates from Cystic Fibrosis Patients. Biomolecules 2019; 9:biom9110646. [PMID: 31653005 PMCID: PMC6920804 DOI: 10.3390/biom9110646] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 10/21/2019] [Accepted: 10/23/2019] [Indexed: 12/13/2022] Open
Abstract
Dermaseptins are an antimicrobial peptide family widely identified from the skin secretions of phyllomeudusinae frogs. Here, we identify Dermaseptin-PC (DM-PC), from the skin secretion of Phyllomedusa coelestis, and further investigate the properties of this peptide, and a number of rationally designed truncated derivatives. The truncated 19-mer derived from the N-terminus exhibited similar antimicrobial potency when compared to the parent peptide, but the haemolytic effect of this truncated peptide was significantly decreased. Based on previous studies, the charge and hydrophobicity of truncated derivatives can affect the bioactivity of these peptides and thus we designed a 10-mer derivative with an optimised positive charge and a cyclohexylalanine (Cha) at the C-terminus for enhancing the hydrophobicity, DMPC-10A, which retained the antimicrobial activity of the parent peptide. To further investigate the influence of Cha at the C-terminus on activity, it was substituted by alanine (Ala) to generate another derivative, DMPC-10, but this was found to be much less potent. In addition, DM-PC, DMPC-19 and DMPC-10A not only rapidly killed planktonic bacteria isolated from cystic fibrosis (CF) patient, but also effectively eradicated their biofilm matrices.
Collapse
Affiliation(s)
- Yuan Ying
- School of Pharmacy, China Medical University, Shenyang 110001, China.
- Natural Drug Discovery Group, School of Pharmacy, Queen's University Belfast, Belfast BT9 7BL, Northern Ireland, UK.
| | - Hui Wang
- School of Pharmacy, China Medical University, Shenyang 110001, China.
| | - Xinping Xi
- Natural Drug Discovery Group, School of Pharmacy, Queen's University Belfast, Belfast BT9 7BL, Northern Ireland, UK.
| | - Chengbang Ma
- Natural Drug Discovery Group, School of Pharmacy, Queen's University Belfast, Belfast BT9 7BL, Northern Ireland, UK.
| | - Yue Liu
- Natural Drug Discovery Group, School of Pharmacy, Queen's University Belfast, Belfast BT9 7BL, Northern Ireland, UK.
| | - Mei Zhou
- Natural Drug Discovery Group, School of Pharmacy, Queen's University Belfast, Belfast BT9 7BL, Northern Ireland, UK.
| | - Qiang Du
- School of Pharmacy, China Medical University, Shenyang 110001, China.
| | - James F Burrows
- Natural Drug Discovery Group, School of Pharmacy, Queen's University Belfast, Belfast BT9 7BL, Northern Ireland, UK.
| | - Minjie Wei
- School of Pharmacy, China Medical University, Shenyang 110001, China.
| | - Tianbao Chen
- Natural Drug Discovery Group, School of Pharmacy, Queen's University Belfast, Belfast BT9 7BL, Northern Ireland, UK.
| | - Lei Wang
- Natural Drug Discovery Group, School of Pharmacy, Queen's University Belfast, Belfast BT9 7BL, Northern Ireland, UK.
| |
Collapse
|
13
|
Fields FR, Freed SD, Carothers KE, Hamid MN, Hammers DE, Ross JN, Kalwajtys VR, Gonzalez AJ, Hildreth AD, Friedberg I, Lee SW. Novel antimicrobial peptide discovery using machine learning and biophysical selection of minimal bacteriocin domains. Drug Dev Res 2019; 81:43-51. [PMID: 31483516 DOI: 10.1002/ddr.21601] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 05/17/2019] [Accepted: 08/20/2019] [Indexed: 02/06/2023]
Abstract
Bacteriocins, the ribosomally produced antimicrobial peptides of bacteria, represent an untapped source of promising antibiotic alternatives. However, bacteriocins display diverse mechanisms of action, a narrow spectrum of activity, and inherent challenges in natural product isolation making in vitro verification of putative bacteriocins difficult. A subset of bacteriocins exert their antimicrobial effects through favorable biophysical interactions with the bacterial membrane mediated by the charge, hydrophobicity, and conformation of the peptide. We have developed a pipeline for bacteriocin-derived compound design and testing that combines sequence-free prediction of bacteriocins using machine learning and a simple biophysical trait filter to generate 20 amino acid peptides that can be synthesized and evaluated for activity. We generated 28,895 total 20-mer candidate peptides and scored them for charge, α-helicity, and hydrophobic moment. Of those, we selected 16 sequences for synthesis and evaluated their antimicrobial, cytotoxicity, and hemolytic activities. Peptides with the overall highest scores for our biophysical parameters exhibited significant antimicrobial activity against Escherichia coli and Pseudomonas aeruginosa. Our combined method incorporates machine learning and biophysical-based minimal region determination to create an original approach to swiftly discover bacteriocin candidates amenable to rapid synthesis and evaluation for therapeutic use.
Collapse
Affiliation(s)
- Francisco R Fields
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana.,Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana.,Chemistry-Biochemistry-Biology Interface Program, University of Notre Dame, Notre Dame, Indiana
| | - Stefan D Freed
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana.,Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana.,Chemistry-Biochemistry-Biology Interface Program, University of Notre Dame, Notre Dame, Indiana
| | - Katelyn E Carothers
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana.,Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana
| | - Md Nafiz Hamid
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, Iowa.,Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa
| | - Daniel E Hammers
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana.,Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana
| | - Jessica N Ross
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana.,Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana
| | - Veronica R Kalwajtys
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana
| | - Alejandro J Gonzalez
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana
| | - Andrew D Hildreth
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana
| | - Iddo Friedberg
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, Iowa.,Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa
| | - Shaun W Lee
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana.,Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana.,Chemistry-Biochemistry-Biology Interface Program, University of Notre Dame, Notre Dame, Indiana
| |
Collapse
|
14
|
Ben Braïek O, Smaoui S. Enterococci: Between Emerging Pathogens and Potential Probiotics. BIOMED RESEARCH INTERNATIONAL 2019; 2019:5938210. [PMID: 31240218 PMCID: PMC6556247 DOI: 10.1155/2019/5938210] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 04/06/2019] [Accepted: 05/14/2019] [Indexed: 11/17/2022]
Abstract
Enterococci are ubiquitous microorganisms that could be found everywhere; in water, plant, soil, foods, and gastrointestinal tract of humans and animals. They were previously used as starters in food fermentation due to their biotechnological traits (enzymatic and proteolytic activities) or protective cultures in food biopreservation due to their produced antimicrobial bacteriocins called enterocins or as probiotics, live cells with different beneficial characteristics such as stimulation of immunity, anti-inflammatory activity, hypocholesterolemic effect, and prevention/treatment of some diseases. However, in the last years, the use of enterococci in foods or as probiotics caused an important debate because of their opportunistic pathogenicity implicated in several nosocomial infections due to virulence factors and antibiotic resistance, particularly the emergence of vancomycin-resistant enterococci. These virulence traits of some enterococci are associated with genetic transfer mechanisms. Therefore, the development of new enterococcal probiotics needs a strict assessment with regard to safety aspects for selecting the truly harmless enterococcal strains for safe applications. This review tries to give some data of the different points of view about this question.
Collapse
Affiliation(s)
- Olfa Ben Braïek
- Laboratory of Transmissible Diseases and Biologically Active Substances (LR99ES27), Faculty of Pharmacy, University of Monastir, Tunisia
| | - Slim Smaoui
- Laboratory of Microorganisms and Biomolecules of the Centre of Biotechnology of Sfax, Tunisia
| |
Collapse
|