1
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Sara M, Yasir M, Kalaiselvan P, Hui A, Kuppusamy R, Kumar N, Chakraborty S, Yu TT, Wong EHH, Molchanova N, Jenssen H, Lin JS, Barron AE, Willcox M. The activity of antimicrobial peptoids against multidrug-resistant ocular pathogens. Cont Lens Anterior Eye 2024; 47:102124. [PMID: 38341309 PMCID: PMC11024869 DOI: 10.1016/j.clae.2024.102124] [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: 07/27/2023] [Revised: 01/11/2024] [Accepted: 02/04/2024] [Indexed: 02/12/2024]
Abstract
BACKGROUND Ocular infections caused by antibiotic-resistant pathogens can result in partial or complete vision loss. The development of pan-resistant microbial strains poses a significant challenge for clinicians as there are limited antimicrobial options available. Synthetic peptoids, which are sequence-specific oligo-N-substituted glycines, offer potential as alternative antimicrobial agents to target multidrug-resistant bacteria. METHODS The antimicrobial activity of synthesised peptoids against multidrug-resistant (MDR) ocular pathogens was evaluated using the microbroth dilution method. Hemolytic propensity was assessed using mammalian erythrocytes. Peptoids were also incubated with proteolytic enzymes, after which their minimum inhibitory activity against bacteria was re-evaluated. RESULTS Several alkylated and brominated peptoids showed good inhibitory activity against multidrug-resistant Pseudomonas aeruginosa strains at concentrations of ≤15 μg mL-1 (≤12 µM). Similarly, most brominated compounds inhibited the growth of methicillin-resistant Staphylococcus aureus at 1.9 to 15 μg mL-1 (12 µM). The N-terminally alkylated peptoids caused less toxicity to erythrocytes. The peptoid denoted as TM5 had a high therapeutic index, being non-toxic to either erythrocytes or corneal epithelial cells, even at 15 to 22 times its MIC. Additionally, the peptoids were resistant to protease activity. CONCLUSIONS Peptoids studied here demonstrated potent activity against various multidrug-resistant ocular pathogens. Their properties make them promising candidates for controlling vision-related morbidity associated with eye infections by antibiotic-resistant strains.
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Affiliation(s)
- Manjulatha Sara
- School of Optometry and Vision Science, UNSW Sydney, Australia.
| | - Muhammad Yasir
- School of Optometry and Vision Science, UNSW Sydney, Australia
| | | | - Alex Hui
- School of Optometry and Vision Science, UNSW Sydney, Australia; Centre for Ocular Research and Education, University of Waterloo, Canada
| | - Rajesh Kuppusamy
- School of Optometry and Vision Science, UNSW Sydney, Australia; School of Chemistry, UNSW Sydney, Australia
| | | | | | - Tsz Tin Yu
- School of Chemistry, UNSW Sydney, Australia
| | | | - Natalia Molchanova
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 4720, USA
| | - Håvard Jenssen
- Department of Science and Environment, Roskilde University, 4000 Roskilde, Denmark
| | - Jennifer S Lin
- Department of Bioengineering, School of Medicine & School of Engineering, Stanford University, Stanford, CA 9430, USA
| | - Annelise E Barron
- Department of Bioengineering, School of Medicine & School of Engineering, Stanford University, Stanford, CA 9430, USA
| | - Mark Willcox
- School of Optometry and Vision Science, UNSW Sydney, Australia.
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2
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Figgins EL, Arora P, Gao D, Porcelli E, Ahmed R, Daep CA, Keele G, Ryan LK, Diamond G. Enhancement of innate immunity in gingival epithelial cells by vitamin D and HDAC inhibitors. FRONTIERS IN ORAL HEALTH 2024; 5:1378566. [PMID: 38567313 PMCID: PMC10986367 DOI: 10.3389/froh.2024.1378566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 03/05/2024] [Indexed: 04/04/2024] Open
Abstract
Introduction The human host defense peptide LL-37 is a component of the innate immune defense mechanisms of the oral cavity against colonization by microbes associated with periodontal disease. We have previously shown that the active form of vitamin D, 1,25(OH)2D3, can induce the expression of LL-37 in gingival epithelial cells (GEC), and prevent the invasion and growth of periopathogenic bacteria in these cells. Further, experimental vitamin D deficiency resulted in increased gingival inflammation and alveolar bone loss. Epidemiological studies have shown associations between vitamin D deficiency and periodontal disease in humans, suggesting application of vitamin D could be a useful therapeutic approach. Further, since we have shown the local activation of vitamin D by enzymes expressed in the GEC, we hypothesized that we could observe this enhancement with the stable, and inexpensive inactive form of vitamin D, which could be further increased with epigenetic regulators. Methods We treated 3-dimensional primary cultures of GEC topically with the inactive form of vitamin D, in the presence and absence of selected histone deacetylase (HDAC) inhibitors. LL-37 mRNA levels were quantified by quantitative RT-PCR, and inhibition of invasion of bacteria was measured by fluorescence microscopy. Results Vitamin D treatment led to an induction of LL-37 mRNA levels, as well as an inhibition of pro-inflammatory cytokine secretion. This effect was further enhanced by HDAC inhibitors, most strongly when the HDAC inhibitor, phenyl butyrate (PBA) was combined with Vitamin D3. This was observed both in solution and in a prototype gel formulation using sodium butyrate. Finally, this combination treatment led to an increase in the antimicrobial activity against infection by Porphyromonas gingivalis and Filifactor alocis, bacteria associated with periodontal lesions, as well as herpes simplex virus, which has also been shown to be associated with periodontal lesions. Conclusions Our results demonstrate that a combination of inactive vitamin D and sodium butyrate could be developed as a safe treatment for periodontal disease.
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Affiliation(s)
- Erika L. Figgins
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, FL, United States
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, KY, United States
| | - Payal Arora
- Global Technology Center, Colgate Palmolive Company, Piscataway, NJ, United States
| | - Denny Gao
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, KY, United States
| | - Emily Porcelli
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, FL, United States
| | - Rabab Ahmed
- Global Technology Center, Colgate Palmolive Company, Piscataway, NJ, United States
| | - Carlo Amorin Daep
- Global Technology Center, Colgate Palmolive Company, Piscataway, NJ, United States
| | - Garrett Keele
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, KY, United States
| | - Lisa K. Ryan
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, KY, United States
- Division of Infectious Disease and Global Medicine, Department of Medicine, University of Florida College of Medicine, Gainesville, FL, United States
- Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, University of Louisville, Louisville, KY, United States
| | - Gill Diamond
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, FL, United States
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, KY, United States
- Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, University of Louisville, Louisville, KY, United States
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3
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Murayama A, Igarashi H, Yamada N, Aly HH, Molchanova N, Lin JS, Nishitsuji H, Shimotohno K, Muramatsu M, Barron AE, Kato T. Antiviral effect of peptoids on hepatitis B virus infection in cell culture. Antiviral Res 2024; 223:105821. [PMID: 38272318 PMCID: PMC10939774 DOI: 10.1016/j.antiviral.2024.105821] [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: 11/08/2023] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 01/27/2024]
Abstract
Although antimicrobial peptides have been shown to inactivate viruses through disruption of their viral envelopes, clinical use of such peptides has been hampered by a number of factors, especially their enzymatically unstable structures. To overcome the shortcomings of antimicrobial peptides, peptoids (sequence-specific N-substituted glycine oligomers) mimicking antimicrobial peptides have been developed. We aimed to demonstrate the antiviral effects of antimicrobial peptoids against hepatitis B virus (HBV) in cell culture. The anti-HBV activity of antimicrobial peptoids was screened and evaluated in an infection system involving the HBV reporter virus and HepG2.2.15-derived HBV. By screening with the HBV reporter virus infection system, three (TM1, TM4, and TM19) of 12 peptoids were identified as reducing the infectivity of HBV, though they did not alter the production levels of HBs antigen in cell culture. These peptoids were not cytotoxic at the evaluated concentrations. Among these peptoids, TM19 was confirmed to reduce HBV infection most potently in a HepG2.2.15-derived HBV infection system that closely demonstrates authentic HBV infection. In cell culture, the most effective administration of TM19 was virus treatment at the infection step, but the reduction in HBV infectivity by pre-treatment or post-treatment of cells with TM19 was minimal. The disrupting effect of TM19 targeting infectious viral particles was clarified in iodixanol density gradient analysis. In conclusion, the peptoid TM19 was identified as a potent inhibitor of HBV. This peptoid prevents HBV infection by disrupting viral particles and is a candidate for a new class of anti-HBV reagents.
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Affiliation(s)
- Asako Murayama
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hitomi Igarashi
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Norie Yamada
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hussein Hassan Aly
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Natalia Molchanova
- Department of Bioengineering, Stanford University School of Medicine & School of Engineering, Stanford, CA, 94305, USA
| | - Jennifer S Lin
- Department of Bioengineering, Stanford University School of Medicine & School of Engineering, Stanford, CA, 94305, USA
| | - Hironori Nishitsuji
- Department of Virology, Fujita Health University School of Medicine, Aichi, Japan
| | - Kunitada Shimotohno
- Genome Medical Sciences Project, National Center for Global Health and Medicine, Chiba, Japan
| | - Masamichi Muramatsu
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan; Department of Infectious Disease Research, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Japan
| | - Annelise E Barron
- Department of Bioengineering, Stanford University School of Medicine & School of Engineering, Stanford, CA, 94305, USA
| | - Takanobu Kato
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan.
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4
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Zhao W, Lin JS, Nielsen JE, Sørensen K, Wadurkar AS, Ji J, Barron AE, Nangia S, Libera MR. Supramolecular Peptoid Structure Strengthens Complexation with Polyacrylic Acid Microgels. Biomacromolecules 2024; 25:1274-1281. [PMID: 38240722 PMCID: PMC11046531 DOI: 10.1021/acs.biomac.3c01242] [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] [Indexed: 02/13/2024]
Abstract
We have studied the complexation between cationic antimicrobials and polyanionic microgels to create self-defensive surfaces that responsively resist bacterial colonization. An essential property is the stable sequestration of the loaded (complexed) antimicrobial within the microgel under a physiological ionic strength. Here, we assess the complexation strength between poly(acrylic acid) [PAA] microgels and a series of cationic peptoids that display supramolecular structures ranging from an oligomeric monomer to a tetramer. We follow changes in loaded microgel diameter with increasing [Na+] as a measure of the counterion doping level. Consistent with prior findings on colistin/PAA complexation, we find that a monomeric peptoid is fully released at ionic strengths well below physiological conditions, despite its +5 charge. In contrast, progressively higher degrees of peptoid supramolecular structure display progressively greater resistance to salting out, which we attribute to the greater entropic stability associated with the complexation of multimeric peptoid bundles.
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Affiliation(s)
- Wenhan Zhao
- Department of Chemical Engineering and Materials Science, Stevens Institute of Technology, Hoboken, New Jersey 07030, United States
| | - Jennifer S Lin
- Department of Bioengineering, School of Medicine & School of Engineering, Stanford University, Stanford, California 94305, United States
| | - Josefine Eilsø Nielsen
- Department of Bioengineering, School of Medicine & School of Engineering, Stanford University, Stanford, California 94305, United States
- Department of Science and Environment, Roskilde University, Roskilde DK-4000, Denmark
| | - Kristian Sørensen
- Department of Bioengineering, School of Medicine & School of Engineering, Stanford University, Stanford, California 94305, United States
| | - Anand Sunil Wadurkar
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States
| | - Jingjing Ji
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States
| | - Annelise E Barron
- Department of Bioengineering, School of Medicine & School of Engineering, Stanford University, Stanford, California 94305, United States
| | - Shikha Nangia
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States
| | - Matthew R Libera
- Department of Chemical Engineering and Materials Science, Stevens Institute of Technology, Hoboken, New Jersey 07030, United States
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5
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Nittayananta W, Lerdsamran H, Chutiwitoonchai N, Promsong A, Srichana T, Netsomboon K, Prasertsopon J, Kerdto J. A novel film spray containing curcumin inhibits SARS-CoV-2 and influenza virus infection and enhances mucosal immunity. Virol J 2024; 21:26. [PMID: 38263162 PMCID: PMC10807123 DOI: 10.1186/s12985-023-02282-x] [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: 11/01/2023] [Accepted: 12/29/2023] [Indexed: 01/25/2024] Open
Abstract
BACKGROUND Infection by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and influenza virus is still a major worldwide health concern. Plants are a good source of bioactive compounds to be used as preventive measures for both inhibiting the virus binding and enhancing mucosal innate immunity. Curcumin has been shown to possess antiviral activity and modulate innate immunity. Therefore, the purpose of this study was to develop an oro-nasal film spray containing curcumin and determine its antiviral activity against SARS-CoV-2 and influenza virus infection, as well as its effects on mucosal innate immunity and inflammatory cytokines in vitro. METHODS The antiviral activity of the film spray against SARS-CoV-2, influenza A/H1N1, A/H3N2, and influenza B was assessed in vitro by plaque reduction assay. Cytotoxicity of the film spray to oral keratinocytes and nasal epithelial cells was assessed by MTT assay, and cytotoxicity to Vero and MDCK cells was assessed by an MTS-based cytotoxicity assay. Oral and nasal innate immune markers in response to the film spray were determined by ELISA and by a commercial Milliplex Map Kit, respectively. RESULTS Our data show that the film spray containing curcumin can inhibit both SARS-CoV-2 and influenza virus infections while maintaining cell viability. Results obtained among 4 viruses revealed that curcumin film spray demonstrated the highest inhibitory activity against SARS-CoV-2 with the lowest EC50 of 3.15 µg/ml and the highest SI value of 4.62, followed by influenza B (EC50 = 6.32 µg/ml, SI = 2.04), influenza A/H1N1 (EC50 = 7.24 µg/ml, SI = 1.78), and influenza A/H3N2 (EC50 > 12.5 µg/ml, SI < 1.03), respectively. Antimicrobial peptides LL-37 and HD-5, IL-6 and TNF-α produced by oral keratinocytes were significantly induced by the film spray, while hBD2 was significantly reduced. CONCLUSION Film spray containing curcumin possesses multiple actions against SARS-CoV-2 infection by inhibiting ACE-2 binding in target cells and enhancing mucosal innate immunity. The film spray can also inhibit influenza virus infection. Therefore, the curcumin film spray may be effective in preventing the viral infection of both SARS-CoV-2 and influenza.
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Affiliation(s)
| | - Hatairat Lerdsamran
- Center for Research Innovation and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Nakhon Pathom, Thailand
| | - Nopporn Chutiwitoonchai
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Aornrutai Promsong
- Faculty of Medicine, Princess of Naradhiwas University, Narathiwat, Thailand
| | - Teerapol Srichana
- Drug Delivery System Excellence Center, Faculty of Pharmaceutical Sciences, Prince of Songkla University, Hat Yai, Songkhla, Thailand
- Department of Pharmaceutical Technology, Faculty of Pharmaceutical Sciences, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | | | - Jarunee Prasertsopon
- Center for Research Innovation and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Nakhon Pathom, Thailand
| | - Jaruta Kerdto
- Thammasat Hospital, Thammasat University, Pathum Thani, Thailand
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6
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Jain RK, Hall CK, Santiso EE. Using Enhanced Sampling Simulations to Study the Conformational Space of Chiral Aromatic Peptoid Monomers. J Chem Theory Comput 2023; 19:9457-9467. [PMID: 37937823 DOI: 10.1021/acs.jctc.3c00803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
Peptoids, or N-substituted glycines, are peptide-like materials that form a wide variety of secondary structures owing to their enhanced flexibility and a diverse collection of possible side chains. Compared to that of peptides, peptoids have a substantially more complex conformational landscape. This is mainly due to the ability of the peptoid amide bond to exist in both cis- and trans-conformations. This makes conventional molecular dynamics simulations and even some enhanced sampling approaches unable to sample the complete energy landscapes. In this article, we present an extension to the CGenFF-NTOID peptoid atomistic forcefield by adding parameters for four side chains to the previously available collection. We employ explicit solvent well-tempered metadynamics simulations to optimize our forcefield parameters and parallel bias metadynamics to study the cis-trans isomerism for SN1-phenylethyl (s1pe) and SN1-naphthylethyl (s1ne) peptoid monomers, the free energy minima generated from which are validated with available experimental data. In the absence of experimental data, we supported our atomistic simulations with ab initio calculations. This work represents an important step toward the computational design of peptoid-based materials.
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Affiliation(s)
- Rakshit Kumar Jain
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27606, United States
| | - Carol K Hall
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27606, United States
| | - Erik E Santiso
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27606, United States
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7
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Tate P, Mastrodomenico V, Cunha C, McClure J, Barron AE, Diamond G, Mounce BC, Kirshenbaum K. Peptidomimetic Oligomers Targeting Membrane Phosphatidylserine Exhibit Broad Antiviral Activity. ACS Infect Dis 2023; 9:1508-1522. [PMID: 37530426 PMCID: PMC10425984 DOI: 10.1021/acsinfecdis.3c00063] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Indexed: 08/03/2023]
Abstract
The development of durable new antiviral therapies is challenging, as viruses can evolve rapidly to establish resistance and attenuate therapeutic efficacy. New compounds that selectively target conserved viral features are attractive therapeutic candidates, particularly for combating newly emergent viral threats. The innate immune system features a sustained capability to combat pathogens through production of antimicrobial peptides (AMPs); however, these AMPs have shortcomings that can preclude clinical use. The essential functional features of AMPs have been recapitulated by peptidomimetic oligomers, yielding effective antibacterial and antifungal agents. Here, we show that a family of AMP mimetics, called peptoids, exhibit direct antiviral activity against an array of enveloped viruses, including the key human pathogens Zika, Rift Valley fever, and chikungunya viruses. These data suggest that the activities of peptoids include engagement and disruption of viral membrane constituents. To investigate how these peptoids target lipid membranes, we used liposome leakage assays to measure membrane disruption. We found that liposomes containing phosphatidylserine (PS) were markedly sensitive to peptoid treatment; in contrast, liposomes formed exclusively with phosphatidylcholine (PC) showed no sensitivity. In addition, chikungunya virus containing elevated envelope PS was more susceptible to peptoid-mediated inactivation. These results indicate that peptoids mimicking the physicochemical characteristics of AMPs act through a membrane-specific mechanism, most likely through preferential interactions with PS. We provide the first evidence for the engagement of distinct viral envelope lipid constituents, establishing an avenue for specificity that may enable the development of a new family of therapeutics capable of averting the rapid development of resistance.
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Affiliation(s)
- Patrick
M. Tate
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - Vincent Mastrodomenico
- Department
of Microbiology and Immunology, Loyola University
Chicago Medical Center, Maywood, Illinois 60130, United States
| | - Christina Cunha
- Department
of Microbiology and Immunology, Loyola University
Chicago Medical Center, Maywood, Illinois 60130, United States
| | | | - Annelise E. Barron
- Maxwell
Biosciences, Austin, Texas 78738, United States
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States
| | - Gill Diamond
- Department
of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, Kentucky 40292, United States
| | - Bryan C. Mounce
- Department
of Microbiology and Immunology, Loyola University
Chicago Medical Center, Maywood, Illinois 60130, United States
| | - Kent Kirshenbaum
- Department
of Chemistry, New York University, New York, New York 10003, United States
- Maxwell
Biosciences, Austin, Texas 78738, United States
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8
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Karim M, Lo CW, Einav S. Preparing for the next viral threat with broad-spectrum antivirals. J Clin Invest 2023; 133:e170236. [PMID: 37259914 PMCID: PMC10232003 DOI: 10.1172/jci170236] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023] Open
Abstract
There is a large global unmet need for the development of countermeasures to combat hundreds of viruses known to cause human disease and for the establishment of a therapeutic portfolio for future pandemic preparedness. Most approved antiviral therapeutics target proteins encoded by a single virus, providing a narrow spectrum of coverage. This, combined with the slow pace and high cost of drug development, limits the scalability of this direct-acting antiviral (DAA) approach. Here, we summarize progress and challenges in the development of broad-spectrum antivirals that target either viral elements (proteins, genome structures, and lipid envelopes) or cellular proviral factors co-opted by multiple viruses via newly discovered compounds or repurposing of approved drugs. These strategies offer new means for developing therapeutics against both existing and emerging viral threats that complement DAAs.
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Affiliation(s)
- Marwah Karim
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, and
| | - Chieh-Wen Lo
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, and
| | - Shirit Einav
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, and
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
- Chan Zuckerberg Biohub San Francisco, San Francisco, California, USA
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9
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Banerjee A, Dutt M. A hybrid approach for coarse-graining helical peptoids: Solvation, secondary structure, and assembly. J Chem Phys 2023; 158:114105. [PMID: 36948821 DOI: 10.1063/5.0138510] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
Protein mimics such as peptoids form self-assembled nanostructures whose shape and function are governed by the side chain chemistry and secondary structure. Experiments have shown that a peptoid sequence with a helical secondary structure assembles into microspheres that are stable under various conditions. The conformation and organization of the peptoids within the assemblies remains unknown and is elucidated in this study via a hybrid, bottom-up coarse-graining approach. The resultant coarse-grained (CG) model preserves the chemical and structural details that are critical for capturing the secondary structure of the peptoid. The CG model accurately captures the overall conformation and solvation of the peptoids in an aqueous solution. Furthermore, the model resolves the assembly of multiple peptoids into a hemispherical aggregate that is in qualitative agreement with the corresponding results from experiments. The mildly hydrophilic peptoid residues are placed along the curved interface of the aggregate. The composition of the residues on the exterior of the aggregate is determined by two conformations adopted by the peptoid chains. Hence, the CG model simultaneously captures sequence-specific features and the assembly of a large number of peptoids. This multiscale, multiresolution coarse-graining approach could help in predicting the organization and packing of other tunable oligomeric sequences of relevance to biomedicine and electronics.
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Affiliation(s)
- Akash Banerjee
- Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - Meenakshi Dutt
- Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
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10
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Kumar V, Lin JS, Molchanova N, Fortkort JA, Reckmann C, Bräse S, Jenssen H, Barron AE, Chugh A. Membrane-acting biomimetic peptoids against visceral leishmaniasis. FEBS Open Bio 2023; 13:519-531. [PMID: 36683396 PMCID: PMC9989931 DOI: 10.1002/2211-5463.13562] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 12/08/2022] [Accepted: 01/20/2023] [Indexed: 01/24/2023] Open
Abstract
Visceral leishmaniasis (VL) is among the most neglected tropical diseases in the world. Drug cell permeability is essential for killing the intracellular residing parasites responsible for VL, making cell-permeating peptides a logical choice to address VL. Unfortunately, the limited biological stability of peptides restricts their usage. Sequence-specific oligo-N-substituted glycines ('peptoids') are a class of peptide mimics that offers an excellent alternative to peptides in terms of ease of synthesis and good biostability. We tested peptoids against the parasite Leishmania donovani in both forms, that is, intracellular amastigotes and promastigotes. N-alkyl hydrophobic chain addition (lipidation) and bromination of oligopeptoids yielded compounds with good antileishmanial activity against both forms, showing the promise of these antiparasitic peptoids as potential drug candidates to treat VL.
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Affiliation(s)
- Vivek Kumar
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, India
| | - Jennifer S Lin
- Department of Bioengineering, Stanford University, Schools of Medicine and of Engineering, CA, USA
| | | | - John A Fortkort
- Department of Bioengineering, Stanford University, Schools of Medicine and of Engineering, CA, USA
| | - Carolin Reckmann
- Institute of Biological and Chemical Systems - Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Germany
| | - Stefan Bräse
- Institute of Biological and Chemical Systems - Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Germany
| | - Håvard Jenssen
- Department of Science and Environment, Roskilde University, Denmark
| | - Annelise E Barron
- Department of Bioengineering, Stanford University, Schools of Medicine and of Engineering, CA, USA
| | - Archana Chugh
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, India
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11
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Yang W, Seo J, Kim JH. Protein-mimetic peptoid nanoarchitectures for pathogen recognition and neutralization. NANOSCALE 2023; 15:975-986. [PMID: 36541218 DOI: 10.1039/d2nr05326h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Recent outbreaks of both new and existing infectious pathogens have threatened healthcare systems around the world. Therefore, it is vital to detect and neutralize pathogens to prevent their spread and treat infected patients. This consideration has led to the development of biosensors and antibiotics inspired by the structure and function of antibodies and antimicrobial peptides (AMPs), which constitute adaptive and innate immunity, efficiently protecting the human body against invading pathogens. Herein, we provide an overview of recent advances in the detection and neutralization of pathogens using protein-mimetic peptoid nanoarchitectures. Peptoids are bio-inspired and sequence-defined polymers composed of repeating N-substituted glycine units. They can spontaneously fold into well-defined three-dimensional nanostructures that encode chemical information depending on their sequences. Loop-functionalized peptoid nanosheets have been constructed by mimicking antibodies containing chemically variable loops as binding motifs for their respective target pathogen. Furthermore, by mimicking the cationic amphipathic features of natural AMPs, helical peptoids and their assemblies have been developed to achieve selective anti-infective activity owing to their intrinsic ability to interact with bacterial membranes and viral envelopes. We believe that this mini-review furnishes in-depth insight into how to construct protein-like nanostructures via the self-assembly of peptoids for application in the detection of pathogens and the treatment of infectious diseases for future healthcare applications.
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Affiliation(s)
- Woojin Yang
- Soft Hybrid Materials Research Center, Korea Institute of Science and Technology, 5 Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea.
| | - Jiwon Seo
- Department of Chemistry, Gwangju Institute of Science and Technology, 123 Cheomdan-gwagiro, Buk-gu, Gwangju 61005, Republic of Korea.
| | - Jae Hong Kim
- Soft Hybrid Materials Research Center, Korea Institute of Science and Technology, 5 Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea.
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12
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Park S, Cho NJ. Lipid Membrane Interface Viewpoint: From Viral Entry to Antiviral and Vaccine Development. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:1-11. [PMID: 36576966 DOI: 10.1021/acs.langmuir.2c02501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Membrane-enveloped viruses are responsible for most viral pandemics in history, and more effort is needed to advance broadly applicable countermeasures to mitigate the impact of future outbreaks. In this Perspective, we discuss how biosensing techniques associated with lipid model membrane platforms are contributing to improving our mechanistic knowledge of membrane fusion and destabilization that is closely linked to viral entry as well as vaccine and antiviral drug development. A key benefit of these platforms is the simplicity of interpreting the results which can be complemented by other techniques to decipher more complicated biological observations and evaluate the biophysical functionalities that can be correlated to biological activities. Then, we introduce exciting application examples of membrane-targeting antivirals that have been refined over time and will continue to improve based on biophysical insights. Two ways to abrogate the function of viral membranes are introduced here: (1) selective disruption of the viral membrane structure and (2) alteration of the membrane component. While both methods are suitable for broadly useful antivirals, the latter also has the potential to produce an inactivated vaccine. Collectively, we emphasize how biosensing tools based on membrane interfacial science can provide valuable information that could be translated into biomedicines and improve their selectivity and performance.
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Affiliation(s)
- Soohyun Park
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Nam-Joon Cho
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
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13
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Pratt EJ, Mancera-Andrade EI, Bicker KL. Synthesis and Characterization of Derivatives of the Antifungal Peptoid RMG8-8. ACS OMEGA 2022; 7:36663-36671. [PMID: 36278036 PMCID: PMC9583092 DOI: 10.1021/acsomega.2c04778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Cryptococcal meningitis, caused by the fungal pathogen Cryptococcus neoformans, is a devastating disease with a mortality rate of over 80%. Due to the increasing prevalence of resistance to antifungals and the high mammalian toxicity of current treatments, the development of new antifungal therapies is vital. In an effort to improve the biological properties of a previously discovered antifungal peptoid, termed RMG8-8, an iterative structure-activity relationship study was conducted. This three-round study sought to optimize the structure of RMG8-8 by focusing on three main structural components: the lipophilic tail, aliphatic side chains, and aromatic side chains. In addition to antifungal testing against C. neoformans, cytotoxicity testing was also performed on all derivatives against human liver cells, and select promising compounds were tested for hemolytic activity against human red blood cells. A number of derivatives containing unique aliphatic or aromatic side chains had antifungal activity similar to RMG8-8 (MIC = 1.56 μg/mL), but all of these compounds were more toxic than RMG8-8. While no derivative was improved across all biological tests, modest improvements were made to the hemolytic activity with compound 9, containing isobutyl side chains in positions 2 and 5, compared to RMG8-8 (HC10 = 130 and 75 μg/mL, respectively). While this study did not yield a dramatically optimized RMG8-8 derivative, this result was not totally unexpected given the remarkable selectivity of this compound from discovery. Nonetheless, this study is an important step in the development of RMG8-8 as a viable antifungal therapeutic.
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14
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Lin J, Bekale LA, Molchanova N, Nielsen JE, Wright M, Bacacao B, Diamond G, Jenssen H, Santa Maria PL, Barron AE. Anti-persister and Anti-biofilm Activity of Self-Assembled Antimicrobial Peptoid Ellipsoidal Micelles. ACS Infect Dis 2022; 8:1823-1830. [PMID: 36018039 PMCID: PMC9469094 DOI: 10.1021/acsinfecdis.2c00288] [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] [Indexed: 01/29/2023]
Abstract
Although persister cells are the root cause of resistance development and relapse of chronic infections, more attention has been focused on developing antimicrobial agents against resistant bacterial strains than on developing anti-persister agents. Frustratingly, the global preclinical antibacterial pipeline does not include any anti-persister drug. Therefore, the central point of this work is to explore antimicrobial peptidomimetics called peptoids (sequence-specific oligo-N-substituted glycines) as a new class of anti-persister drugs. In this study, we demonstrate that one particular antimicrobial peptoid, the sequence-specific pentamer TM5, is active against planktonic persister cells and sterilizes biofilms formed by both Gram-negative and Gram-positive bacteria. Moreover, we demonstrate the potential of TM5 to inhibit cytokine production induced by lipopolysaccharides from Gram-negative bacteria. We anticipate that this work can pave the way to the development of new anti-persister agents based on antimicrobial peptoids of this class to simultaneously help address the crisis of bacterial resistance and reduce the occurrence of the relapse of chronic infections.
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Affiliation(s)
- Jennifer
S. Lin
- Department
of Bioengineering, School of Medicine & School of Engineering, Stanford University, Stanford, California 94305, United States
| | - Laurent A. Bekale
- Department
of Otolaryngology, Head and Neck Surgery, School of Medicine, Stanford University, Stanford, California 94305, United States
| | - Natalia Molchanova
- The
Molecular Foundry, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - Josefine Eilsø Nielsen
- Department
of Bioengineering, School of Medicine & School of Engineering, Stanford University, Stanford, California 94305, United States,Department
of Science and Environment, Roskilde University, 4000 Roskilde, Denmark
| | - Megan Wright
- Department
of Otolaryngology, Head and Neck Surgery, School of Medicine, Stanford University, Stanford, California 94305, United States
| | - Brian Bacacao
- Department
of Otolaryngology, Head and Neck Surgery, School of Medicine, Stanford University, Stanford, California 94305, United States
| | - Gill Diamond
- Department
of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, Kentucky 40202, United States
| | - Håvard Jenssen
- Department
of Science and Environment, Roskilde University, 4000 Roskilde, Denmark
| | - Peter L. Santa Maria
- Department
of Otolaryngology, Head and Neck Surgery, School of Medicine, Stanford University, Stanford, California 94305, United States,
| | - Annelise E. Barron
- Department
of Bioengineering, School of Medicine & School of Engineering, Stanford University, Stanford, California 94305, United States,
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15
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Zupin L, dos Santos-Silva CA, Al Mughrbi ARH, Vilela LMB, Benko-Iseppon AM, Crovella S. Bioactive Antimicrobial Peptides: A New Weapon to Counteract Zoonosis. Microorganisms 2022; 10:microorganisms10081591. [PMID: 36014009 PMCID: PMC9414035 DOI: 10.3390/microorganisms10081591] [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: 06/30/2022] [Revised: 07/29/2022] [Accepted: 08/03/2022] [Indexed: 11/16/2022] Open
Abstract
Zoonoses have recently become the center of attention of the general population and scientific community. Notably, more than 30 new human pathogens have been identified in the last 30 years, 75% of which can be classified as zoonosis. The complete eradication of such types of infections is far out of reach, considering the limited understanding of animal determinants in zoonoses and their causes of emergence. Therefore, efforts must be doubled in examining the spread, persistence, and pathogenicity of zoonosis and studying possible clinical interventions and antimicrobial drug development. The search for antimicrobial bioactive compounds has assumed great emphasis, considering the emergence of multi-drug-resistant microorganisms. Among the biomolecules of emerging scientific interest are antimicrobial peptides (AMPs), potent biomolecules that can potentially act as important weapons against infectious diseases. Moreover, synthetic AMPs are easily tailored (bioinformatically) to target specific features of the pathogens to hijack, inducing no or very low resistance. Although very promising, previous studies on SAMPs’ efficacy are still at their early stages. Indeed, further studies and better characterization on their mechanism of action with in vitro and in vivo assays are needed so as to proceed to their clinical application on human beings.
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Affiliation(s)
- Luisa Zupin
- Institute for Maternal and Child Health—IRCCS Burlo Garofolo, 34137 Trieste, Italy
- Correspondence: (L.Z.); (S.C.)
| | | | | | - Livia Maria Batista Vilela
- Centro de Biociências, Departamento de Genética, Universidade Federal de Pernambuco, Recife 50670-420, Brazil
| | - Ana Maria Benko-Iseppon
- Centro de Biociências, Departamento de Genética, Universidade Federal de Pernambuco, Recife 50670-420, Brazil
| | - Sergio Crovella
- Biological Science Program, Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, Doha 2713, Qatar
- Correspondence: (L.Z.); (S.C.)
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16
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Abstract
Staphylococcus aureus is one of the most common pathogens associated with infection in wounds. The current standard of care uses a combination of disinfection and drainage followed by conventional antibiotics such as methicillin. Methicillin and vancomycin resistance has rendered these treatments ineffective, often causing the reemergence of infection. This study examines the use of antimicrobial peptoids (sequence-specific poly-N-substituted glycines) designed to mimic naturally occurring cationic, amphipathic host defense peptides, as an alternative to conventional antibiotics. These peptoids also show efficient and fast (<30 min) killing of methicillin-susceptible S. aureus (MSSA) and methicillin-resistant S. aureus (MRSA) at low micromolar concentrations without having apparent cytotoxic side effects in vivo. Additionally, these novel peptoids show excellent efficacy against biofilm formation and detachment for both MSSA and MRSA. In comparison, conventional antibiotics were unable to detach or prevent formation of biofilms. One cationic 12mer, Peptoid 1, shows great promise, as it could prevent formation of and detach biofilms at concentrations as low as 1.6 μM. The use of a bioluminescent S. aureus murine incision wound model demonstrated clearance of infection in peptoid-treated mice within 8 days, conveying another advantage these peptoids have over conventional antibiotics. These results provide clear evidence of the potential for antimicrobial peptoids for the treatment of S. aureus wound infections. IMPORTANCEStaphylococcus aureus resistance is a consistent problem with a large impact on the health care system. Infections with resistant S. aureus can cause serious adverse effects and can result in death. These antimicrobial peptoids show efficient killing of bacteria both as a biofilm and as free bacteria, often doing so in less than 30 min. As such, these antimicrobials have the potential to alleviate the burden that Staphylococcus infections have on the health care system and cause better outcomes for infected patients.
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17
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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: 38] [Impact Index Per Article: 19.0] [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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18
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Zhang L, Ghosh SK, Basavarajappa SC, Chen Y, Shrestha P, Penfield J, Brewer A, Ramakrishnan P, Buck M, Weinberg A. HBD-2 binds SARS-CoV-2 RBD and blocks viral entry: Strategy to combat COVID-19. iScience 2022; 25:103856. [PMID: 35128350 PMCID: PMC8808565 DOI: 10.1016/j.isci.2022.103856] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 09/14/2021] [Accepted: 01/28/2022] [Indexed: 12/26/2022] Open
Abstract
New approaches to complement vaccination are needed to combat the spread of SARS-CoV-2 and stop COVID-19-related deaths and medical complications. Human beta defensin 2 (hBD-2) is a naturally occurring epithelial cell-derived host defense peptide that has anti-viral properties. Our comprehensive in-silico studies demonstrate that hBD-2 binds the site on the CoV-2-RBD that docks with the ACE2 receptor. Biophysical measurements confirm that hBD-2 indeed binds to the CoV-2-receptor-binding domain (RBD) (KD ∼ 2μM by surface plasmon resonance), preventing it from binding to ACE2-expressing cells. Importantly, hBD-2 shows specificity by blocking CoV-2/spike pseudoviral infection, but not VSVG-mediated infection, of ACE2-expressing human cells with an IC50 of 2.8 ± 0.4 μM. These promising findings offer opportunities to develop hBD-2 and/or its derivatives and mimetics to safely and effectively use as agents to prevent SARS-CoV-2 infection. HBD-2 binds spike-RBD at the ACE2 interaction site in silico Biophysical and biological assays confirm hBD-2 binding to spike-RBD HBD-2 blocks spike-RBD:ACE2 binding HBD-2 prevents CoV-2/spike pseudovirions from infecting ACE2-expressing human cells
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Affiliation(s)
- Liqun Zhang
- Chemical Engineering, Tennessee Technological University, Cookeville, TN 38505, USA
| | - Santosh K. Ghosh
- Biological Sciences, School of Dental Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | | | - Yinghua Chen
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Pravesh Shrestha
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Jackson Penfield
- Chemical Engineering, Tennessee Technological University, Cookeville, TN 38505, USA
| | - Ann Brewer
- Chemical Engineering, Tennessee Technological University, Cookeville, TN 38505, USA
| | - Parameswaran Ramakrishnan
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
- Corresponding author
| | - Matthias Buck
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
- Corresponding author
| | - Aaron Weinberg
- Biological Sciences, School of Dental Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
- Corresponding author
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19
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Nielsen JE, Alford MA, Yung DBY, Molchanova N, Fortkort JA, Lin JS, Diamond G, Hancock REW, Jenssen H, Pletzer D, Lund R, Barron AE. Self-Assembly of Antimicrobial Peptoids Impacts Their Biological Effects on ESKAPE Bacterial Pathogens. ACS Infect Dis 2022; 8:533-545. [PMID: 35175731 DOI: 10.1021/acsinfecdis.1c00536] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Antimicrobial peptides (AMPs) are promising pharmaceutical candidates for the prevention and treatment of infections caused by multidrug-resistant ESKAPE pathogens, which are responsible for the majority of hospital-acquired infections. Clinical translation of AMPs has been limited, in part by apparent toxicity on systemic dosing and by instability arising from susceptibility to proteolysis. Peptoids (sequence-specific oligo-N-substituted glycines) resist proteolytic digestion and thus are of value as AMP mimics. Only a few natural AMPs such as LL-37 and polymyxin self-assemble in solution; whether antimicrobial peptoids mimic these properties has been unknown. Here, we examine the antibacterial efficacy and dynamic self-assembly in aqueous media of eight peptoid mimics of cationic AMPs designed to self-assemble and two nonassembling controls. These amphipathic peptoids self-assembled in different ways, as determined by small-angle X-ray scattering; some adopt helical bundles, while others form core-shell ellipsoidal or worm-like micelles. Interestingly, many of these peptoid assemblies show promising antibacterial, antibiofilm activity in vitro in media, under host-mimicking conditions and antiabscess activity in vivo. While self-assembly correlated overall with antibacterial efficacy, this correlation was imperfect. Certain self-assembled morphologies seem better-suited for antibacterial activity. In particular, a peptoid exhibiting a high fraction of long, worm-like micelles showed reduced antibacterial, antibiofilm, and antiabscess activity against ESKAPE pathogens compared with peptoids that form ellipsoidal or bundled assemblies. This is the first report of self-assembling peptoid antibacterials with activity against in vivo biofilm-like infections relevant to clinical medicine.
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Affiliation(s)
- Josefine Eilsø Nielsen
- Department of Bioengineering, School of Medicine, Stanford University, Stanford, California 94305, United States
- Department of Chemistry, University of Oslo, Oslo 0315, Norway
| | - Morgan Ashley Alford
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Deborah Bow Yue Yung
- Department of Microbiology and Immunology, University of Otago, Dunedin 9054, New Zealand
| | - Natalia Molchanova
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - John A. Fortkort
- Department of Bioengineering, School of Medicine, Stanford University, Stanford, California 94305, United States
| | - Jennifer S. Lin
- Department of Bioengineering, School of Medicine, Stanford University, Stanford, California 94305, United States
| | - Gill Diamond
- Department of Oral Immunology and Infectious Diseases, University of Louisville, School of Dentistry, Louisville, Kentucky 40202, United States
| | - Robert E. W. Hancock
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Håvard Jenssen
- Department of Science and Environment, Roskilde University, Roskilde 4000, Denmark
| | - Daniel Pletzer
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Microbiology and Immunology, University of Otago, Dunedin 9054, New Zealand
| | - Reidar Lund
- Department of Chemistry, University of Oslo, Oslo 0315, Norway
| | - Annelise E. Barron
- Department of Bioengineering, School of Medicine, Stanford University, Stanford, California 94305, United States
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20
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Sureram S, Arduino I, Ueoka R, Rittà M, Francese R, Srivibool R, Darshana D, Piel J, Ruchirawat S, Muratori L, Lembo D, Kittakoop P, Donalisio M. The Peptide A-3302-B Isolated from a Marine Bacterium Micromonospora sp. Inhibits HSV-2 Infection by Preventing the Viral Egress from Host Cells. Int J Mol Sci 2022; 23:947. [PMID: 35055133 PMCID: PMC8778767 DOI: 10.3390/ijms23020947] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/07/2022] [Accepted: 01/13/2022] [Indexed: 02/04/2023] Open
Abstract
Herpesviruses are highly prevalent in the human population, and frequent reactivations occur throughout life. Despite antiviral drugs against herpetic infections, the increasing appearance of drug-resistant viral strains and their adverse effects prompt the research of novel antiherpetic drugs for treating lesions. Peptides obtained from natural sources have recently become of particular interest for antiviral therapy applications. In this work, we investigated the antiviral activity of the peptide A-3302-B, isolated from a marine bacterium, Micromonospora sp., strain MAG 9-7, against herpes simplex virus type 1, type 2, and human cytomegalovirus. Results showed that the peptide exerted a specific inhibitory activity against HSV-2 with an EC50 value of 14 μM. Specific antiviral assays were performed to investigate the mechanism of action of A-3302-B. We demonstrated that the peptide did not affect the expression of viral proteins, but it inhibited the late events of the HSV-2 replicative cycle. In detail, it reduced the cell-to-cell virus spread and the transmission of the extracellular free virus by preventing the egress of HSV-2 progeny from the infected cells. The dual antiviral and previously reported anti-inflammatory activities of A-3302-B, and its effect against an acyclovir-resistant HSV-2 strain are attractive features for developing a therapeutic to reduce the transmission of HSV-2 infections.
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Affiliation(s)
- Sanya Sureram
- Chulabhorn Research Institute, Kamphaeng Phet 6 Road, Laksi, Bangkok 10210, Thailand; (S.S.); (S.R.)
| | - Irene Arduino
- Department of Clinical and Biological Sciences, University of Turin, Regione Gonzole 10, 10043 Orbassano, Italy; (I.A.); (M.R.); (R.F.); (D.L.)
| | - Reiko Ueoka
- Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland; (R.U.); (J.P.)
| | - Massimo Rittà
- Department of Clinical and Biological Sciences, University of Turin, Regione Gonzole 10, 10043 Orbassano, Italy; (I.A.); (M.R.); (R.F.); (D.L.)
| | - Rachele Francese
- Department of Clinical and Biological Sciences, University of Turin, Regione Gonzole 10, 10043 Orbassano, Italy; (I.A.); (M.R.); (R.F.); (D.L.)
| | | | - Dhanushka Darshana
- Program in Chemical Sciences, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Kamphaeng Phet 6 Road, Laksi, Bangkok 10210, Thailand;
| | - Jörn Piel
- Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland; (R.U.); (J.P.)
| | - Somsak Ruchirawat
- Chulabhorn Research Institute, Kamphaeng Phet 6 Road, Laksi, Bangkok 10210, Thailand; (S.S.); (S.R.)
- Program in Chemical Sciences, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Kamphaeng Phet 6 Road, Laksi, Bangkok 10210, Thailand;
- Center of Excellence on Environmental Health and Toxicology (EHT), OPS, Ministry of Higher Education, Science, Research and Innovation, Bangkok 10210, Thailand
| | - Luisa Muratori
- Department of Clinical and Biological Sciences, Neuroscience Institute of the “Cavalieri Ottolenghi” Foundation (NICO), University of Turin, 10043 Orbassano, Italy;
| | - David Lembo
- Department of Clinical and Biological Sciences, University of Turin, Regione Gonzole 10, 10043 Orbassano, Italy; (I.A.); (M.R.); (R.F.); (D.L.)
| | - Prasat Kittakoop
- Chulabhorn Research Institute, Kamphaeng Phet 6 Road, Laksi, Bangkok 10210, Thailand; (S.S.); (S.R.)
- Program in Chemical Sciences, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Kamphaeng Phet 6 Road, Laksi, Bangkok 10210, Thailand;
- Center of Excellence on Environmental Health and Toxicology (EHT), OPS, Ministry of Higher Education, Science, Research and Innovation, Bangkok 10210, Thailand
| | - Manuela Donalisio
- Department of Clinical and Biological Sciences, University of Turin, Regione Gonzole 10, 10043 Orbassano, Italy; (I.A.); (M.R.); (R.F.); (D.L.)
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21
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Mojsoska B. Solid-phase synthesis of novel antimicrobial peptoids with α- and β-chiral side chains. Methods Enzymol 2022; 663:327-340. [DOI: 10.1016/bs.mie.2021.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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22
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Herlan CN, Feser D, Schepers U, Bräse S. Bio-instructive materials on-demand - combinatorial chemistry of peptoids, foldamers, and beyond. Chem Commun (Camb) 2021; 57:11131-11152. [PMID: 34611672 DOI: 10.1039/d1cc04237h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Combinatorial chemistry allows for the rapid synthesis of large compound libraries for high throughput screenings in biology, medicinal chemistry, or materials science. Especially compounds from a highly modular design are interesting for the proper investigation of structure-to-activity relationships. Permutations of building blocks result in many similar but unique compounds. The influence of certain structural features on the entire structure can then be monitored and serve as a starting point for the rational design of potent molecules for various applications. Peptoids, a highly diverse class of bioinspired oligomers, suit perfectly for combinatorial chemistry. Their straightforward synthesis on a solid support using repetitive reaction steps ensures easy handling and high throughput. Applying this modular approach, peptoids are readily accessible, and their interchangeable side-chains allow for various structures. Thus, peptoids can easily be tuned in their solubility, their spatial structure, and, consequently, their applicability in various fields of research. Since their discovery, peptoids have been applied as antimicrobial agents, artificial membranes, molecular transporters, and much more. Studying their three-dimensional structure, various foldamers with fascinating, unique properties were discovered. This non-comprehensive review will state the most interesting discoveries made over the past years and arouse curiosity about what may come.
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Affiliation(s)
- Claudine Nicole Herlan
- Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann von Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Dominik Feser
- Institute of Functional Interfaces (IFG), Karlsruhe Institute of Technology (KIT), Hermann von Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Ute Schepers
- Institute of Functional Interfaces (IFG), Karlsruhe Institute of Technology (KIT), Hermann von Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.,Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), Fritz Haber Weg 6, 76131 Karlsruhe, Germany
| | - Stefan Bräse
- Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann von Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany. .,Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), Fritz Haber Weg 6, 76131 Karlsruhe, Germany
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23
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Róg T, Girych M, Bunker A. Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design. Pharmaceuticals (Basel) 2021; 14:1062. [PMID: 34681286 PMCID: PMC8537670 DOI: 10.3390/ph14101062] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 11/17/2022] Open
Abstract
We review the use of molecular dynamics (MD) simulation as a drug design tool in the context of the role that the lipid membrane can play in drug action, i.e., the interaction between candidate drug molecules and lipid membranes. In the standard "lock and key" paradigm, only the interaction between the drug and a specific active site of a specific protein is considered; the environment in which the drug acts is, from a biophysical perspective, far more complex than this. The possible mechanisms though which a drug can be designed to tinker with physiological processes are significantly broader than merely fitting to a single active site of a single protein. In this paper, we focus on the role of the lipid membrane, arguably the most important element outside the proteins themselves, as a case study. We discuss work that has been carried out, using MD simulation, concerning the transfection of drugs through membranes that act as biological barriers in the path of the drugs, the behavior of drug molecules within membranes, how their collective behavior can affect the structure and properties of the membrane and, finally, the role lipid membranes, to which the vast majority of drug target proteins are associated, can play in mediating the interaction between drug and target protein. This review paper is the second in a two-part series covering MD simulation as a tool in pharmaceutical research; both are designed as pedagogical review papers aimed at both pharmaceutical scientists interested in exploring how the tool of MD simulation can be applied to their research and computational scientists interested in exploring the possibility of a pharmaceutical context for their research.
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Affiliation(s)
- Tomasz Róg
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Mykhailo Girych
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Alex Bunker
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, 00014 Helsinki, Finland;
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Li D, Chen P, Shi T, Mehmood A, Qiu J. HD5 and LL-37 Inhibit SARS-CoV and SARS-CoV-2 Binding to Human ACE2 by Molecular Simulation. Interdiscip Sci 2021; 13:766-777. [PMID: 34363600 PMCID: PMC8346780 DOI: 10.1007/s12539-021-00462-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/30/2021] [Accepted: 07/02/2021] [Indexed: 02/06/2023]
Abstract
The coronavirus (COVID-19) pandemic is still spreading all over the world. As reported, angiotensin-converting enzyme-2 (ACE2) is a receptor of SARS-CoV-2 spike protein that initializes viral entry into host cells. Previously, the human defensin 5 (HD5) has been experimentally confirmed to be functional against the SARS-CoV-2. The present study proposes a human cathelicidin known as LL37 that strongly binds to the carboxypeptidase domain of human ACE2 compared to HD5. Therefore, LL37 bears a great potential to be tested as an anti-SARS-CoVD-2 peptide. We investigated the molecular interactions formed between the LL37 and ACE2 as well as HD5 and ACE2 tailed by their thermodynamic stability. The MM-PBSA and free energy landscape analysis outcomes confirmed its possible inhibitory effect against the SARS-CoV-2. The results obtained here could help propose a promising therapeutic strategy against the havoc caused by SARS-CoV-2 infections.
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Affiliation(s)
- Daixi Li
- Institute of Biothermal Science and Technology, University of Shanghai for Science and Technology, Shanghai, 200093, China.
| | - Peiqin Chen
- Institute of Biothermal Science and Technology, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Ting Shi
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Aamir Mehmood
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Jingfei Qiu
- AI Research Center, Peng Cheng Laboratory, Shenzhen, Guangdong, 518055, People's Republic of China
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Ghosh SK, Weinberg A. Ramping Up Antimicrobial Peptides Against Severe Acute Respiratory Syndrome Coronavirus-2. Front Mol Biosci 2021; 8:620806. [PMID: 34235176 PMCID: PMC8255374 DOI: 10.3389/fmolb.2021.620806] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 05/27/2021] [Indexed: 12/17/2022] Open
Abstract
Human-derived antimicrobial peptides (AMPs), such as defensins and cathelicidin LL-37, are members of the innate immune system and play a crucial role in early pulmonary defense against viruses. These AMPs achieve viral inhibition through a variety of mechanisms including, but not limited to, direct binding to virions, binding to and modulating host cell-surface receptors, blocking viral replication, and aggregation of viral particles and indirectly by functioning as chemokines to enhance or curb adaptive immune responses. Given the fact that we are in a pandemic of unprecedented severity and the urgent need for therapeutic options to combat severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), naturally expressed AMPs and their derivatives have the potential to combat coronavirus disease 2019 (COVID-19) and impede viral infectivity in various ways. Provided the fact that development of effective treatments is an urgent public health priority, AMPs and their derivatives are being explored as potential prophylactic and therapeutic candidates. Additionally, cell-based platforms such as human mesenchymal stem cell (hMSC) therapy are showing success in saving the lives of severely ill patients infected with SARS-CoV-2. This could be partially due to AMPs released from hMSCs that also act as immunological rheostats to modulate the host inflammatory response. This review highlights the utilization of AMPs in strategies that could be implemented as novel therapeutics, either alone or in combination with other platforms, to treat CoV-2-infected individuals.
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Affiliation(s)
| | - Aaron Weinberg
- Department of Biological Sciences, Case Western Reserve University, Cleveland, OH, United States
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