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Frigini EN, Porasso RD, Beke-Somfai T, López Cascales JJ, Enriz RD, Pantano S. The Mechanism of Antimicrobial Small-Cationic Peptides from Coarse-Grained Simulations. J Chem Inf Model 2023; 63:6877-6889. [PMID: 37905818 DOI: 10.1021/acs.jcim.3c01348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Antimicrobial cationic peptides (AMPs) are excellent candidates for use as therapeutic antimicrobial agents. Among them, short peptides possessing sequences of 9-11 amino acids have some advantages over long-sequence peptides. However, one of the main limitations of short peptides is that their mechanism of action at the molecular level is not well-known. In this article, we report a model based on multiscale molecular dynamics simulations of short peptides interacting with vesicles containing palmitoyl-oleoyl-phosphatidylglycerol (POPG)/palmitoyl-oleoyl-phosphatidylethanolamine (POPE). Simulations using this approach have allowed us to understand the different behaviors of peptides with antimicrobial activity with respect to those that do not produce this effect. We found remarkable agreement with a series of experimental results directly supporting our model. Moreover, these results allow us to understand the mechanism of action at the molecular level of these short peptides. Our simulations suggest that mechanical inhomogeneities appear in the membrane, promoting membrane rupture when a threshold concentration of peptides adsorbed on the membrane is achieved. These results explain the high structural demand for these peptides to maintain a delicate balance between the affinity for the bilayer surface, a low peptide-peptide repulsion (in order to reach the threshold concentration), and an acceptable tendency to penetrate into the bilayer. This mechanism is different from those proposed for peptides with long amino acid sequences. Such information is very useful from the medicinal chemistry point of view for the design of new small antimicrobial peptides.
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Affiliation(s)
- Ezequiel N Frigini
- Facultad de Química, Bioquímica y Farmacia, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Universidad Nacional de San Luis, Ejército de los Andes 950, San Luis 5700, Argentina
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo 11400, Uruguay
| | - Rodolfo D Porasso
- Instituto de Matemáticas Aplicada San Luis (IMASL), CONICET, Facultad de Ciencias Físico Matemáticas y Naturales, Universidad Nacional de San Luis, Av. Ejército de los Andes 950, San Luis 5700, Argentina
| | - Tamás Beke-Somfai
- Research Centre for Natural Sciences, Institute of Materials and Environmental Chemistry, H-1117 Budapest, Hungary
| | - José Javier López Cascales
- Universidad Politécnica de Cartagena, Grupo de Bioinformática y Macromoleculas (BioMac), Area de Química Física, Aulario II, Campus de Alfonso XIII, 30203 Cartagena, Murcia, Spain
| | - Ricardo D Enriz
- Facultad de Química, Bioquímica y Farmacia, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Universidad Nacional de San Luis, Ejército de los Andes 950, San Luis 5700, Argentina
| | - Sergio Pantano
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo 11400, Uruguay
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2
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Efficacy of natural antimicrobial peptides versus peptidomimetic analogues: a systematic review. Future Med Chem 2022; 14:1899-1921. [PMID: 36421051 DOI: 10.4155/fmc-2022-0160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Aims: This systematic review was carried out to determine whether synthetic peptidomimetics exhibit significant advantages over antimicrobial peptides in terms of in vitro potency. Structural features - molecular weight, charge and length - were examined for correlations with activity. Methods: Original research articles reporting minimum inhibitory concentration values against Escherichia coli, indexed until 31 December 2020, were searched in PubMed/ScienceDirect/Google Scholar and evaluated using mixed-effects models. Results: In vitro antimicrobial activity of peptidomimetics resembled that of antimicrobial peptides. Net charge significantly affected minimum inhibitory concentration values (p < 0.001) with a trend of 4.6% decrease for increments in charge by +1. Conclusion: AMPs and antibacterial peptidomimetics exhibit similar potencies, providing an opportunity to exploit the advantageous stability and bioavailability typically associated with peptidomimetics.
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3
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Ragonis-Bachar P, Rayan B, Barnea E, Engelberg Y, Upcher A, Landau M. Natural Antimicrobial Peptides Self-assemble as α/β Chameleon Amyloids. Biomacromolecules 2022; 23:3713-3727. [PMID: 35947777 DOI: 10.1021/acs.biomac.2c00582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Amyloid protein fibrils and some antimicrobial peptides (AMPs) share biophysical and structural properties. This observation suggests that ordered self-assembly can act as an AMP-regulating mechanism, and, vice versa, that human amyloids play a role in host defense against pathogens, as opposed to their common association with neurodegenerative and systemic diseases. Based on previous structural information on toxic amyloid peptides, we developed a sequence-based bioinformatics platform and, led by its predictions, experimentally identified 14 fibril-forming AMPs (ffAMPs) from living organisms, which demonstrated cross-β and cross-α amyloid properties. The results support the amyloid-antimicrobial link. The high prevalence of ffAMPs produced by amphibians and marine creatures among other species suggests that they confer unique advantageous properties in distinctive environments, potentially providing stability and adherence properties. Most of the newly identified 14 ffAMPs showed lipid-induced and/or time-dependent secondary structure transitions in the fibril form, indicating structural and functional cross-α/β chameleons. Specifically, ffAMP cytotoxicity against human cells correlated with the inherent or lipid-induced α-helical fibril structure. The findings raise hypotheses about the role of fibril secondary structure switching in regulation of processes, such as the transition between a stable storage conformation and an active state with toxicity against specific cell types.
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Affiliation(s)
- Peleg Ragonis-Bachar
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Bader Rayan
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Eilon Barnea
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Yizhaq Engelberg
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Alexander Upcher
- Ilse Katz Institute for Nanoscale Science and Technology, Ben Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Meytal Landau
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel.,European Molecular Biology Laboratory (EMBL) and Centre for Structural Systems Biology, Hamburg 22607, Germany
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Goldschmidt Gőz V, Duong KHY, Horváth D, Ferentzi K, Farkas V, Perczel A. Application of Sugar Amino Acids: Flow Chemistry Used for α/β‐Chimera Synthesis. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Viktória Goldschmidt Gőz
- MTA-ELTE Protein Modeling Research Group Eötvös Loránd Research Network (ELKH) ELTE Eötvös Loránd University Pázmány P. stny. 1/A 1117 Budapest Hungary
| | - Kim Hoang Yen Duong
- Laboratory of Structural Chemistry and Biology Institute of Chemistry ELTE Eötvös Loránd University Pázmány P. stny. 1/A 1117 Budapest Hungary
- Hevesy György PhD School of Chemistry Institute of Chemistry ELTE Eötvös Loránd University Pázmány P. stny. 1/A 1117 Budapest Hungary
| | - Dániel Horváth
- Laboratory of Structural Chemistry and Biology Institute of Chemistry ELTE Eötvös Loránd University Pázmány P. stny. 1/A 1117 Budapest Hungary
| | - Kristóf Ferentzi
- Laboratory of Structural Chemistry and Biology Institute of Chemistry ELTE Eötvös Loránd University Pázmány P. stny. 1/A 1117 Budapest Hungary
- Hevesy György PhD School of Chemistry Institute of Chemistry ELTE Eötvös Loránd University Pázmány P. stny. 1/A 1117 Budapest Hungary
| | - Viktor Farkas
- MTA-ELTE Protein Modeling Research Group Eötvös Loránd Research Network (ELKH) ELTE Eötvös Loránd University Pázmány P. stny. 1/A 1117 Budapest Hungary
| | - András Perczel
- MTA-ELTE Protein Modeling Research Group Eötvös Loránd Research Network (ELKH) ELTE Eötvös Loránd University Pázmány P. stny. 1/A 1117 Budapest Hungary
- Laboratory of Structural Chemistry and Biology Institute of Chemistry ELTE Eötvös Loránd University Pázmány P. stny. 1/A 1117 Budapest Hungary
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5
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Lima B, Ricci M, Garro A, Juhász T, Szigyártó IC, Papp ZI, Feresin G, Garcia de la Torre J, Lopez Cascales J, Fülöp L, Beke-Somfai T, Enriz RD. New short cationic antibacterial peptides. Synthesis, biological activity and mechanism of action. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183665. [PMID: 34097861 DOI: 10.1016/j.bbamem.2021.183665] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 05/07/2021] [Accepted: 06/01/2021] [Indexed: 11/28/2022]
Abstract
We report a theoretical and experimental study on a new series of small-sized antibacterial peptides. Synthesis and bioassays for these peptides are reported here. In addition, we evaluated different physicochemical parameters that modulate antimicrobial activity (charge, secondary structure, amphipathicity, hydrophobicity and polarity). We also performed molecular dynamic simulations to assess the interaction between these peptides and their molecular target (the membrane). Biophysical characterization of the peptides was carried out with different techniques, such as circular dichroism (CD), linear dichroism (LD), infrared spectroscopy (IR), dynamic light scattering (DLS), fluorescence spectroscopy and TEM studies using model systems (liposomes) for mammalian and bacterial membranes. The results of this study allow us to draw important conclusions on three different aspects. Theoretical and experimental results indicate that small-sized peptides have a particular mechanism of action that is different to that of large peptides. These results provide additional support for a previously proposed four-step mechanism of action. The possible pharmacophoric requirement for these small-sized peptides is discussed. Furthermore, our results indicate that a net +4 charge is the adequate for 9 amino acid long peptides to produce antibacterial activity. The information reported here is very important for designing new antibacterial peptides with these structural characteristics.
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Affiliation(s)
- Beatriz Lima
- Instituto de Biotecnología, Universidad Nacional de San Juan, Av. Libertador General San Martín 1109 (O), CP 5400 San Juan, Argentina
| | - Maria Ricci
- Research Centre for Natural Sciences, Institute of Materials and Environmental Chemistry, H-1117 Budapest, Hungary
| | - Adriana Garro
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Chacabuco 915, 5700 San Luis, Argentina
| | - Tünde Juhász
- Research Centre for Natural Sciences, Institute of Materials and Environmental Chemistry, H-1117 Budapest, Hungary
| | - Imola Csilla Szigyártó
- Research Centre for Natural Sciences, Institute of Materials and Environmental Chemistry, H-1117 Budapest, Hungary
| | - Zita I Papp
- Department of Medical Chemistry, University of Szeged, H-6720 Szeged, Dóm tér 8, Hungary
| | - Gabriela Feresin
- Instituto de Biotecnología, Universidad Nacional de San Juan, Av. Libertador General San Martín 1109 (O), CP 5400 San Juan, Argentina
| | - Jose Garcia de la Torre
- Facultad de Química, Departamento de Química Física, Universidad de Murcia, Campus de Espinardo, 30100 Espinardo, Murcia, Spain
| | - Javier Lopez Cascales
- Grupo de Bioinformática y Macromoléculas (BioMac), Área de Química Física, Universidad Politécnica de Cartagena, Aulario II, ́ Campus de Alfonso XIII, 30203 Cartagena, Murcia, Spain
| | - Lívia Fülöp
- Department of Medical Chemistry, University of Szeged, H-6720 Szeged, Dóm tér 8, Hungary.
| | - Tamás Beke-Somfai
- Research Centre for Natural Sciences, Institute of Materials and Environmental Chemistry, H-1117 Budapest, Hungary.
| | - Ricardo D Enriz
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Chacabuco 915, 5700 San Luis, Argentina.
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6
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Larzábal M, Baldoni HA, Suvire FD, Curto LM, Gomez GE, Da Silva WM, Giudicessi SL, Camperi SA, Delfino JM, Cataldi AA, Enriz D. An inhibitory mechanism of action of coiled‐coil peptides against type three secretion system from enteropathogenicEscherichia coli. J Pept Sci 2019; 25:e3149. [DOI: 10.1002/psc.3149] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 12/28/2018] [Accepted: 01/08/2019] [Indexed: 12/17/2022]
Affiliation(s)
| | - Hector A. Baldoni
- Facultad de Química, Bioquímica y FarmaciaUniversidad Nacional de San Luis San Luis Argentina
- IMASL‐CONICET San Luis Argentina
| | - Fernando D. Suvire
- Facultad de Química, Bioquímica y FarmaciaUniversidad Nacional de San Luis San Luis Argentina
- IMIBIO‐CONICET San Luis Argentina
| | - Lucrecia M. Curto
- Facultad de Farmacia y Bioquímica, Departamento de Química BiológicaUniversidad de Buenos Aires (UBA) Buenos Aires Argentina
- Universidad de Buenos Aires‐CONICET, Instituto de Química y Fisicoquímica Biológicas (IQUIFIB) Buenos Aires Argentina
| | - Gabriela E. Gomez
- Facultad de Farmacia y Bioquímica, Departamento de Química BiológicaUniversidad de Buenos Aires (UBA) Buenos Aires Argentina
- Universidad de Buenos Aires‐CONICET, Instituto de Química y Fisicoquímica Biológicas (IQUIFIB) Buenos Aires Argentina
| | | | - Silvana L. Giudicessi
- Facultad de Farmacia y Bioquímica, Cátedra de BiotecnologíaUniversidad de Buenos Aires (UBA) Buenos Aires Argentina
- CONICET—Universidad de Buenos Aires, Instituto de Nanobiotecnología (NANOBIOTEC) Buenos Aires Argentina
| | - Silvia A. Camperi
- Facultad de Farmacia y Bioquímica, Cátedra de BiotecnologíaUniversidad de Buenos Aires (UBA) Buenos Aires Argentina
- CONICET—Universidad de Buenos Aires, Instituto de Nanobiotecnología (NANOBIOTEC) Buenos Aires Argentina
| | - Jose M. Delfino
- Facultad de Farmacia y Bioquímica, Departamento de Química BiológicaUniversidad de Buenos Aires (UBA) Buenos Aires Argentina
- Universidad de Buenos Aires‐CONICET, Instituto de Química y Fisicoquímica Biológicas (IQUIFIB) Buenos Aires Argentina
| | | | - Daniel Enriz
- Facultad de Química, Bioquímica y FarmaciaUniversidad Nacional de San Luis San Luis Argentina
- IMIBIO‐CONICET San Luis Argentina
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7
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López
Cascales JJ, Zenak S, García de la Torre J, Lezama OG, Garro A, Enriz RD. Small Cationic Peptides: Influence of Charge on Their Antimicrobial Activity. ACS OMEGA 2018; 3:5390-5398. [PMID: 30221230 PMCID: PMC6130792 DOI: 10.1021/acsomega.8b00293] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 04/11/2018] [Indexed: 05/28/2023]
Abstract
The first stage of the action mechanism of small cationic peptides with antimicrobial activity is ruled by electrostatic interactions between the peptide and the pathogen cell membrane. Thus, an increase in its activity could be expected with an increase in the positive charge on the peptide. By contrast, the opposite behavior has been observed when the charge increases to reach a critical value, beyond which the activity falls. This work studies the perturbation effects in a cell membrane model for two small cationic peptides with similar length and morphology but with different cationic charges. The synthesis and antibacterial activity of the two peptides used in this study are described. The thermodynamic study associated with the insertion of these peptides into the membrane and the perturbing effects on the bilayer structure provide valuable insights into the molecular action mechanism associated with the charge of these small cationic peptides.
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Affiliation(s)
- José Javier López
Cascales
- Grupo
de Bioinformatica y Macromoleculas (BioMac), Area de Química
Física, Universidad Politécnica
de Cartagena, Aulario
II, Campus de Alfonso XIII, 30203 Cartagena, Murcia, Spain
| | - Siham Zenak
- Laboratoire
d’Etude Physique des Matériaux, Département de
Physique Energétique, Faculté de Physique, Université des Sciences et de la Technologie
d’Oran, BP 1505
El M’Naouer, Oran 31000, Algeria
| | - José García de la Torre
- Facultad
de Química, Departamento de Química Física, Universidad de Murcia, Campus de Espinardo, 30100 Espinardo, Murcia, Spain
| | | | - Adriana Garro
- Facultad
de Química, Bioquímica y Farmacia, IMIBIO-CONICET, Universidad Nacional de San Luis, Chacabuco 917, 5700 San Luis, Argentina
| | - Ricardo Daniel Enriz
- Facultad
de Química, Bioquímica y Farmacia, IMIBIO-CONICET, Universidad Nacional de San Luis, Chacabuco 917, 5700 San Luis, Argentina
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