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Makowski M, Franco OL, Santos NC, Melo MN. Lipid Shape as a Membrane Activity Modulator of a Fusogenic Antimicrobial Peptide. J Chem Inf Model 2025; 65:4554-4567. [PMID: 40110793 DOI: 10.1021/acs.jcim.4c02020] [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: 03/22/2025]
Abstract
An intriguing feature of many bacterial membranes is their prevalence of non-bilayer-forming lipids, such as the cone-shaped phosphatidylethanolamines and cardiolipins. Many membrane-active antimicrobial peptides lower the bilayer-to-hexagonal phase transition energy barrier in membranes containing such types of cone-shaped lipids. Here, we systematically studied how the molecular shape of lipids affects the activity of antimicrobial peptide EcDBS1R4, which is known to be an efficient fusogenic peptide. Using coarse-grained molecular dynamics simulations, we show the ability of EcDBS1R4 to form "hourglass-shaped" pores, which is inhibited by cone-shaped lipids. The abundance of cone-shaped lipids further correlates with the propensity of this peptide to oligomerize preferentially in antiparallel dimers. We also observe that EcDBS1R4 promotes the segregation of the anionic lipids. When coupled to dimerization, this charge segregation leads to regions in the bilayer that are devoid of peptides and rich in zwitterionic lipids. Our results indicate a protective role of cone-shaped lipids in bacterial membranes against pore-mediated permeabilization by EcDBS1R4.
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Affiliation(s)
- Marcin Makowski
- GIMM - Gulbenkian Institute for Molecular Medicine, Av. Prof. Egas Moniz, Lisbon 1649-035, Portugal
- Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, Lisbon 1649-028, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras 2780-157, Portugal
- Facultad de Ciencias Químicas, Departamento de Química Física, Universidad Complutense de Madrid, Avda. Complutense s/n, Madrid 28040, Spain
- Instituto de Investigación Biomédica Hospital Doce de Octubre (imas12), Avenida de Córdoba s/n, Madrid 28041, Spain
- Instituto Pluridisciplinar, Paseo Juan XXIII 1, Madrid 28040, Spain
| | - Octávio L Franco
- Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Campus Darcy Ribeiro, Asa Norte, Brasília, Distrito Federal 70910900, Brazil
- Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916 Módulo B, Asa Norte, Brasília, Distrito Federal 70790160, Brazil
- S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica, Dom Bosco Avenida Tamandaré 6000, Campo Grande, Mato Grosso do Sul 79117900, Brazil
| | - Nuno C Santos
- GIMM - Gulbenkian Institute for Molecular Medicine, Av. Prof. Egas Moniz, Lisbon 1649-035, Portugal
- Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, Lisbon 1649-028, Portugal
| | - Manuel N Melo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras 2780-157, Portugal
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2
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Gutierrez CDO, Almeida LHDO, Sardi JDCO, Almeida CV, de Oliveira CFR, Marchetto R, Crusca E, Buccini DF, Franco OL, Cardoso MH, Macedo MLR. Boosting the antibacterial potential of a linear encrypted peptide in a Kunitz-type inhibitor (ApTI) through physicochemical-guided approaches. Biochimie 2024; 227:161-171. [PMID: 39029576 DOI: 10.1016/j.biochi.2024.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 06/26/2024] [Accepted: 07/16/2024] [Indexed: 07/21/2024]
Abstract
Bacterial resistance has become a serious public health problem in recent years, thus encouraging the search for new antimicrobial agents. Here, we report an antimicrobial peptide (AMP), called PEPAD, which was designed based on an encrypted peptide from a Kunitz-type plant peptidase inhibitor. PEPAD was capable of rapidly inhibiting and eliminating numerous bacterial species at micromolar concentrations (from 4μM to 10 μM), with direct membrane activity. It was also observed that the peptide can act synergistically with ciprofloxacin and showed no toxicity in the G. mellonella in vivo assay. Circular dichroism assays revealed that the peptide's secondary structure adopts different scaffolds depending on the environment in which it is inserted. In lipids mimicking bacterial cell membranes, PEPAD adopts a more stable α-helical structure, which is consistent with its membrane-associated mechanism of action. When in contact with lipids mimicking mammalian cells, PEPAD adopts a disordered structure, losing its function and suggesting cellular selectivity. Therefore, these findings make PEPAD a promising candidate for future antimicrobial therapies with low toxicity to the host.
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Affiliation(s)
- Camila de Oliveira Gutierrez
- Laboratório de Purificação de Proteínas e Suas Funções Biológicas, Faculdade de Ciências Farmacêuticas, Alimentos e Nutrição, Universidade Federal de Mato Grosso Do Sul, Campo Grande, MS, Brazil
| | - Luís Henrique de Oliveira Almeida
- Laboratório de Purificação de Proteínas e Suas Funções Biológicas, Faculdade de Ciências Farmacêuticas, Alimentos e Nutrição, Universidade Federal de Mato Grosso Do Sul, Campo Grande, MS, Brazil
| | - Janaina de Cássia Orlandi Sardi
- Laboratório de Purificação de Proteínas e Suas Funções Biológicas, Faculdade de Ciências Farmacêuticas, Alimentos e Nutrição, Universidade Federal de Mato Grosso Do Sul, Campo Grande, MS, Brazil
| | - Claudiane Vilharroel Almeida
- Laboratório de Purificação de Proteínas e Suas Funções Biológicas, Faculdade de Ciências Farmacêuticas, Alimentos e Nutrição, Universidade Federal de Mato Grosso Do Sul, Campo Grande, MS, Brazil
| | - Caio Fernando Ramalho de Oliveira
- Laboratório de Purificação de Proteínas e Suas Funções Biológicas, Faculdade de Ciências Farmacêuticas, Alimentos e Nutrição, Universidade Federal de Mato Grosso Do Sul, Campo Grande, MS, Brazil
| | - Reinaldo Marchetto
- Universidade Estadual Paulista (UNESP), Instituto de Química, Araraquara, São Paulo, Brazil
| | - Edson Crusca
- Universidade Estadual Paulista (UNESP), Instituto de Química, Araraquara, São Paulo, Brazil
| | | | - Octavio Luiz Franco
- S-Inova Biotech, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil; Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil
| | - Marlon Henrique Cardoso
- Laboratório de Purificação de Proteínas e Suas Funções Biológicas, Faculdade de Ciências Farmacêuticas, Alimentos e Nutrição, Universidade Federal de Mato Grosso Do Sul, Campo Grande, MS, Brazil; S-Inova Biotech, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil; Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil
| | - Maria Lígia Rodrigues Macedo
- Laboratório de Purificação de Proteínas e Suas Funções Biológicas, Faculdade de Ciências Farmacêuticas, Alimentos e Nutrição, Universidade Federal de Mato Grosso Do Sul, Campo Grande, MS, Brazil.
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3
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Quigua-Orozco RM, Andrade IEP, Oshiro KGN, Rezende SB, Santos ADO, Pereira JAL, da Silva VG, Buccini DF, Porto WF, Macedo MLR, Cardoso MH, Franco OL. In silico optimization of analogs derived pro-adrenomedullin peptide to evaluate antimicrobial potential. Chem Biol Drug Des 2024; 104:e14588. [PMID: 39048531 DOI: 10.1111/cbdd.14588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 06/04/2024] [Accepted: 07/09/2024] [Indexed: 07/27/2024]
Abstract
Diverse computational approaches have been widely used to assist in designing antimicrobial peptides with enhanced activities. This tactic has also been used to address the need for new treatment alternatives to combat resistant bacterial infections. Herein, we have designed eight variants from a natural peptide, pro-adrenomedullin N-terminal 20 peptide (PAMP), using an in silico pattern insertion approach, the Joker algorithm. All the variants show an α-helical conformation, but with differences in the helix percentages according to circular dichroism (CD) results. We found that the C-terminal portion of PAMP may be relevant for its antimicrobial activities, as revealed by the molecular dynamics, CD, and antibacterial results. The analogs showed variable antibacterial potential, but most were not cytotoxic. Nevertheless, PAMP2 exhibited the most potent activities against human and animal-isolated bacteria, showing cytotoxicity only at a substantially higher concentration than its minimal inhibitory concentration (MIC). Our results suggest that the enhanced activity in the profile of PAMP2 may be related to their particular physicochemical properties, along with the adoption of an amphipathic α-helical arrangement with the conserved C-terminus portion. Finally, the peptides designed in this study can constitute scaffolds for the design of improved sequences.
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Affiliation(s)
- Raquel M Quigua-Orozco
- S-Inova Biotech, Programa de Pós-Graduação Em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Mato Grosso do Sul, Brazil
| | - Isadora E P Andrade
- Programa de Pós-Graduação Em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brasília, Distrito Federal, Brazil
| | - Karen G N Oshiro
- S-Inova Biotech, Programa de Pós-Graduação Em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Mato Grosso do Sul, Brazil
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação Em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
| | - Samilla B Rezende
- S-Inova Biotech, Programa de Pós-Graduação Em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Mato Grosso do Sul, Brazil
| | - Alexandre Duarte O Santos
- S-Inova Biotech, Programa de Pós-Graduação Em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Mato Grosso do Sul, Brazil
| | - Julia A L Pereira
- S-Inova Biotech, Programa de Pós-Graduação Em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Mato Grosso do Sul, Brazil
| | - Viviane G da Silva
- S-Inova Biotech, Programa de Pós-Graduação Em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Mato Grosso do Sul, Brazil
| | - Danieli F Buccini
- S-Inova Biotech, Programa de Pós-Graduação Em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Mato Grosso do Sul, Brazil
| | - William F Porto
- Programa de Pós-Graduação Em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brasília, Distrito Federal, Brazil
| | - Maria L R Macedo
- Laboratório de Purificação de Proteínas e Suas Funções Biológicas, Universidade Federal de Mato Grosso Do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Marlon H Cardoso
- S-Inova Biotech, Programa de Pós-Graduação Em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Mato Grosso do Sul, Brazil
- Programa de Pós-Graduação Em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brasília, Distrito Federal, Brazil
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação Em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
- Laboratório de Purificação de Proteínas e Suas Funções Biológicas, Universidade Federal de Mato Grosso Do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Octávio L Franco
- S-Inova Biotech, Programa de Pós-Graduação Em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Mato Grosso do Sul, Brazil
- Programa de Pós-Graduação Em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brasília, Distrito Federal, Brazil
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação Em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
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Liu Y, Cui P, Tan R, Ru S. Rapid Membrane-Penetrating Hybrid Peptides Achieve Efficient Dual Antimicrobial and Antibiofilm Activity through a Triple Bactericidal Mechanism. ACS OMEGA 2024; 9:26133-26148. [PMID: 38911764 PMCID: PMC11191078 DOI: 10.1021/acsomega.4c01577] [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: 02/19/2024] [Revised: 05/21/2024] [Accepted: 05/24/2024] [Indexed: 06/25/2024]
Abstract
Antimicrobial peptides (AMPs) are a type of biomaterial used against multidrug resistant (MDR) bacteria. This study reports the design of a peptide family rich in tryptophan and lysine obtained by optimizing a natural AMP using single factor modification and pheromone hybridization to expedite the penetration and improve the antimicrobial activity of AMPs. S-4, L-4, and P-4 showed α-helical structures, exhibited extremely fast membrane penetration rates in vitro, and could kill MDR bacteria efficiently within 30 min. Intracellular fluorescence localization suggested rapid membrane-penetrating of AMPs within 1 min, making it more difficult for bacteria to develop resistance. Furthermore, they could effectively inhibit and destroy bacterial biofilms with dual antimicrobial and antibiofilm activity. In the treatment of skin infections caused by MDR-Acinetobacter baumannii in vivo , AMPs could effectively alleviate inflammation without toxic side effects. Additionally, the triple antimicrobial damage of AMPs was described in detail. AMPs rapidly penetrate the cell membrane, inducing cell membrane damage, triggering oxidative damage with a storm of reactive oxygen species and leading to bacterial death through leakage of cellular contents by complexing with DNA. The multiple damage is an important means by which AMPs can prevent bacterial resistance adequately.
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Affiliation(s)
| | | | - Rong Tan
- Lab of Environmental Health
and Ecological Engineering, College of Marine Life Science, Ocean University of China, Qingdao 266003, China
| | - Shaoguo Ru
- Lab of Environmental Health
and Ecological Engineering, College of Marine Life Science, Ocean University of China, Qingdao 266003, China
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5
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Liang Q, Liu Z, Liang Z, Zhu C, Li D, Kong Q, Mou H. Development strategies and application of antimicrobial peptides as future alternatives to in-feed antibiotics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:172150. [PMID: 38580107 DOI: 10.1016/j.scitotenv.2024.172150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/14/2024] [Accepted: 03/30/2024] [Indexed: 04/07/2024]
Abstract
The use of in-feed antibiotics has been widely restricted due to the significant environmental pollution and food safety concerns they have caused. Antimicrobial peptides (AMPs) have attracted widespread attention as potential future alternatives to in-feed antibiotics owing to their demonstrated antimicrobial activity and environment friendly characteristics. However, the challenges of weak bioactivity, immature stability, and low production yields of natural AMPs impede practical application in the feed industry. To address these problems, efforts have been made to develop strategies for approaching the AMPs with enhanced properties. Herein, we summarize approaches to improving the properties of AMPs as potential alternatives to in-feed antibiotics, mainly including optimization of structural parameters, sequence modification, selection of microbial hosts, fusion expression, and industrially fermentation control. Additionally, the potential for application of AMPs in animal husbandry is discussed. This comprehensive review lays a strong theoretical foundation for the development of in-feed AMPs to achieve the public health globally.
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Affiliation(s)
- Qingping Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
| | - Zhemin Liu
- Fundamental Science R&D Center of Vazyme Biotech Co. Ltd., Nanjing 210000, China
| | - Ziyu Liang
- Section of Neurobiology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Changliang Zhu
- College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
| | - Dongyu Li
- College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
| | - Qing Kong
- College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
| | - Haijin Mou
- College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China.
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6
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Orozco RMQ, Oshiro KGN, Pinto IB, Buccini DF, Almeida CV, Marin VN, de Souza CM, Macedo MLR, Cardoso MH, Franco OL. Employment of mastoparan-like peptides to prevent Staphylococcus aureus associated with bovine mastitis. J Bacteriol 2024; 206:e0007124. [PMID: 38629875 PMCID: PMC11112992 DOI: 10.1128/jb.00071-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 03/25/2024] [Indexed: 05/24/2024] Open
Abstract
Bovine mastitis is a frequent infection in lactating cattle, causing great economic losses. Staphylococcus aureus represents the main etiological agent, which causes recurrent and persistent intramammary infections because conventional antibiotics are ineffective against it. Mastoparan-like peptides are multifunctional molecules with broad antimicrobial potential, constituting an attractive alternative. Nevertheless, their toxicity to host cells has hindered their therapeutic application. Previously, our group engineered three mastoparan-L analogs, namely mastoparan-MO, mastoparan-R1, and [I5, R8] MP, to improve cell selectivity and potential. Here, we were interested in comparing the antibacterial efficacy of mastoparan-L and its analogs against bovine mastitis isolates of S. aureus strains, making a correlation with the physicochemical properties and structural arrangement changes promoted by the sequence modifications. As a result, the analog's hemolytic and/or antimicrobial activity was balanced. All the peptides displayed α-helical folding in hydrophobic and membrane-mimetic environments, as determined by circular dichroism. The peptide [I5, R8] MP stood out for its enhanced selectivity and antibacterial features related to mastoparan-L and the other derivatives. Biophysical approaches revealed that [I5, R8] MP rapidly depolarizes the bacterial membrane of S. aureus, causing cell death by subsequent membrane disruption. Our results demonstrated that the [I5, R8] MP peptide could be a starting point for the development of peptide-based drugs for the treatment of bovine mastitis, with the advantage of no residue in milk, which would help reduce the use of classical antibiotics.IMPORTANCEStaphylococcus aureus is a leading cause of mastitis, the world's most important dairy cattle disease. The multidrug resistance and zoonotic potential of S. aureus, besides the likelihood of antibiotic residues in milk, are of critical concern to public and animal health. Antimicrobial peptides offer a novel antimicrobial strategy. Here, we demonstrate that [I5, R8] MP is a potent and selective peptide, which acts on S. aureus by targeting the bacterial membrane. Therefore, understanding the physicochemical determinants and the modes of action of this class of antimicrobials opens novel prospects for peptide development with enhanced activities in the bovine mastitis context.
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Affiliation(s)
- Raquel M. Q. Orozco
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
| | - Karen G. N. Oshiro
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
- Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brasília, Brazil
| | - Ingrid B. Pinto
- Laboratório de Síntese e Transformações de Moléculas Orgânicas, Instituo de Química, Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil
| | - Danieli F. Buccini
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
| | - Claudiane V. Almeida
- Laboratório de Purificação de Proteínas e suas Funções Biológicas, Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil
| | - Valentina Nieto Marin
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
| | - Camila Maurmann de Souza
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brasília, Brazil
| | - Maria L. R. Macedo
- Laboratório de Purificação de Proteínas e suas Funções Biológicas, Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil
| | - Marlon H. Cardoso
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
- Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brasília, Brazil
- Laboratório de Purificação de Proteínas e suas Funções Biológicas, Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brasília, Brazil
| | - Octávio L. Franco
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
- Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brasília, Brazil
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brasília, Brazil
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Reffuveille F, Dghoughi Y, Colin M, Torres MDT, de la Fuente-Nunez C. Antibiofilm approaches as a new paradigm for treating infections. PROGRESS IN BIOMEDICAL ENGINEERING (BRISTOL, ENGLAND) 2024; 6:023001. [PMID: 39506977 PMCID: PMC11540418 DOI: 10.1088/2516-1091/ad1cd6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/08/2024]
Abstract
The lack of effective antibiotics for drug-resistant infections has led the World Health Organization to declare antibiotic resistance a global priority. Most bacterial infections are caused by microbes growing in structured communities called biofilms. Bacteria growing in biofilms are less susceptible to antibiotics than their planktonic counterparts. Despite their significant clinical implications, bacterial biofilms have not received the attention they warrant, with no approved antibiotics specifically designed for their eradication. In this paper, we aim to shed light on recent advancements in antibiofilm strategies that offer compelling alternatives to traditional antibiotics. Additionally, we will briefly explore the potential synergy between computational approaches, including the emerging field of artificial intelligence, and the accelerated design and discovery of novel antibiofilm molecules in the years ahead.
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Affiliation(s)
- Fany Reffuveille
- Université de Reims Champagne-Ardenne, Biomatériaux et Inflammation en Site Osseux, BIOS EA 4691, SFR Cap Santé, 51097 Reims, France
- Université de Reims Champagne-Ardenne, UFR Pharmacie, Service de Microbiologie, 51097 Reims, France
| | - Yasser Dghoughi
- Université de Reims Champagne-Ardenne, Biomatériaux et Inflammation en Site Osseux, BIOS EA 4691, SFR Cap Santé, 51097 Reims, France
| | - Marius Colin
- Université de Reims Champagne-Ardenne, Biomatériaux et Inflammation en Site Osseux, BIOS EA 4691, SFR Cap Santé, 51097 Reims, France
- Université de Reims Champagne-Ardenne, UFR Pharmacie, Service de Microbiologie, 51097 Reims, France
| | - Marcelo D T Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, United States of America
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, United States of America
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, United States of America
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, United States of America
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, United States of America
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8
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Surekha S, Lamiyan AK, Gupta V. Antibiotic Resistant Biofilms and the Quest for Novel Therapeutic Strategies. Indian J Microbiol 2024; 64:20-35. [PMID: 38468748 PMCID: PMC10924852 DOI: 10.1007/s12088-023-01138-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/03/2023] [Indexed: 03/13/2024] Open
Abstract
Antimicrobial resistance (AMR) is one of the major leading causes of death around the globe. Present treatment pipelines are insufficient to overcome the critical situation. Prominent biofilm forming human pathogens which can thrive in infection sites using adaptive features results in biofilm persistence. Considering the present scenario, prudential investigations into the mechanisms of resistance target them to improve antibiotic efficacy is required. Regarding this, developing newer and effective treatment options using edge cutting technologies in medical research is the need of time. The reasons underlying the adaptive features in biofilm persistence have been centred on different metabolic and physiological aspects. The high tolerance levels against antibiotics direct researchers to search for novel bioactive molecules that can help combat the problem. In view of this, the present review outlines the focuses on an opportunity of different strategies which are in testing pipeline can thus be developed into products ready to use.
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Affiliation(s)
- Saumya Surekha
- Department of Biochemistry, Panjab University, Chandigarh, India
| | | | - Varsha Gupta
- GMCH: Government Medical College and Hospital, Chandigarh, India
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9
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Pedron CN, Torres MDT, Oliveira CS, Silva AF, Andrade GP, Wang Y, Pinhal MAS, Cerchiaro G, da Silva Junior PI, da Silva FD, Radhakrishnan R, de la Fuente-Nunez C, Oliveira Junior VX. Molecular hybridization strategy for tuning bioactive peptide function. Commun Biol 2023; 6:1067. [PMID: 37857855 PMCID: PMC10587126 DOI: 10.1038/s42003-023-05254-7] [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: 05/18/2022] [Accepted: 08/17/2023] [Indexed: 10/21/2023] Open
Abstract
The physicochemical and structural properties of antimicrobial peptides (AMPs) determine their mechanism of action and biological function. However, the development of AMPs as therapeutic drugs has been traditionally limited by their toxicity for human cells. Tuning the physicochemical properties of such molecules may abolish toxicity and yield synthetic molecules displaying optimal safety profiles and enhanced antimicrobial activity. Here, natural peptides were modified to improve their activity by the hybridization of sequences from two different active peptide sequences. Hybrid AMPs (hAMPs) were generated by combining the amphipathic faces of the highly toxic peptide VmCT1, derived from scorpion venom, with parts of four other naturally occurring peptides having high antimicrobial activity and low toxicity against human cells. This strategy led to the design of seven synthetic bioactive variants, all of which preserved their structure and presented increased antimicrobial activity (3.1-128 μmol L-1). Five of the peptides (three being hAMPs) presented high antiplasmodial at 0.8 μmol L-1, and virtually no undesired toxic effects against red blood cells. In sum, we demonstrate that peptide hybridization is an effective strategy for redirecting biological activity to generate novel bioactive molecules with desired properties.
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Affiliation(s)
- Cibele Nicolaski Pedron
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, 09210580, Brazil
- Departamento de Bioquímica, Universidade Federal de São Paulo, São Paulo, SP, 04044020, Brazil
| | - Marcelo Der Torossian Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Cyntia Silva Oliveira
- Departamento de Bioquímica, Universidade Federal de São Paulo, São Paulo, SP, 04044020, Brazil
| | - Adriana Farias Silva
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo, SP, 04044020, Brazil
| | - Gislaine Patricia Andrade
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, 09210580, Brazil
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo, SP, 04044020, Brazil
| | - Yiming Wang
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Giselle Cerchiaro
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, 09210580, Brazil
| | | | - Fernanda Dias da Silva
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, 09210580, Brazil
| | - Ravi Radhakrishnan
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA.
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, USA.
| | - Vani Xavier Oliveira Junior
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, 09210580, Brazil.
- Departamento de Bioquímica, Universidade Federal de São Paulo, São Paulo, SP, 04044020, Brazil.
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10
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Wang X, Yang X, Wang Q, Meng D. Unnatural amino acids: promising implications for the development of new antimicrobial peptides. Crit Rev Microbiol 2023; 49:231-255. [PMID: 35254957 DOI: 10.1080/1040841x.2022.2047008] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The increasing incidence and rapid spread of bacterial resistance to conventional antibiotics are a serious global threat to public health, highlighting the need to develop new antimicrobial alternatives. Antimicrobial peptides (AMPs) represent a class of promising natural antibiotic candidates due to their broad-spectrum activity and low tendency to induce resistance. However, the development of AMPs for medical use is hampered by several obstacles, such as moderate activity, lability to proteolytic degradation, and low bioavailability. To date, many researchers have focussed on the optimization or design of novel artificial AMPs with desired properties. Unnatural amino acids (UAAs) are valuable building blocks in the manufacture of a variety of pharmaceuticals, and have been used to develop artificial AMPs with specific structural and physicochemical properties. Rational incorporation of UAAs has become a very promising approach to endow AMPs with strong and long-lasting activity but no toxicity. This review aims to summarize key approaches that have been used to incorporate UAAs to develop novel AMPs with improved properties and better performance. It is anticipated that this review will guide future design considerations for UAA-based antimicrobial applications.
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Affiliation(s)
- Xiuhong Wang
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin, People's Republic of China
| | - Xiaomin Yang
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin, People's Republic of China
| | - Qiaoe Wang
- Key Laboratory of Cosmetic, China National Light Industry, Beijing Technology and Business University, Beijing, People's Republic of China
| | - Demei Meng
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin, People's Republic of China.,Tianjin Gasin-DH Preservation Technology Co., Ltd, Tianjin, People's Republic of China
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11
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Su Y, Yrastorza JT, Matis M, Cusick J, Zhao S, Wang G, Xie J. Biofilms: Formation, Research Models, Potential Targets, and Methods for Prevention and Treatment. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2203291. [PMID: 36031384 PMCID: PMC9561771 DOI: 10.1002/advs.202203291] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/31/2022] [Indexed: 05/28/2023]
Abstract
Due to the continuous rise in biofilm-related infections, biofilms seriously threaten human health. The formation of biofilms makes conventional antibiotics ineffective and dampens immune clearance. Therefore, it is important to understand the mechanisms of biofilm formation and develop novel strategies to treat biofilms more effectively. This review article begins with an introduction to biofilm formation in various clinical scenarios and their corresponding therapy. Established biofilm models used in research are then summarized. The potential targets which may assist in the development of new strategies for combating biofilms are further discussed. The novel technologies developed recently for the prevention and treatment of biofilms including antimicrobial surface coatings, physical removal of biofilms, development of new antimicrobial molecules, and delivery of antimicrobial agents are subsequently presented. Finally, directions for future studies are pointed out.
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Affiliation(s)
- Yajuan Su
- Department of Surgery‐Transplant and Mary & Dick Holland Regenerative Medicine ProgramCollege of MedicineUniversity of Nebraska Medical CenterOmahaNE68198USA
| | - Jaime T. Yrastorza
- Department of Surgery‐Transplant and Mary & Dick Holland Regenerative Medicine ProgramCollege of MedicineUniversity of Nebraska Medical CenterOmahaNE68198USA
| | - Mitchell Matis
- Department of Surgery‐Transplant and Mary & Dick Holland Regenerative Medicine ProgramCollege of MedicineUniversity of Nebraska Medical CenterOmahaNE68198USA
| | - Jenna Cusick
- Department of Surgery‐Transplant and Mary & Dick Holland Regenerative Medicine ProgramCollege of MedicineUniversity of Nebraska Medical CenterOmahaNE68198USA
| | - Siwei Zhao
- Department of Surgery‐Transplant and Mary & Dick Holland Regenerative Medicine ProgramCollege of MedicineUniversity of Nebraska Medical CenterOmahaNE68198USA
| | - Guangshun Wang
- Department of Pathology and MicrobiologyCollege of MedicineUniversity of Nebraska Medical CenterOmahaNE68198USA
| | - Jingwei Xie
- Department of Surgery‐Transplant and Mary & Dick Holland Regenerative Medicine ProgramCollege of MedicineUniversity of Nebraska Medical CenterOmahaNE68198USA
- Department of Mechanical and Materials EngineeringCollege of EngineeringUniversity of Nebraska‐LincolnLincolnNE68588USA
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12
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Cardoso MH, Chan LY, Cândido ES, Buccini DF, Rezende SB, Torres MDT, Oshiro KGN, Silva ÍC, Gonçalves S, Lu TK, Santos NC, de la Fuente-Nunez C, Craik DJ, Franco OL. An N-capping asparagine-lysine-proline (NKP) motif contributes to a hybrid flexible/stable multifunctional peptide scaffold. Chem Sci 2022; 13:9410-9424. [PMID: 36093022 PMCID: PMC9383710 DOI: 10.1039/d1sc06998e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 07/10/2022] [Indexed: 11/21/2022] Open
Abstract
Structural diversity drives multiple biological activities and mechanisms of action in linear peptides. Here we describe an unusual N-capping asparagine-lysine-proline (NKP) motif that confers a hybrid multifunctional scaffold to a computationally designed peptide (PaDBS1R7). PaDBS1R7 has a shorter α-helix segment than other computationally designed peptides of similar sequence but with key residue substitutions. Although this motif acts as an α-helix breaker in PaDBS1R7, the Asn5 presents exclusive N-capping effects, forming a belt to establish hydrogen bonds for an amphipathic α-helix stabilization. The combination of these different structural profiles was described as a coil/N-cap/α-helix scaffold, which was also observed in diverse computational peptide mutants. Biological studies revealed that all peptides displayed antibacterial activities. However, only PaDBS1R7 displayed anticancer properties, eradicated Pseudomonas aeruginosa biofilms, decreased bacterial counts by 100-1000-fold in vivo, reduced lipopolysaccharide-induced macrophages stress, and stimulated fibroblast migration for wound healing. This study extends our understanding of an N-capping NKP motif to engineering hybrid multifunctional peptide drug candidates with potent anti-infective and immunomodulatory properties.
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Affiliation(s)
- Marlon H Cardoso
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco Avenida Tamandaré 6000 Campo Grande - MS 79117900 Brazil
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília SGAN 916 Módulo B, Asa Norte, Brasília - DF 70790160 Brazil
- Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Campus Darcy Ribeiro Asa Norte Brasília - DF 70910900 Brazil
- Instituto de Biociências (INBIO), Universidade Federal de Mato Grosso do Sul, Cidade Universitária 79070900 Campo Grande Mato Grosso do Sul Brazil
| | - Lai Y Chan
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland Brisbane QLD, 4072 Australia
| | - Elizabete S Cândido
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco Avenida Tamandaré 6000 Campo Grande - MS 79117900 Brazil
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília SGAN 916 Módulo B, Asa Norte, Brasília - DF 70790160 Brazil
| | - Danieli F Buccini
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco Avenida Tamandaré 6000 Campo Grande - MS 79117900 Brazil
| | - Samilla B Rezende
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco Avenida Tamandaré 6000 Campo Grande - MS 79117900 Brazil
| | - Marcelo D T Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, Penn Institute for Computational Science, University of Pennsylvania Philadelphia Pennsylvania USA
| | - Karen G N Oshiro
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco Avenida Tamandaré 6000 Campo Grande - MS 79117900 Brazil
- Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Campus Darcy Ribeiro Asa Norte Brasília - DF 70910900 Brazil
| | - Ítala C Silva
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa Lisbon Portugal
| | - Sónia Gonçalves
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa Lisbon Portugal
| | - Timothy K Lu
- Synthetic Biology Group, MIT Synthetic Biology Center, The Center for Microbiome Informatics and Therapeutics, Research Laboratory of Electronics, Department of Biological Engineering, Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology Cambridge - MA 02139 USA
| | - Nuno C Santos
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa Lisbon Portugal
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, Penn Institute for Computational Science, University of Pennsylvania Philadelphia Pennsylvania USA
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland Brisbane QLD, 4072 Australia
| | - Octávio L Franco
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco Avenida Tamandaré 6000 Campo Grande - MS 79117900 Brazil
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília SGAN 916 Módulo B, Asa Norte, Brasília - DF 70790160 Brazil
- Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Campus Darcy Ribeiro Asa Norte Brasília - DF 70910900 Brazil
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13
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Prediction of Linear Cationic Antimicrobial Peptides Active against Gram-Negative and Gram-Positive Bacteria Based on Machine Learning Models. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12073631] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Antimicrobial peptides (AMPs) are considered as promising alternatives to conventional antibiotics in order to overcome the growing problems of antibiotic resistance. Computational prediction approaches receive an increasing interest to identify and design the best candidate AMPs prior to the in vitro tests. In this study, we focused on the linear cationic peptides with non-hemolytic activity, which are downloaded from the Database of Antimicrobial Activity and Structure of Peptides (DBAASP). Referring to the MIC (Minimum inhibition concentration) values, we have assigned a positive label to a peptide if it shows antimicrobial activity; otherwise, the peptide is labeled as negative. Here, we focused on the peptides showing antimicrobial activity against Gram-negative and against Gram-positive bacteria separately, and we created two datasets accordingly. Ten different physico-chemical properties of the peptides are calculated and used as features in our study. Following data exploration and data preprocessing steps, a variety of classification algorithms are used with 100-fold Monte Carlo Cross-Validation to build models and to predict the antimicrobial activity of the peptides. Among the generated models, Random Forest has resulted in the best performance metrics for both Gram-negative dataset (Accuracy: 0.98, Recall: 0.99, Specificity: 0.97, Precision: 0.97, AUC: 0.99, F1: 0.98) and Gram-positive dataset (Accuracy: 0.95, Recall: 0.95, Specificity: 0.95, Precision: 0.90, AUC: 0.97, F1: 0.92) after outlier elimination is applied. This prediction approach might be useful to evaluate the antibacterial potential of a candidate peptide sequence before moving to the experimental studies.
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Torres MDT, Melo MCR, Flowers L, Crescenzi O, Notomista E, de la Fuente-Nunez C. Mining for encrypted peptide antibiotics in the human proteome. Nat Biomed Eng 2022; 6:67-75. [PMID: 34737399 DOI: 10.1038/s41551-021-00801-1] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 08/25/2021] [Indexed: 12/30/2022]
Abstract
The emergence of drug-resistant bacteria calls for the discovery of new antibiotics. Yet, for decades, traditional discovery strategies have not yielded new classes of antimicrobial. Here, by mining the human proteome via an algorithm that relies on the sequence length, net charge, average hydrophobicity and other physicochemical properties of antimicrobial peptides, we report the identification of 2,603 encrypted peptide antibiotics that are encoded in proteins with biological function unrelated to the immune system. We show that the encrypted peptides kill pathogenic bacteria by targeting their membrane, modulate gut and skin commensals, do not readily select for bacterial resistance, and possess anti-infective activity in skin abscess and thigh infection mouse models. We also show, in vitro and in the two mouse models of infection, that encrypted antibiotic peptides from the same biogeographical area display synergistic antimicrobial activity. Our algorithmic strategy allows for the rapid mining of proteomic data and opens up new routes for the discovery of candidate antibiotics.
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Affiliation(s)
- Marcelo D T Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Marcelo C R Melo
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Laurice Flowers
- Departments of Dermatology and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Orlando Crescenzi
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Eugenio Notomista
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA.
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, USA.
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15
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Oliveira CS, Torres MDT, Pedron CN, Andrade VB, Silva PI, Silva FD, de la Fuente-Nunez C, Oliveira VX. Synthetic Peptide Derived from Scorpion Venom Displays Minimal Toxicity and Anti-infective Activity in an Animal Model. ACS Infect Dis 2021; 7:2736-2745. [PMID: 34463484 DOI: 10.1021/acsinfecdis.1c00261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Multidrug-resistant bacteria represent a global health problem increasingly leading to infections that are untreatable with our existing antibiotic arsenal. Therefore, it is critical to identify novel effective antimicrobials. Venoms represent an underexplored source of potential antibiotic molecules. Here, we engineered a peptide (IsCT1-NH2) derived from the venom of the scorpion Opisthacanthus madagascariensis, whose application as an antimicrobial had been traditionally hindered by its high toxicity. Through peptide design and the knowledge obtained in preliminary studies with single and double-substituted analogs, we engineered IsCT1 derivatives with multiple amino acid substitutions to assess the impact of net charge on antimicrobial activity and toxicity. We demonstrate that increased net charge (from +3 to +6) significantly reduced toxicity toward human erythrocytes. Our lead synthetic peptide, [A]1[K]3[F]5[K]8-IsCT1-NH2 (net charge of +4), exhibited increased antimicrobial activity against Gram-negative and Gram-positive bacteria in vitro and enhanced anti-infective activity in a mouse model. Mechanism of action studies revealed that the increased antimicrobial activity of our lead molecule was due, at least in part, to its enhanced ability to permeabilize the outer membrane and depolarize the cytoplasmic membrane. In summary, we describe a simple method based on net charge tuning to turn highly toxic venom-derived peptides into viable therapeutics.
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Affiliation(s)
- Cyntia Silva Oliveira
- Escola Paulista de Medicina, Programa de pós-graduação em Biologia Molecular, Universidade Federal de São Paulo, São Paulo, SP 04044020, Brazil
| | - Marcelo Der Torossian Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Cibele Nicolaski Pedron
- Escola Paulista de Medicina, Programa de pós-graduação em Biologia Molecular, Universidade Federal de São Paulo, São Paulo, SP 04044020, Brazil
| | - Viviane Brito Andrade
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP 09210580, Brazil
| | - Pedro Ismael Silva
- Instituto Butantan, Laboratório Especial de Toxinologia Aplicada, São Paulo, SP 05503900, Brazil
| | - Fernanda Dias Silva
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP 09210580, Brazil
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Vani Xavier Oliveira
- Escola Paulista de Medicina, Programa de pós-graduação em Biologia Molecular, Universidade Federal de São Paulo, São Paulo, SP 04044020, Brazil
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP 09210580, Brazil
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16
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17
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Almeida CV, de Oliveira CFR, Dos Santos EL, Dos Santos HF, Júnior EC, Marchetto R, da Cruz LA, Ferreira AMT, Gomes VM, Taveira GB, Costa BO, Franco OL, Cardoso MH, Macedo MLR. Differential interactions of the antimicrobial peptide, RQ18, with phospholipids and cholesterol modulate its selectivity for microorganism membranes. Biochim Biophys Acta Gen Subj 2021; 1865:129937. [PMID: 34052310 DOI: 10.1016/j.bbagen.2021.129937] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 05/15/2021] [Accepted: 05/24/2021] [Indexed: 10/21/2022]
Abstract
BACKGROUND Antimicrobial peptides (AMPs) are molecules with potential application for the treatment of microorganism infections. We, herein, describe the structure, activity, and mechanism of action of RQ18, an α-helical AMP that displays antimicrobial activity against Gram-positive and Gram-negative bacteria, and yeasts from the Candida genus. METHODS A physicochemical-guided design assisted by computer tools was used to obtain our lead peptide candidate, named RQ18. This peptide was assayed against Gram-positive and Gram-negative bacteria, yeasts, and mammalian cells to determine its selectivity index. The secondary structure and the mechanism of action of RQ18 were investigated using circular dichroism, large unilamellar vesicles, and molecular dynamic simulations. RESULTS RQ18 was not cytotoxic to human lung fibroblasts, peripheral blood mononuclear cells, red blood cells, or Vero cells at MIC values, exhibiting a high selectivity index. Circular dichroism analysis and molecular dynamic simulations revealed that RQ18 presents varying structural profiles in aqueous solution, TFE/water mixtures, SDS micelles, and lipid bilayers. The peptide was virtually unable to release carboxyfluorescein from large unilamellar vesicles composed of POPC/cholesterol, model that mimics the eukaryotic membrane, indicating that vesicles' net charges and the presence of cholesterol may be related with RQ18 selectivity for bacterial and fungal cell surfaces. CONCLUSIONS RQ18 was characterized as a membrane-active peptide with dual antibacterial and antifungal activities, without compromising mammalian cells viability, thus reinforcing its therapeutic application. GENERAL SIGNIFICANCE These results provide further insight into the complex process of AMPs interaction with biological membranes, in special with systems that mimic prokaryotic and eukaryotic cell surfaces.
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Affiliation(s)
- Claudiane V Almeida
- Universidade Federal de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Caio F R de Oliveira
- Universidade Federal de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil; Universidade Federal da Grande Dourados, Dourados, Mato Grosso do Sul, Brazil; Oncolytic Anticancer Drugs, Dourados, Mato Grosso do Sul, Brazil
| | - Edson L Dos Santos
- Universidade Federal da Grande Dourados, Dourados, Mato Grosso do Sul, Brazil
| | - Helder F Dos Santos
- Universidade Federal da Grande Dourados, Dourados, Mato Grosso do Sul, Brazil
| | - Edson C Júnior
- Instituto de Química, Departamento de Bioquímica e Química Tecnológica, Universidade Estadual Paulista Júlio de Mesquita Filho, Araraquara, São Paulo, Brazil
| | - Reinaldo Marchetto
- Instituto de Química, Departamento de Bioquímica e Química Tecnológica, Universidade Estadual Paulista Júlio de Mesquita Filho, Araraquara, São Paulo, Brazil
| | - Leticia A da Cruz
- Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, Brazil
| | - Alda Maria T Ferreira
- Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, Brazil
| | - Valdirene M Gomes
- Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Gabriel B Taveira
- Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Bruna O Costa
- S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Mato Grosso do Sul, Brazil
| | - Octávio L Franco
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil; S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Mato Grosso do Sul, Brazil
| | - Marlon H Cardoso
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil; S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Mato Grosso do Sul, Brazil
| | - Maria Lígia R Macedo
- Universidade Federal de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil.
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Investigation of antibiofilm activity, antibacterial activity, and mechanistic studies of an amphiphilic peptide against Acinetobacter baumannii. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183600. [PMID: 33675719 DOI: 10.1016/j.bbamem.2021.183600] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 02/12/2021] [Accepted: 02/27/2021] [Indexed: 12/15/2022]
Abstract
Biofilm-producing pathogens, such as Acinetobacter baumannii, have aroused escalating attention. Because these bacteria could secrete mixture with close-knit architecture and complicated components to resist traditional antibiotics. Here, we reported an amphiphilic peptide denoted as zp3 (GIIAGIIIKIKK-NH2), which showed favorable bioactivity against Acinetobacter baumannii ATCC 19606 (minimal inhibitory concentration, MIC = 4 μM) and low cytotoxicity to mammalian cells Vero (half maximal inhibitory concentration, IC50 > 100 μM). Importantly, zp3 could inhibit the formation of biofilm at micromole level and eliminate around 50% preformed biofilm at 32 μM after 6 h treatment. This peptide was able to bind with biofilm while maintaining a helical structure in a mimic biofilm-rich environment. In vivo test demonstrated that zp3 rescued 33.3% of larvae after 48 h infection and reduced 1 log live bacteria inside the animal body after 6 h treatment. The bactericidal mode for zp3 was attributed to the combination of influencing ions balance at low concentration and inducing permeability alteration and pore formation on the Acinetobacter baumannii membrane at high concentration. Application on medical textiles also proved that zp3 could perform a good antibacterial activity in practice.
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19
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Torres MDT, Cao J, Franco OL, Lu TK, de la Fuente-Nunez C. Synthetic Biology and Computer-Based Frameworks for Antimicrobial Peptide Discovery. ACS NANO 2021; 15:2143-2164. [PMID: 33538585 PMCID: PMC8734659 DOI: 10.1021/acsnano.0c09509] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Antibiotic resistance is one of the greatest challenges of our time. This global health problem originated from a paucity of truly effective antibiotic classes and an increased incidence of multi-drug-resistant bacterial isolates in hospitals worldwide. Indeed, it has been recently estimated that 10 million people will die annually from drug-resistant infections by the year 2050. Therefore, the need to develop out-of-the-box strategies to combat antibiotic resistance is urgent. The biological world has provided natural templates, called antimicrobial peptides (AMPs), which exhibit multiple intrinsic medical properties including the targeting of bacteria. AMPs can be used as scaffolds and, via engineering, can be reconfigured for optimized potency and targetability toward drug-resistant pathogens. Here, we review the recent development of tools for the discovery, design, and production of AMPs and propose that the future of peptide drug discovery will involve the convergence of computational and synthetic biology principles.
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Affiliation(s)
- Marcelo D T Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Jicong Cao
- Synthetic Biology Group, MIT Synthetic Biology Center, Department of Biological Engineering and Electrical Engineering and Computer Science, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Octavio L Franco
- Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília, DF 70790160, Brazil
- S-inova Biotech, Universidade Católica Dom Bosco, Campo Grande, MS 79117010, Brazil
| | - Timothy K Lu
- Synthetic Biology Group, MIT Synthetic Biology Center, Department of Biological Engineering and Electrical Engineering and Computer Science, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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20
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Silveira GGOS, Torres MDT, Ribeiro CFA, Meneguetti BT, Carvalho CME, de la Fuente-Nunez C, Franco OL, Cardoso MH. Antibiofilm Peptides: Relevant Preclinical Animal Infection Models and Translational Potential. ACS Pharmacol Transl Sci 2021; 4:55-73. [PMID: 33615161 DOI: 10.1021/acsptsci.0c00191] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Indexed: 12/21/2022]
Abstract
Biofilm-forming bacteria may be 10-1000 times more resistant to antibiotics than planktonic bacteria and represent about 75% of bacterial infections in humans. Antibiofilm treatments are scarce, and no effective therapies have been reported so far. In this context, antibiofilm peptides (ABPs) represent an exciting class of agents with potent activity against biofilms both in vitro and in vivo. Moreover, murine models of bacterial biofilm infections have been used to evaluate the in vivo effectiveness of ABPs. Therefore, here we highlight the translational potential of ABPs and provide an overview of the different clinically relevant murine models to assess ABP efficacy, including wound, foreign body, chronic lung, and oral models of infection. We discuss key challenges to translate ABPs to the clinic and the pros and cons of the existing murine biofilm models for reliable assessment of the efficacy of ABPs.
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Affiliation(s)
- Gislaine G O S Silveira
- S-Inova Biotech, Programa de Pós-Graduação Stricto Sensu em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Mato Grosso do Sul 79117-010, Brazil
| | - Marcelo D T Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States.,Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States.,Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Camila F A Ribeiro
- S-Inova Biotech, Programa de Pós-Graduação Stricto Sensu em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Mato Grosso do Sul 79117-010, Brazil
| | - Beatriz T Meneguetti
- S-Inova Biotech, Programa de Pós-Graduação Stricto Sensu em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Mato Grosso do Sul 79117-010, Brazil
| | - Cristiano M E Carvalho
- S-Inova Biotech, Programa de Pós-Graduação Stricto Sensu em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Mato Grosso do Sul 79117-010, Brazil
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States.,Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States.,Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Octávio L Franco
- S-Inova Biotech, Programa de Pós-Graduação Stricto Sensu em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Mato Grosso do Sul 79117-010, Brazil.,Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal 71966-700, Brazil
| | - Marlon H Cardoso
- S-Inova Biotech, Programa de Pós-Graduação Stricto Sensu em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Mato Grosso do Sul 79117-010, Brazil.,Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal 71966-700, Brazil
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21
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Torres MDT, Voskian S, Brown P, Liu A, Lu TK, Hatton TA, de la Fuente-Nunez C. Coatable and Resistance-Proof Ionic Liquid for Pathogen Eradication. ACS NANO 2021; 15:966-978. [PMID: 33438392 DOI: 10.1021/acsnano.0c07642] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Antibiotic-resistant bacteria infect close to 3 million people, and kill 35,000, each year in the United States. Ionic liquid (IL)-based antimicrobial agents have the potential to diversify our ever-diminishing antibiotic arsenal. Here, we describe an IL with potent submicromolar antimicrobial activity in vitro against clinically relevant Gram-negative and Gram-positive bacterial pathogens as well as anti-infective activity in a mouse model. The IL kills pathogenic bacteria such as Acinetobacter baumannii, Salmonella enterica, and Escherichia coli by disrupting their outer membrane and does not select for bacterial resistance. We show incorporation of our IL into surface coatings to generate a type of antibiofilm material. The IL-loaded ionogel surfaces demonstrate high-antimicrobial and antifouling activity by killing bacteria in both static and dynamic tests. Our IL-based antibiofilm surfaces are low-cost and easy to manufacture, can be formed on glass, latex, plastic, and metal surfaces, such as catheters and other medical devices where high local concentrations of antimicrobials are needed, and may have applications in other clinical and industrial settings.
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Affiliation(s)
- Marcelo D T Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Sahag Voskian
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Paul Brown
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Andong Liu
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Boston Children's Hospital, Boston, Massachusetts 02115, United States
| | - Timothy K Lu
- Synthetic Biology Group, MIT Synthetic Biology Center, Department of Biological Engineering, and Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, United States
| | - T Alan Hatton
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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22
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Repurposing a peptide toxin from wasp venom into antiinfectives with dual antimicrobial and immunomodulatory properties. Proc Natl Acad Sci U S A 2020; 117:26936-26945. [PMID: 33046640 DOI: 10.1073/pnas.2012379117] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Novel antibiotics are urgently needed to combat multidrug-resistant pathogens. Venoms represent previously untapped sources of novel drugs. Here we repurposed mastoparan-L, the toxic active principle derived from the venom of the wasp Vespula lewisii, into synthetic antimicrobials. We engineered within its N terminus a motif conserved among natural peptides with potent immunomodulatory and antimicrobial activities. The resulting peptide, mast-MO, adopted an α-helical structure as determined by NMR, exhibited increased antibacterial properties comparable to standard-of-care antibiotics both in vitro and in vivo, and potentiated the activity of different classes of antibiotics. Mechanism-of-action studies revealed that mast-MO targets bacteria by rapidly permeabilizing their outer membrane. In animal models, the peptide displayed direct antimicrobial activity, led to enhanced ability to attract leukocytes to the infection site, and was able to control inflammation. Permutation studies depleted the remaining toxicity of mast-MO toward human cells, yielding derivatives with antiinfective activity in animals. We demonstrate a rational design strategy for repurposing venoms into promising antimicrobials.
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23
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Torres MDT, Silva AF, Andrade GP, Pedron CN, Cerchiaro G, Ribeiro AO, Oliveira VX, de la Fuente‐Nunez C. The wasp venom antimicrobial peptide polybia-CP and its synthetic derivatives display antiplasmodial and anticancer properties. Bioeng Transl Med 2020; 5:e10167. [PMID: 33005737 PMCID: PMC7510464 DOI: 10.1002/btm2.10167] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 05/10/2020] [Accepted: 05/11/2020] [Indexed: 12/11/2022] Open
Abstract
The wasp venom-derived antimicrobial peptide polybia-CP has been previously shown to exhibit potent antimicrobial activity, but it is also highly toxic. Previously, using a physicochemical-guided peptide design strategy, we reversed its toxicity while preserving and even enhancing its antibacterial properties. Here, we report on several additional unanticipated biological properties of polybia-CP and derivatives, namely their ability to target Plasmodium sporozoites and cancer cells. We leverage a physicochemical-guided approach to identify features that operate as functional hotspots making these peptides viable antiplasmodial and anticancer agents. Helical content and net positive charge are identified as key structural and physicochemical determinants for antiplasmodial activity. In addition to helicity and net charge, hydrophobicity-related properties of polybia-CP and derivatives were found to be equally critical to target cancer cells. We demonstrate that by tuning these physicochemical parameters, it is possible to design synthetic peptides with enhanced submicromolar antiplasmodial potency and micromolar anticancer activity. This study reveals novel and previously undescribed functions for Polybia-CP and analogs. Additionally, we demonstrate that a physicochemical-guided rational design strategy can be used for identifying functional hotspots in peptide molecules and for tuning structure-function to generate novel and potent new-to-nature therapies.
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Affiliation(s)
- Marcelo D. T. Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, Penn Institute for Computational Science, and Department of BioengineeringUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Adriana F. Silva
- Centro de Ciências Naturais e HumanasUniversidade Federal do ABCSanto AndréSPBrazil
- Departamento de BioquímicaUniversidade Federal de São PauloSão PauloSPBrazil
| | - Gislaine P. Andrade
- Centro de Ciências Naturais e HumanasUniversidade Federal do ABCSanto AndréSPBrazil
| | - Cibele N. Pedron
- Centro de Ciências Naturais e HumanasUniversidade Federal do ABCSanto AndréSPBrazil
| | - Giselle Cerchiaro
- Centro de Ciências Naturais e HumanasUniversidade Federal do ABCSanto AndréSPBrazil
| | - Anderson O. Ribeiro
- Centro de Ciências Naturais e HumanasUniversidade Federal do ABCSanto AndréSPBrazil
| | - Vani X. Oliveira
- Centro de Ciências Naturais e HumanasUniversidade Federal do ABCSanto AndréSPBrazil
- Departamento de BiofísicaUniversidade Federal de São PauloSão PauloSPBrazil
| | - Cesar de la Fuente‐Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, Penn Institute for Computational Science, and Department of BioengineeringUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
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24
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Dang TT, Chan LY, Huang YH, Nguyen LTT, Kaas Q, Huynh T, Craik DJ. Exploring the Sequence Diversity of Cyclotides from Vietnamese Viola Species. JOURNAL OF NATURAL PRODUCTS 2020; 83:1817-1828. [PMID: 32437150 DOI: 10.1021/acs.jnatprod.9b01218] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Viola is the largest genus in the Violaceae plant family and is known for its ubiquitous natural production of cyclotides. Many Viola species are used as medicinal herbs across Asia and are often consumed by humans in teas for the treatment of diseases, including ulcers and asthma. Previous studies reported the isolation of cyclotides from Viola species in many countries in the hope of discovering novel compounds with anti-cancer activities; however, Viola species from Vietnam have not been investigated to date. Here, the discovery of cyclotides from three Viola species (V. arcuata, V. tonkinensis, and V. austrosinensis) collected in the northern mountainous region of Vietnam is reported. Ten cyclotides were isolated from these three Viola species: four are novel and six were previously reported to be expressed in other plants. The structures of three of the new bracelet cyclotides are similar to that of cycloviolacin O2. Because cycloviolacin O2 has previously been shown to have potent activity against a wide range of cancer cell lines including HeLa (human cervical cancer cells) and PC-3 (human prostate cancer cells), the cancer cytotoxicity of the cyclotides isolated from V. arcuata was assessed. All tested cyclotides were cytotoxic against cancer cells, albeit to varying degrees. The sequences discovered in this study significantly expand the understanding of cyclotide diversity, especially in comparison with other cyclotides found in plants from the Asian region.
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Affiliation(s)
- Tien T Dang
- The Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Lai Y Chan
- The Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Yen-Hua Huang
- The Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Linh T T Nguyen
- The Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Quentin Kaas
- The Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Tien Huynh
- Department of Biosciences and Food Technology, RMIT University, Victoria 3001, Australia
| | - David J Craik
- The Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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25
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Porto WF, Irazazabal LN, Humblot V, Haney EF, Ribeiro SM, Hancock REW, Ladram A, Franco OL. EcDBS1R6: A novel cationic antimicrobial peptide derived from a signal peptide sequence. Biochim Biophys Acta Gen Subj 2020; 1864:129633. [PMID: 32416198 DOI: 10.1016/j.bbagen.2020.129633] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 04/10/2020] [Accepted: 05/08/2020] [Indexed: 12/23/2022]
Abstract
BACKGROUND Bacterial infections represent a major worldwide health problem the antimicrobial peptides (AMPs) have been considered as potential alternative agents for treating these infections. Here we demonstrated the antimicrobial activity of EcDBS1R6, a peptide derived from a signal peptide sequence of Escherichia coli that we previously turned into an AMP by making changes through the Joker algorithm. METHODS Antimicrobial activity was measured by broth microdilution method. Membrane integrity was measured using fluorescent probes and through scanning electron microscopy imaging. A sliding window of truncated peptides was used to determine the EcDBS1R6 active core. Molecular dynamics in TFE/water environment was used to assess the EcDBS1R6 structure. RESULTS Signal peptides are known to naturally interact with membranes; however, the modifications introduced by Joker transformed this peptide into a membrane-active agent capable of killing bacteria. The C-terminus was unable to fold into an α-helix whereas its fragments showed poor or no antimicrobial activity, suggesting that the EcDBS1R6 antibacterial core was located at the helical N-terminus, corresponding to the signal peptide portion of the parent peptide. CONCLUSION The strategy of transforming signal peptides into AMPs appears to be promising and could be used to produce novel antimicrobial agents. GENERAL SIGNIFICANCE The process of transforming an inactive signal peptide into an antimicrobial peptide could open a new venue for creating new AMPs derived from signal peptides.
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Affiliation(s)
- William F Porto
- S-Inova Biotech, Pós-graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil; Porto Reports, Brasília, DF, Brazil
| | - Luz N Irazazabal
- Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia Universidade Católica de Brasília, Brasília, DF, Brazil; Molecular Pathology Post-graduate Program, University of Brasília, Brasília, Distrito Federal, Brazil
| | - Vincent Humblot
- Sorbonne Université, CNRS, Laboratoire de Réactivité de Surface, LRS, F-75252 Paris, France
| | - Evan F Haney
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, 2259 Lower Mall Research Station, Vancouver, British Columbia V6T 1Z4, Canada
| | - Suzana M Ribeiro
- Programa de Pós-Graduação em Ciências da Saúde, Universidade Federal da Grande Dourados, Dourados, MS, Brazil
| | - Robert E W Hancock
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, 2259 Lower Mall Research Station, Vancouver, British Columbia V6T 1Z4, Canada
| | - Ali Ladram
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, IBPS, BIOSIPE, F-75252 Paris, France
| | - Octavio L Franco
- S-Inova Biotech, Pós-graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil; Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia Universidade Católica de Brasília, Brasília, DF, Brazil; Molecular Pathology Post-graduate Program, University of Brasília, Brasília, Distrito Federal, Brazil.
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26
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da Silva ACB, Sardi JDCO, de Oliveira DGL, de Oliveira CFR, Dos Santos HF, Dos Santos EL, Crusca E, Cardoso MH, Franco OL, Macedo MLR. Development of a novel anti-biofilm peptide derived from profilin of Spodoptera frugiperda. BIOFOULING 2020; 36:516-527. [PMID: 32619153 DOI: 10.1080/08927014.2020.1776857] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 05/14/2020] [Accepted: 05/21/2020] [Indexed: 06/11/2023]
Abstract
Candida yeast infections are the fourth leading cause of death worldwide. Peptides with antimicrobial activity are a promising alternative treatment for such infections. Here, the antifungal activity of a new antimicrobial peptide-PEP-IA18-was evaluated against Candida species. PEP-IA18 was designed from the primary sequence of profilin, a protein from Spodoptera frugiperda, and displayed potent activity against Candida albicans and Candida tropicalis, showing a minimum inhibitory concentration (MIC) of 2.5 µM. Furthermore, the mechanism of action of PEP-IA18 involved interaction with the cell membrane (ergosterol complexation). Treatment at MIC and/or 10 × MIC significantly reduced biofilm formation and viability. PEP-IA18 showed low toxicity toward human fibroblasts and only revealed hemolytic activity at high concentrations. Thus, PEP-IA18 exhibited antifungal and anti-biofilm properties with potential applicability in the treatment of infections caused by Candida species.
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Affiliation(s)
- Amanda Carolina Borges da Silva
- Protein Purification Laboratory and Biological Functions, Faculty of Pharmaceutical Sciences, Food and Nutrition, Federal University of Mato Grosso do Sul, Campo Grande, MS, Brazil
| | - Janaina de Cassia Orlandi Sardi
- Protein Purification Laboratory and Biological Functions, Faculty of Pharmaceutical Sciences, Food and Nutrition, Federal University of Mato Grosso do Sul, Campo Grande, MS, Brazil
| | - Daniella Gorete Lourenço de Oliveira
- Protein Purification Laboratory and Biological Functions, Faculty of Pharmaceutical Sciences, Food and Nutrition, Federal University of Mato Grosso do Sul, Campo Grande, MS, Brazil
| | - Caio Fernando Ramalho de Oliveira
- Center for Biotechnology and Bioprospecting Studies Applied to Metabolism (GEBBAM), Federal University of Grande Dourados, Dourados, MS, Brazil
| | - Helder Freitas Dos Santos
- Center for Biotechnology and Bioprospecting Studies Applied to Metabolism (GEBBAM), Federal University of Grande Dourados, Dourados, MS, Brazil
| | - Edson Lucas Dos Santos
- Center for Biotechnology and Bioprospecting Studies Applied to Metabolism (GEBBAM), Federal University of Grande Dourados, Dourados, MS, Brazil
| | - Edson Crusca
- Department of Biochemistry, Institute of Chemistry, São Paulo State University, Araraquara, São Paulo, Brazil
| | - Marlon Henrique Cardoso
- S-inova Biotech, Graduate Program in Biotechnology, Dom Bosco Catholic University, Campo Grande, MS, Brazil
- Center for Proteomic and Biochemical Analysis, Graduate Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, Brasília, DF, Brazil
- Graduate Program in Molecular Pathology, Faculty of Medicine, University of Brasilia, Brasília, DF, Brazil
| | - Octávio Luiz Franco
- S-inova Biotech, Graduate Program in Biotechnology, Dom Bosco Catholic University, Campo Grande, MS, Brazil
- Center for Proteomic and Biochemical Analysis, Graduate Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, Brasília, DF, Brazil
- Graduate Program in Molecular Pathology, Faculty of Medicine, University of Brasilia, Brasília, DF, Brazil
| | - Maria Lígia Rodrigues Macedo
- Protein Purification Laboratory and Biological Functions, Faculty of Pharmaceutical Sciences, Food and Nutrition, Federal University of Mato Grosso do Sul, Campo Grande, MS, Brazil
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27
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Cardoso MH, Orozco RQ, Rezende SB, Rodrigues G, Oshiro KGN, Cândido ES, Franco OL. Computer-Aided Design of Antimicrobial Peptides: Are We Generating Effective Drug Candidates? Front Microbiol 2020; 10:3097. [PMID: 32038544 PMCID: PMC6987251 DOI: 10.3389/fmicb.2019.03097] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 12/20/2019] [Indexed: 11/16/2022] Open
Abstract
Antimicrobial peptides (AMPs), especially antibacterial peptides, have been widely investigated as potential alternatives to antibiotic-based therapies. Indeed, naturally occurring and synthetic AMPs have shown promising results against a series of clinically relevant bacteria. Even so, this class of antimicrobials has continuously failed clinical trials at some point, highlighting the importance of AMP optimization. In this context, the computer-aided design of AMPs has put together crucial information on chemical parameters and bioactivities in AMP sequences, thus providing modes of prediction to evaluate the antibacterial potential of a candidate sequence before synthesis. Quantitative structure-activity relationship (QSAR) computational models, for instance, have greatly contributed to AMP sequence optimization aimed at improved biological activities. In addition to machine-learning methods, the de novo design, linguistic model, pattern insertion methods, and genetic algorithms, have shown the potential to boost the automated design of AMPs. However, how successful have these approaches been in generating effective antibacterial drug candidates? Bearing this in mind, this review will focus on the main computational strategies that have generated AMPs with promising activities against pathogenic bacteria, as well as anti-infective potential in different animal models, including sepsis and cutaneous infections. Moreover, we will point out recent studies on the computer-aided design of antibiofilm peptides. As expected from automated design strategies, diverse candidate sequences with different structural arrangements have been generated and deposited in databases. We will, therefore, also discuss the structural diversity that has been engendered.
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Affiliation(s)
- Marlon H Cardoso
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil.,Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brazil
| | - Raquel Q Orozco
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil.,Instituto de Ciências Biológicas, Departamento de Biologia, Programa de Pós-Graduação em Ciências Biológicas (Imunologia/Genética e Biotecnologia), Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | - Samilla B Rezende
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
| | - Gisele Rodrigues
- Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brazil
| | - Karen G N Oshiro
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil.,Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brasília, Brazil
| | - Elizabete S Cândido
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil.,Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brazil
| | - Octávio L Franco
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil.,Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brazil.,Instituto de Ciências Biológicas, Departamento de Biologia, Programa de Pós-Graduação em Ciências Biológicas (Imunologia/Genética e Biotecnologia), Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil.,Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brasília, Brazil
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28
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Der Torossian Torres M, de la Fuente-Nunez C. Reprogramming biological peptides to combat infectious diseases. Chem Commun (Camb) 2019; 55:15020-15032. [PMID: 31782426 DOI: 10.1039/c9cc07898c] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
With the rapid spread of resistance among parasites and bacterial pathogens, antibiotic-resistant infections have drawn much attention worldwide. Consequently, there is an urgent need to develop new strategies to treat neglected diseases and drug-resistant infections. Here, we outline several new strategies that have been developed to counter pathogenic microorganisms by designing and constructing antimicrobial peptides (AMPs). In addition to traditional discovery and design mechanisms guided by chemical biology, synthetic biology and computationally-based approaches offer useful tools for the discovery and generation of bioactive peptides. We believe that the convergence of such fields, coupled with systematic experimentation in animal models, will help translate biological peptides into the clinic. The future of anti-infective therapeutics is headed towards specifically designed molecules whose form is driven by computer-based frameworks. These molecules are selective, stable, and active at therapeutic doses.
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Affiliation(s)
- Marcelo Der Torossian Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, and Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, and Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
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29
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de Barros E, Gonçalves RM, Cardoso MH, Santos NC, Franco OL, Cândido ES. Snake Venom Cathelicidins as Natural Antimicrobial Peptides. Front Pharmacol 2019; 10:1415. [PMID: 31849667 PMCID: PMC6895205 DOI: 10.3389/fphar.2019.01415] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 11/07/2019] [Indexed: 01/10/2023] Open
Abstract
Bioactive small molecules isolated from animals, plants, fungi and bacteria, including natural antimicrobial peptides, have shown great therapeutic potential worldwide. Among these peptides, snake venom cathelicidins are being widely exploited, because the variation in the composition of the venom reflects a range of biological activities that may be of biotechnological interest. Cathelicidins are short, cationic, and amphipathic molecules. They play an important role in host defense against microbial infections. We are currently facing a strong limitation on pharmacological interventions for infection control, which has become increasingly complex due to the lack of effective therapeutic options. In this review, we will focus on natural snake venom cathelicidins as promising candidates for the development of new antibacterial agents to fight antibiotic-resistant bacteria. We will highlight their antibacterial and antibiofilm activities, mechanism of action, and modulation of the innate immune response.
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Affiliation(s)
- Elizângela de Barros
- Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
- S-Inova Biotech, Universidade Católica Dom Bosco, Campo Grande, Brazil
| | - Regina M. Gonçalves
- Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
- S-Inova Biotech, Universidade Católica Dom Bosco, Campo Grande, Brazil
| | - Marlon H. Cardoso
- S-Inova Biotech, Universidade Católica Dom Bosco, Campo Grande, Brazil
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brazil
| | - Nuno C. Santos
- Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
- S-Inova Biotech, Universidade Católica Dom Bosco, Campo Grande, Brazil
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Octávio L. Franco
- Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
- S-Inova Biotech, Universidade Católica Dom Bosco, Campo Grande, Brazil
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brazil
| | - Elizabete S. Cândido
- Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
- S-Inova Biotech, Universidade Católica Dom Bosco, Campo Grande, Brazil
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brazil
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30
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Agbale CM, Sarfo JK, Galyuon IK, Juliano SA, Silva GGO, Buccini DF, Cardoso MH, Torres MDT, Angeles-Boza AM, de la Fuente-Nunez C, Franco OL. Antimicrobial and Antibiofilm Activities of Helical Antimicrobial Peptide Sequences Incorporating Metal-Binding Motifs. Biochemistry 2019; 58:3802-3812. [PMID: 31448597 DOI: 10.1021/acs.biochem.9b00440] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Antimicrobial peptides (AMPs) represent alternative strategies to combat the global health problem of antibiotic resistance. However, naturally occurring AMPs are generally not sufficiently active for use as antibiotics. Optimized synthetic versions incorporating additional design principles are needed. Here, we engineered amino-terminal Cu(II) and Ni(II) (ATCUN) binding motifs, which can enhance biological function, into the native sequence of two AMPs, CM15 and citropin1.1. The incorporation of metal-binding motifs modulated the antimicrobial activity of synthetic peptides against a panel of carbapenem-resistant enterococci (CRE) bacteria, including carbapenem-resistant Klebsiella pneumoniae (KpC+) and Escherichia coli (KpC+). Activity modulation depended on the type of ATCUN variant utilized. Membrane permeability assays revealed that the in silico selected lead template, CM15, and its ATCUN analogs increased bacterial cell death. Mass spectrometry, circular dichroism, and molecular dynamics simulations indicated that coordinating ATCUN derivatives with Cu(II) ions did not increase the helical tendencies of the AMPs. CM15 ATCUN variants, when combined with Meropenem, streptomycin, or chloramphenicol, showed synergistic effects against E. coli (KpC+ 1812446) biofilms. Motif addition also reduced the hemolytic activity of the wild-type AMP and improved the survival rate of mice in a systemic infection model. The dependence of these bioactivities on the particular amino acids of the ATCUN motif highlights the possible use of size, charge, and hydrophobicity to fine-tune AMP biological function. Our data indicate that incorporating metal-binding motifs into peptide sequences leads to synthetic variants with modified biological properties. These principles may be applied to augment the activities of other peptide sequences.
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Affiliation(s)
- Caleb M Agbale
- S-INOVA Biotech, Programa de Pós-Graduação em Biotecnologia , Universidade Católica Dom Bosco , Campo Grande , Mato Grosso Do Sul, MS 79117-900 , Brazil.,Department of Biochemistry, School of Biological Sciences, College of Agriculture and Natural Sciences , University of Cape Coast , Cape Coast , Ghana.,Department of Molecular Biology and Biotechnology, School of Biological Sciences, College of Agriculture and Natural Sciences , University of Cape Coast , Cape Coast , Ghana
| | - Justice K Sarfo
- S-INOVA Biotech, Programa de Pós-Graduação em Biotecnologia , Universidade Católica Dom Bosco , Campo Grande , Mato Grosso Do Sul, MS 79117-900 , Brazil
| | - Isaac K Galyuon
- Department of Molecular Biology and Biotechnology, School of Biological Sciences, College of Agriculture and Natural Sciences , University of Cape Coast , Cape Coast , Ghana
| | - Samuel A Juliano
- Department of Chemistry , University of Connecticut , Storrs , Connecticut 06269 , United States
| | - Gislaine G O Silva
- S-INOVA Biotech, Programa de Pós-Graduação em Biotecnologia , Universidade Católica Dom Bosco , Campo Grande , Mato Grosso Do Sul, MS 79117-900 , Brazil
| | - Danieli F Buccini
- S-INOVA Biotech, Programa de Pós-Graduação em Biotecnologia , Universidade Católica Dom Bosco , Campo Grande , Mato Grosso Do Sul, MS 79117-900 , Brazil
| | - Marlon H Cardoso
- S-INOVA Biotech, Programa de Pós-Graduação em Biotecnologia , Universidade Católica Dom Bosco , Campo Grande , Mato Grosso Do Sul, MS 79117-900 , Brazil.,Centro de Análises de Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia , Universidade Católica de Brasília , Brasília , DF 70790-160 , Brazil.,Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina , Universidade de Brasília , Brasília , DF 70910-900 , Brazil
| | - Marcelo D T Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Perelman School of Medicine, and Department of Bioengineering , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Alfredo M Angeles-Boza
- Department of Chemistry , University of Connecticut , Storrs , Connecticut 06269 , United States.,Institute of Materials Science , University of Connecticut , Storrs , Connecticut 06269 , United States
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Perelman School of Medicine, and Department of Bioengineering , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Octavio L Franco
- S-INOVA Biotech, Programa de Pós-Graduação em Biotecnologia , Universidade Católica Dom Bosco , Campo Grande , Mato Grosso Do Sul, MS 79117-900 , Brazil.,Centro de Análises de Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia , Universidade Católica de Brasília , Brasília , DF 70790-160 , Brazil.,Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina , Universidade de Brasília , Brasília , DF 70910-900 , Brazil
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31
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Oshiro KGN, Cândido ES, Chan LY, Torres MDT, Monges BED, Rodrigues SG, Porto WF, Ribeiro SM, Henriques ST, Lu TK, de la Fuente-Nunez C, Craik DJ, Franco OL, Cardoso MH. Computer-Aided Design of Mastoparan-like Peptides Enables the Generation of Nontoxic Variants with Extended Antibacterial Properties. J Med Chem 2019; 62:8140-8151. [DOI: 10.1021/acs.jmedchem.9b00915] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Karen G. N. Oshiro
- Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brasília 70910900, Brazil
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande 79117900, Brazil
| | - Elizabete S. Cândido
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande 79117900, Brazil
- Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília 70790160, Brazil
| | - Lai Y. Chan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Marcelo D. T. Torres
- Synthetic Biology Group, MIT Synthetic Biology Center; The Center for Microbiome Informatics and Therapeutics; Research Laboratory of Electronics, Department of Biological Engineering, and Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, United States
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, 09210170, Brazil
| | - Bruna E. D. Monges
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande 79117900, Brazil
| | - Silvia G. Rodrigues
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande 79117900, Brazil
| | - William F. Porto
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande 79117900, Brazil
- Porto Reports, Brasília, DF 70790160, Brazil
| | - Suzana M. Ribeiro
- Programa de Pós-Graduação em Ciências da Saúde, Universidade Federal da Grande Dourados, Dourados, MS 79825070, Brazil
| | - Sónia T. Henriques
- Faculty of Health, School of Biomedical Sciences, Institute of Health & Biomedical Innovation, Queensland University of Technology, Translational Research Institute, Brisbane, QLD 4102, Australia
| | - Timothy K. Lu
- Synthetic Biology Group, MIT Synthetic Biology Center; The Center for Microbiome Informatics and Therapeutics; Research Laboratory of Electronics, Department of Biological Engineering, and Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, United States
| | - Cesar de la Fuente-Nunez
- Synthetic Biology Group, MIT Synthetic Biology Center; The Center for Microbiome Informatics and Therapeutics; Research Laboratory of Electronics, Department of Biological Engineering, and Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, United States
| | - David J. Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Octávio L. Franco
- Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brasília 70910900, Brazil
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande 79117900, Brazil
- Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília 70790160, Brazil
| | - Marlon H. Cardoso
- Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brasília 70910900, Brazil
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande 79117900, Brazil
- Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília 70790160, Brazil
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
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32
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Torres MD, Sothiselvam S, Lu TK, de la Fuente-Nunez C. Peptide Design Principles for Antimicrobial Applications. J Mol Biol 2019; 431:3547-3567. [DOI: 10.1016/j.jmb.2018.12.015] [Citation(s) in RCA: 184] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 12/19/2018] [Accepted: 12/22/2018] [Indexed: 02/08/2023]
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33
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Cândido ES, Cardoso MH, Chan LY, Torres MDT, Oshiro KGN, Porto WF, Ribeiro SM, Haney EF, Hancock REW, Lu TK, de la Fuente-Nunez C, Craik DJ, Franco OL. Short Cationic Peptide Derived from Archaea with Dual Antibacterial Properties and Anti-Infective Potential. ACS Infect Dis 2019; 5:1081-1086. [PMID: 31016969 DOI: 10.1021/acsinfecdis.9b00073] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Bacterial biofilms and associated infections represent one of the biggest challenges in the clinic, and as an alternative to counter bacterial infections, antimicrobial peptides have attracted great attention in the past decade. Here, ten short cationic antimicrobial peptides were generated through a sliding-window strategy on the basis of the 19-amino acid residue peptide, derived from a Pyrobaculum aerophilum ribosomal protein. PaDBS1R6F10 exhibited anti-infective potential as it decreased the bacterial burden in murine Pseudomonas aeruginosa cutaneous infections by more than 1000-fold. Adverse cytotoxic and hemolytic effects were not detected against mammalian cells. The peptide demonstrated structural plasticity in terms of its secondary structure in the different environments tested. PaDBS1R6F10 represents a promising antimicrobial agent against bacteria infections, without harming human cells.
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Affiliation(s)
- Elizabete S. Cândido
- Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916 Módulo B, Asa Norte, Brasília, Distrito Federal 70790160, Brazil
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Avenida Tamandaré 6000, Campo Grande, Mato Grosso do Sul 79117900, Brazil
| | - Marlon H. Cardoso
- Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916 Módulo B, Asa Norte, Brasília, Distrito Federal 70790160, Brazil
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Avenida Tamandaré 6000, Campo Grande, Mato Grosso do Sul 79117900, Brazil
- Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Campus Darcy Ribeiro, Asa Norte, Brasília, Distrito Federal 70910900, Brazil
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Brisbane, Queensland 4072, Australia
| | - Lai Y. Chan
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Brisbane, Queensland 4072, Australia
| | - Marcelo D. T. Torres
- Synthetic Biology Group, MIT Synthetic Biology Center; The Center for Microbiome Informatics and Therapeutics; Research Laboratory of Electronics, Department of Biological Engineering, and Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, United States of America
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, São Paulo 09210170, Brazil
| | - Karen G. N. Oshiro
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Avenida Tamandaré 6000, Campo Grande, Mato Grosso do Sul 79117900, Brazil
- Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Campus Darcy Ribeiro, Asa Norte, Brasília, Distrito Federal 70910900, Brazil
| | - William F. Porto
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Avenida Tamandaré 6000, Campo Grande, Mato Grosso do Sul 79117900, Brazil
- Porto Reports, Brasília, Distrito Federal 70790160, Brazil
| | - Suzana M. Ribeiro
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Avenida Tamandaré 6000, Campo Grande, Mato Grosso do Sul 79117900, Brazil
| | - Evan F. Haney
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Robert E. W. Hancock
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Timothy K. Lu
- Synthetic Biology Group, MIT Synthetic Biology Center; The Center for Microbiome Informatics and Therapeutics; Research Laboratory of Electronics, Department of Biological Engineering, and Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, United States of America
| | - Cesar de la Fuente-Nunez
- Synthetic Biology Group, MIT Synthetic Biology Center; The Center for Microbiome Informatics and Therapeutics; Research Laboratory of Electronics, Department of Biological Engineering, and Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, United States of America
| | - David J. Craik
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Brisbane, Queensland 4072, Australia
| | - Octávio L. Franco
- Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916 Módulo B, Asa Norte, Brasília, Distrito Federal 70790160, Brazil
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Avenida Tamandaré 6000, Campo Grande, Mato Grosso do Sul 79117900, Brazil
- Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Campus Darcy Ribeiro, Asa Norte, Brasília, Distrito Federal 70910900, Brazil
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