1
|
Ramazi S, Mohammadi N, Allahverdi A, Khalili E, Abdolmaleki P. A review on antimicrobial peptides databases and the computational tools. Database (Oxford) 2022; 2022:baac011. [PMID: 35305010 PMCID: PMC9216472 DOI: 10.1093/database/baac011] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 02/04/2022] [Accepted: 02/28/2022] [Indexed: 12/29/2022]
Abstract
Antimicrobial Peptides (AMPs) have been considered as potential alternatives for infection therapeutics since antibiotic resistance has been raised as a global problem. The AMPs are a group of natural peptides that play a crucial role in the immune system in various organisms AMPs have features such as a short length and efficiency against microbes. Importantly, they have represented low toxicity in mammals which makes them potential candidates for peptide-based drugs. Nevertheless, the discovery of AMPs is accompanied by several issues which are associated with labour-intensive and time-consuming wet-lab experiments. During the last decades, numerous studies have been conducted on the investigation of AMPs, either natural or synthetic type, and relevant data are recently available in many databases. Through the advancement of computational methods, a great number of AMP data are obtained from publicly accessible databanks, which are valuable resources for mining patterns to design new models for AMP prediction. However, due to the current flaws in assessing computational methods, more interrogations are warranted for accurate evaluation/analysis. Considering the diversity of AMPs and newly reported ones, an improvement in Machine Learning algorithms are crucial. In this review, we aim to provide valuable information about different types of AMPs, their mechanism of action and a landscape of current databases and computational tools as resources to collect AMPs and beneficial tools for the prediction and design of a computational model for new active AMPs.
Collapse
Affiliation(s)
- Shahin Ramazi
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Jalal Ale Ahmad Highway, Tehran 14115-111, Iran
| | - Neda Mohammadi
- Department of Medical Biotechnology, Faculty of Allied Medical Sciences, Iran University of Medical Sciences, Hemmat Highway, Tehran 1449614535, Iran
- Institute of Pharmacology and Toxicology, University of Bonn, Biomedical Center, Venusberg Campus 1, Bonn 53127, Germany
| | - Abdollah Allahverdi
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Jalal Ale Ahmad Highway, Tehran 14115-111, Iran
| | - Elham Khalili
- Department of Plant Biology, Faculty of Biological Sciences, Tarbiat Modares University, Jalal Ale Ahmad Highway, Tehran 14115-111, Iran
| | - Parviz Abdolmaleki
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Jalal Ale Ahmad Highway, Tehran 14115-111, Iran
| |
Collapse
|
2
|
Barbosa JC, Gonçalves S, Makowski M, Silva ÍC, Caetano T, Schneider T, Mösker E, Süssmuth RD, Santos NC, Mendo S. Insights into the mode of action of the two-peptide lantibiotic lichenicidin. Colloids Surf B Biointerfaces 2022; 211:112308. [PMID: 34973602 DOI: 10.1016/j.colsurfb.2021.112308] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 11/30/2022]
Abstract
Lantibiotics are promising candidates to address the worldwide problem of antibiotic resistance. They belong to a class of natural compounds exhibiting strong activity against clinically relevant Gram-positive bacterial strains, including methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococci (VRE). Lichenicidin is a class II two-peptide lantibiotic. The presence of the two mature peptides, Bliα and Bliβ, is necessary for full activity against target bacteria. This work aims at clarifying the synergistic activity of both peptides in their interaction with the target membranes. The effect of lichenicidin was tested against S. aureus cells and large unilamellar vesicles. Lichenicidin increases the net surface charge of S. aureus, as shown by zeta-potential measurements, without reaching electroneutralization. In addition, lichenicidin causes cell surface perturbations that culminate in the leakage of its internal contents, as observed by atomic force microscopy. Bliα seems to have low affinity for S. aureus, however, it contributes to increase the affinity of Bliβ, because together they present higher affinity than separately. In contrast, Bliα seems to provide an anchoring site for lichenicidin in lipid II-containing membranes. Interestingly, Bliβ alone can induce high levels of membrane leakage, but this effect appears to be faster in the presence of Bliα. Based on this information, we propose a mechanism of action of lichenicidin.
Collapse
Affiliation(s)
- Joana C Barbosa
- Department of Biology & Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal.
| | - Sónia Gonçalves
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, Lisbon, Portugal.
| | - Marcin Makowski
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, Lisbon, Portugal.
| | - Ítala C Silva
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, Lisbon, Portugal.
| | - Tânia Caetano
- Department of Biology & Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal.
| | - Tanja Schneider
- Institute for Pharmaceutical Microbiology, University of Bonn, Bonn, Germany.
| | - Eva Mösker
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany.
| | | | - Nuno C Santos
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, Lisbon, Portugal.
| | - Sónia Mendo
- Department of Biology & Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal.
| |
Collapse
|
3
|
Wang H, Zhao J, Zhao H, Li H, Wang J. CL-ACP: a parallel combination of CNN and LSTM anticancer peptide recognition model. BMC Bioinformatics 2021; 22:512. [PMID: 34670488 PMCID: PMC8527680 DOI: 10.1186/s12859-021-04433-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 10/05/2021] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Anticancer peptides are defence substances with innate immune functions that can selectively act on cancer cells without harming normal cells and many studies have been conducted to identify anticancer peptides. In this paper, we introduce the anticancer peptide secondary structures as additional features and propose an effective computational model, CL-ACP, that uses a combined network and attention mechanism to predict anticancer peptides. RESULTS The CL-ACP model uses secondary structures and original sequences of anticancer peptides to construct the feature space. The long short-term memory and convolutional neural network are used to extract the contextual dependence and local correlations of the feature space. Furthermore, a multi-head self-attention mechanism is used to strengthen the anticancer peptide sequences. Finally, three categories of feature information are classified by cascading. CL-ACP was validated using two types of datasets, anticancer peptide datasets and antimicrobial peptide datasets, on which it achieved good results compared to previous methods. CL-ACP achieved the highest AUC values of 0.935 and 0.972 on the anticancer peptide and antimicrobial peptide datasets, respectively. CONCLUSIONS CL-ACP can effectively recognize antimicrobial peptides, especially anticancer peptides, and the parallel combined neural network structure of CL-ACP does not require complex feature design and high time cost. It is suitable for application as a useful tool in antimicrobial peptide design.
Collapse
Affiliation(s)
- Huiqing Wang
- College of Information and Computer, Taiyuan University of Technology, Taiyuan, 030024, China
| | - Jian Zhao
- College of Information and Computer, Taiyuan University of Technology, Taiyuan, 030024, China.
| | - Hong Zhao
- College of Information and Computer, Taiyuan University of Technology, Taiyuan, 030024, China
| | - Haolin Li
- College of Information and Computer, Taiyuan University of Technology, Taiyuan, 030024, China
| | - Juan Wang
- College of Information and Computer, Taiyuan University of Technology, Taiyuan, 030024, China
| |
Collapse
|
4
|
Felício MR, Silveira GGOS, Oshiro KGN, Meneguetti BT, Franco OL, Santos NC, Gonçalves S. Polyalanine peptide variations may have different mechanisms of action against multidrug-resistant bacterial pathogens. J Antimicrob Chemother 2021; 76:1174-1186. [PMID: 33501992 DOI: 10.1093/jac/dkaa560] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 12/15/2020] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES The number of bacterial pathogens resistant to the currently available antibiotics has dramatically increased, with antimicrobial peptides (AMPs) being among the most promising potential new drugs. In this study, the applicability and mechanisms of action of Pa-MAP 2 and Pa-MAP 1.9, two AMPs synthetically designed based on a natural AMP template, were evaluated. METHODS Pa-MAP 2 and Pa-MAP 1.9 were tested against a clinically isolated multidrug-resistant (MDR) Escherichia coli strain. Biophysical approaches were used to evaluate the preference of both peptides for specific lipid membranes, and bacterial surface changes imaged by atomic force microscopy (AFM). The efficacy of both peptides was assessed both in vitro and in vivo. RESULTS Experimental results showed that both peptides have antimicrobial activity against the E. coli MDR strain. Zeta potential and surface plasmon resonance assays showed that they interact extensively with negatively charged membranes, changing from a random coil structure, when free in solution, to an α-helical structure after membrane interaction. The antibacterial efficacy was evaluated in vitro, by several techniques, and in vivo, using a wound infection model, showing a concentration-dependent antibacterial effect. Different membrane properties were evaluated to understand the mechanism underlying peptide action, showing that both promote destabilization of the bacterial surface, as imaged by AFM, and change properties such as membrane surface and dipole potential. CONCLUSIONS Despite their similarity, data indicate that the mechanisms of action of the peptides are different, with Pa-MAP 1.9 being more effective than Pa-MAP 2. These results highlight their potential use as antimicrobial agents against MDR bacteria.
Collapse
Affiliation(s)
- Mário R Felício
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Gislaine G O S Silveira
- S-Inova Biotech, Pós-graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil
| | - Karen G N Oshiro
- S-Inova Biotech, Pós-graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil
- Programa de Pós-Graduação em Patologia Molecular, Universidade de Brasília, Brasília, DF, Brazil
| | - Beatriz T Meneguetti
- S-Inova Biotech, Pós-graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil
| | - Octávio L Franco
- S-Inova Biotech, Pós-graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil
- Programa de Pós-Graduação em Patologia Molecular, Universidade de Brasília, Brasília, DF, Brazil
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil
| | - Nuno C Santos
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Sónia Gonçalves
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| |
Collapse
|
5
|
Harper CE, Hernandez CJ. Cell biomechanics and mechanobiology in bacteria: Challenges and opportunities. APL Bioeng 2020; 4:021501. [PMID: 32266323 PMCID: PMC7113033 DOI: 10.1063/1.5135585] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 02/27/2020] [Indexed: 12/11/2022] Open
Abstract
Physical forces play a profound role in the survival and function of all known forms of life. Advances in cell biomechanics and mechanobiology have provided key insights into the physiology of eukaryotic organisms, but much less is known about the roles of physical forces in bacterial physiology. This review is an introduction to bacterial mechanics intended for persons familiar with cells and biomechanics in mammalian cells. Bacteria play a major role in human health, either as pathogens or as beneficial commensal organisms within the microbiome. Although bacteria have long been known to be sensitive to their mechanical environment, understanding the effects of physical forces on bacterial physiology has been limited by their small size (∼1 μm). However, advancements in micro- and nano-scale technologies over the past few years have increasingly made it possible to rigorously examine the mechanical stress and strain within individual bacteria. Here, we review the methods currently used to examine bacteria from a mechanical perspective, including the subcellular structures in bacteria and how they differ from those in mammalian cells, as well as micro- and nanomechanical approaches to studying bacteria, and studies showing the effects of physical forces on bacterial physiology. Recent findings indicate a large range in mechanical properties of bacteria and show that physical forces can have a profound effect on bacterial survival, growth, biofilm formation, and resistance to toxins and antibiotics. Advances in the field of bacterial biomechanics have the potential to lead to novel antibacterial strategies, biotechnology approaches, and applications in synthetic biology.
Collapse
Affiliation(s)
- Christine E. Harper
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York 14853, USA
| | | |
Collapse
|
6
|
Buck AK, Elmore DE, Darling LEO. Using fluorescence microscopy to shed light on the mechanisms of antimicrobial peptides. Future Med Chem 2019; 11:2445-2458. [PMID: 31517514 PMCID: PMC6787493 DOI: 10.4155/fmc-2019-0095] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 06/18/2019] [Indexed: 12/18/2022] Open
Abstract
Antimicrobial peptides (AMPs) are promising in the fight against increasing bacterial resistance, but the development of AMPs with enhanced activity requires a thorough understanding of their mechanisms of action. Fluorescence microscopy is one of the most flexible and effective tools to characterize AMPs, particularly in its ability to measure the membrane interactions and cellular localization of peptides. Recent advances have increased the scope of research questions that can be addressed via microscopy through improving spatial and temporal resolution. Unique combinations of fluorescent labels and dyes can simultaneously consider different aspects of peptide-membrane interaction mechanisms. This review emphasizes the central role that fluorescence microscopy will continue to play in the interrogation of AMP structure-function relationships and the engineering of more potent peptides.
Collapse
Affiliation(s)
- Anne K Buck
- Biochemistry Program, Wellesley College, Wellesley, MA 02481, USA
| | - Donald E Elmore
- Department of Chemistry & Biochemistry Program, Wellesley College, Wellesley, MA 02481, USA
| | - Louise EO Darling
- Department of Biological Sciences & Biochemistry Program, Wellesley College, Wellesley, MA 02481, USA
| |
Collapse
|
7
|
Synergistic and antibiofilm activity of the antimicrobial peptide P5 against carbapenem-resistant Pseudomonas aeruginosa. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:1329-1337. [DOI: 10.1016/j.bbamem.2019.05.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 05/07/2019] [Accepted: 05/10/2019] [Indexed: 01/14/2023]
|