1
|
Porto WF, Ferreira KCV, Ribeiro SM, Franco OL. Sense the moment: A highly sensitive antimicrobial activity predictor based on hydrophobic moment. Biochim Biophys Acta Gen Subj 2021; 1866:130070. [PMID: 34953809 DOI: 10.1016/j.bbagen.2021.130070] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 11/27/2021] [Accepted: 12/15/2021] [Indexed: 12/31/2022]
Abstract
BACKGROUND Computer-aided identification and design tools are indispensable for developing antimicrobial agents for controlling antibiotic-resistant bacteria. Antimicrobial peptides (AMPs) have aroused intense interest, since they have a broad spectrum of activity, and therefore, several systems for predicting antimicrobial peptides have been developed, using scalar physicochemical properties; however, regardless of the machine learning algorithm, these systems often fail in discriminating AMPs from their shuffled versions, leading to the need for new training methods to overcome this bias. Aiming to solve this bias, here we present "Sense the Moment", a prediction system capable of discriminating AMPs and shuffled versions. METHODS The system was trained using 776 entries: 388 from known AMPs and another 388 based on shuffled versions of known AMPs. Each entry contained the geometric average of three hydrophobic moments measured with different scales. RESULTS The model showed good accuracy (>80%) and excellent sensitivity (>90%) for AMP prediction, exceeding deep-learning-based methods. CONCLUSION Our results demonstrate the system's applicability, aiding in identifying and discarding non-AMPs, since the number of false negatives is lower than false positives. GENERAL SIGNIFICANCE The application of this model in virtual screening protocols for identifying and/or creating antimicrobial agents could aid in the identification of potential drugs to control pathogenic microorganisms and in solving the antibiotic resistance crisis. AVAILABILITY The system was implemented as a web application, available at <http://portoreports.com/stm/>.
Collapse
Affiliation(s)
| | - Karla C V Ferreira
- Pós-Graduação em Ciências Genômicas e Biotecnologia Universidade Católica 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
| | - Suzana M Ribeiro
- Programa de Pós-Graduação em Ciências da Saúde, Universidade Federal da Grande Dourados, Dourados, MS, Brazil
| | - Octavio L Franco
- Pós-Graduação em Ciências Genômicas e Biotecnologia Universidade Católica 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; S-Inova Biotech, Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil.
| |
Collapse
|
2
|
Araujo Sousa B, Nascimento Silva O, Farias Porto W, Lima Rocha T, Paulino Silva L, Ferreira Leal AP, Buccini DF, Oluwagbamigbe Fajemiroye J, de Araujo Caldas R, Franco OL, Grossi-de-Sá MF, de la Fuente Nunez C, Moreno SE. Identification of the Active Principle Conferring Anti-Inflammatory and Antinociceptive Properties in Bamboo Plant. Molecules 2021; 26:3054. [PMID: 34065427 PMCID: PMC8160853 DOI: 10.3390/molecules26103054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/29/2021] [Accepted: 03/31/2021] [Indexed: 11/16/2022] Open
Abstract
Early plants began colonizing earth about 450 million years ago. During the process of coevolution, their metabolic cellular pathways produced a myriad of natural chemicals, many of which remain uncharacterized biologically. Popular preparations containing some of these molecules have been used medicinally for thousands of years. In Brazilian folk medicine, plant extracts from the bamboo plant Guadua paniculata Munro have been used for the treatment of infections and pain. However, the chemical basis of these therapeutic effects has not yet been identified. Here, we performed protein biochemistry and downstream pharmacological assays to determine the mechanisms underlying the anti-inflammatory and antinociceptive effects of an aqueous extract of the G. paniculata rhizome, which we termed AqGP. The anti-inflammatory and antinociceptive effects of AqGP were assessed in mice. We identified and purified a protein (AgGP), with an amino acid sequence similar to that of thaumatins (~20 kDa), capable of repressing inflammation through downregulation of neutrophil recruitment and of decreasing hyperalgesia in mice. In conclusion, we have identified the molecule and the molecular mechanism responsible for the anti-inflammatory and antinociceptive properties of a plant commonly used in Brazilian folk medicine.
Collapse
Affiliation(s)
- Bruna Araujo Sousa
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília CEP 70790-160, DF, Brazil; (B.A.S.); (W.F.P.); (O.L.F.); (M.F.G.-d.-S.)
| | - Osmar Nascimento Silva
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande CEP 79117-900, MS, Brazil; (O.N.S.); (A.P.F.L.); (D.F.B.); (R.d.A.C.)
- Centro Universitário de Anápolis, Unievangélica, Anápolis CEP 75083-515, GO, Brazil;
| | - William Farias Porto
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília CEP 70790-160, DF, Brazil; (B.A.S.); (W.F.P.); (O.L.F.); (M.F.G.-d.-S.)
- Porto Reports, Brasília CEP 72236-011, DF, Brazil
| | - Thales Lima Rocha
- Embrapa Recursos Genéticos e Biotecnologia (Cenargen), Brasília CEP 70770-917, DF, Brazil; (T.L.R.); (L.P.S.)
| | - Luciano Paulino Silva
- Embrapa Recursos Genéticos e Biotecnologia (Cenargen), Brasília CEP 70770-917, DF, Brazil; (T.L.R.); (L.P.S.)
| | - Ana Paula Ferreira Leal
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande CEP 79117-900, MS, Brazil; (O.N.S.); (A.P.F.L.); (D.F.B.); (R.d.A.C.)
| | - Danieli Fernanda Buccini
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande CEP 79117-900, MS, Brazil; (O.N.S.); (A.P.F.L.); (D.F.B.); (R.d.A.C.)
| | - James Oluwagbamigbe Fajemiroye
- Centro Universitário de Anápolis, Unievangélica, Anápolis CEP 75083-515, GO, Brazil;
- Núcleo de Estudos e Pesquisas Tóxico-Farmacológicas, Universidade Federal de Goiás, Goiânia 74605-220, GO, Brazil
| | - Ruy de Araujo Caldas
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande CEP 79117-900, MS, Brazil; (O.N.S.); (A.P.F.L.); (D.F.B.); (R.d.A.C.)
| | - Octávio Luiz Franco
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília CEP 70790-160, DF, Brazil; (B.A.S.); (W.F.P.); (O.L.F.); (M.F.G.-d.-S.)
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande CEP 79117-900, MS, Brazil; (O.N.S.); (A.P.F.L.); (D.F.B.); (R.d.A.C.)
- Departamento de Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brasília CEP 70910-900, DF, Brazil
| | - Maria Fátima Grossi-de-Sá
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília CEP 70790-160, DF, Brazil; (B.A.S.); (W.F.P.); (O.L.F.); (M.F.G.-d.-S.)
- Embrapa Recursos Genéticos e Biotecnologia (Cenargen), Brasília CEP 70770-917, DF, Brazil; (T.L.R.); (L.P.S.)
| | - Cesar de la Fuente Nunez
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA;
- Department of Biological Engineering, The Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Electrical Engineering and Computer Science, The Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Susana Elisa Moreno
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande CEP 79117-900, MS, Brazil; (O.N.S.); (A.P.F.L.); (D.F.B.); (R.d.A.C.)
| |
Collapse
|
3
|
Fatoki TH, Ibraheem O, Ogunyemi IO, Akinmoladun AC, Ugboko HU, Adeseko CJ, Awofisayo OA, Olusegun SJ, Enibukun JM. Network analysis, sequence and structure dynamics of key proteins of coronavirus and human host, and molecular docking of selected phytochemicals of nine medicinal plants. J Biomol Struct Dyn 2020; 39:6195-6217. [PMID: 32686993 DOI: 10.1080/07391102.2020.1794971] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The novel coronavirus of 2019 (nCoV-19) has become a pandemic, affecting over 205 nations with over 7,410,000 confirmed cases which has resulted to over 418,000 deaths worldwide. This study aimed to identify potential therapeutic compounds and phytochemicals of medicinal plants that have potential to modulate the expression network of genes that are involve in SARS-CoV-2 pathology in human host and to understand the dynamics key proteins involved in the virus-host interactions. The method used include gene network analysis, molecular docking, and sequence and structure dynamics simulations. The results identified DNA-dependent protein kinase (DNA-PK) and Protein kinase CK2 as key players in SARS-CoV-2 lifecycle. Among the predicted drugs compounds, clemizole, monorden, spironolactone and tanespimycin showed high binding energies; among the studied repurposing compounds, remdesivir, simeprevir and valinomycin showed high binding energies; among the predicted acidic compounds, acetylursolic acid and hardwickiic acid gave high binding energies; while among the studied anthraquinones and glycosides compounds, ellagitannin and friedelanone showed high binding energies against 3-Chymotrypsin-like protease (3CLpro), Papain-like protease (PLpro), helicase (nsp13), RNA-dependent RNA polymerase (nsp12), 2'-O-ribose methyltransferase (nsp16) of SARS-CoV-2 and DNA-PK and CK2alpha in human. The order of affinity for CoV proteins is 5Y3E > 6NUS > 6JYT > 2XYR > 3VB6. Finally, medicinal plants with phytochemicals such as caffeine, ellagic acid, quercetin and their derivatives could possibly remediate COVID-19.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Toluwase Hezekiah Fatoki
- Translational Bioinformatics Unit, Department of Biochemistry, Federal University Oye Ekiti, Oye Ekiti, Ekiti State, Nigeria
| | - Omodele Ibraheem
- Translational Bioinformatics Unit, Department of Biochemistry, Federal University Oye Ekiti, Oye Ekiti, Ekiti State, Nigeria
| | | | | | - Harriet U Ugboko
- Microbiology Research Unit, Department of Biological Sciences, Covenant University, Ota, Ogun State, Nigeria
| | | | - Oladoja A Awofisayo
- Department of Pharmaceutical and Medicinal Chemistry, University of Uyo, Uyo, Nigeria
| | | | | |
Collapse
|
4
|
Yuan F, Tian Y, Qin W, Li J, Yang D, Zhao B, Yin F, Li Z. Evaluation of topologically distinct constrained antimicrobial peptides with broad-spectrum antimicrobial activity. Org Biomol Chem 2019; 16:5764-5770. [PMID: 30004546 DOI: 10.1039/c8ob00483h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Antimicrobial peptides (AMPs) are short cationic peptides with a high affinity for membranes and emerged as a promising therapeutic approach with potential for treating infectious diseases. Chemical stabilization of short peptides proved to be a successful approach for enhancing their bio-physical properties. Herein, we designed and synthesized a panel of conformationally constrained antimicrobial peptides with either α-helical or β-hairpin conformation using templating strategies. These synthetic short constrained peptides possess different topological distributions of hydrophobic and hydrophilic residues and displayed distinct antimicrobial activity. Notably, the conformationally constrained α-helical peptides displayed a faster internalization into the bacteria cells compared to their β-hairpin analogues. These synthetic short constrained peptides showed killing effects on a broad spectrum of microorganisms mainly through pore formation and membrane damage which provided a potentially promising skeleton for the next generation of stabilized antimicrobial peptides.
Collapse
Affiliation(s)
- Fang Yuan
- Institute of Scientific and Technical Information of China, Beijing, 100038, China
| | | | | | | | | | | | | | | |
Collapse
|
5
|
In silico optimization of a guava antimicrobial peptide enables combinatorial exploration for peptide design. Nat Commun 2018; 9:1490. [PMID: 29662055 PMCID: PMC5902452 DOI: 10.1038/s41467-018-03746-3] [Citation(s) in RCA: 159] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Accepted: 03/02/2018] [Indexed: 12/29/2022] Open
Abstract
Plants are extensively used in traditional medicine, and several plant antimicrobial peptides have been described as potential alternatives to conventional antibiotics. However, after more than four decades of research no plant antimicrobial peptide is currently used for treating bacterial infections, due to their length, post-translational modifications or high dose requirement for a therapeutic effect . Here we report the design of antimicrobial peptides derived from a guava glycine-rich peptide using a genetic algorithm. This approach yields guavanin peptides, arginine-rich α-helical peptides that possess an unusual hydrophobic counterpart mainly composed of tyrosine residues. Guavanin 2 is characterized as a prototype peptide in terms of structure and activity. Nuclear magnetic resonance analysis indicates that the peptide adopts an α-helical structure in hydrophobic environments. Guavanin 2 is bactericidal at low concentrations, causing membrane disruption and triggering hyperpolarization. This computational approach for the exploration of natural products could be used to design effective peptide antibiotics. Antimicrobial peptides are considered promising alternatives to antibiotics. Here the authors developed a computational algorithm that starts with peptides naturally occurring in plants and optimizes this starting material to yield new variants which are highly distinct from the parent peptide.
Collapse
|
6
|
Nielsen DS, Shepherd NE, Xu W, Lucke AJ, Stoermer MJ, Fairlie DP. Orally Absorbed Cyclic Peptides. Chem Rev 2017; 117:8094-8128. [PMID: 28541045 DOI: 10.1021/acs.chemrev.6b00838] [Citation(s) in RCA: 262] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Peptides and proteins are not orally bioavailable in mammals, although a few peptides are intestinally absorbed in small amounts. Polypeptides are generally too large and polar to passively diffuse through lipid membranes, while most known active transport mechanisms facilitate cell uptake of only very small peptides. Systematic evaluations of peptides with molecular weights above 500 Da are needed to identify parameters that influence oral bioavailability. Here we describe 125 cyclic peptides containing four to thirty-seven amino acids that are orally absorbed by mammals. Cyclization minimizes degradation in the gut, blood, and tissues by removing cleavable N- and C-termini and by shielding components from metabolic enzymes. Cyclization also folds peptides into bioactive conformations that determine exposure of polar atoms to solvation by water and lipids and therefore can influence oral bioavailability. Key chemical properties thought to influence oral absorption and bioavailability are analyzed, including molecular weight, octanol-water partitioning, hydrogen bond donors/acceptors, rotatable bonds, and polar surface area. The cyclic peptides violated to different degrees all of the limits traditionally considered to be important for oral bioavailability of drug-like small molecules, although fewer hydrogen bond donors and reduced flexibility generally favored oral absorption.
Collapse
Affiliation(s)
- Daniel S Nielsen
- Division of Chemistry and Structural Biology, and ‡Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD 4072, Australia
| | - Nicholas E Shepherd
- Division of Chemistry and Structural Biology, and ‡Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD 4072, Australia
| | - Weijun Xu
- Division of Chemistry and Structural Biology, and ‡Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD 4072, Australia
| | - Andrew J Lucke
- Division of Chemistry and Structural Biology, and ‡Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD 4072, Australia
| | - Martin J Stoermer
- Division of Chemistry and Structural Biology, and ‡Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD 4072, Australia
| | - David P Fairlie
- Division of Chemistry and Structural Biology, and ‡Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD 4072, Australia
| |
Collapse
|
7
|
Porto W, Pires A, Franco O. Computational tools for exploring sequence databases as a resource for antimicrobial peptides. Biotechnol Adv 2017; 35:337-349. [DOI: 10.1016/j.biotechadv.2017.02.001] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 01/12/2017] [Accepted: 02/08/2017] [Indexed: 12/22/2022]
|
8
|
Cunha NBD, Barbosa AEADD, de Almeida RG, Porto WF, Maximiano MR, Álvares LCS, Munhoz CBR, Eugênio CUO, Viana AAB, Franco OL, Dias SC. Cloning and characterization of novel cyclotides genes from South American plants. Biopolymers 2017; 106:784-795. [PMID: 27554590 DOI: 10.1002/bip.22938] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Revised: 08/10/2016] [Accepted: 08/21/2016] [Indexed: 01/06/2023]
Abstract
Cyclotides are multifunctional plant cyclic peptides containing 28-37 amino acid residues and a pattern of three disulfide bridges, forming a motif known as the cyclic cystine knot. Due to their high biotechnological potential, the sequencing and characterization of cyclotide genes are crucial not only for cloning and establishing heterologous expression strategies, but also to understand local plant evolution in the context of host-pathogen relationships. Here, two species from the Brazilian Cerrado, Palicourea rigida (Rubiaceae) and Pombalia lanata (A.St.-Hil.) Paula-Souza (Violaceae), were used for cloning and characterizing novel cyclotide genes. Using 3' and 5' RACE PCR and sequencing, two full cDNAs, named parigidin-br2 (P. rigida) and hyla-br1 (P. lanata), were isolated and shown to have similar genetic structures to other cyclotides. Both contained the conserved ER-signal domain, N-terminal prodomain, mature cyclotide domain and a C-terminal region. Genomic sequencing of parigidin-br2 revealed two different gene copies: one intronless allele and one presenting a rare 131-bp intron. In contrast, genomic sequencing of hyla-br1 revealed an intronless gene-a common characteristic of members of the Violaceae family. Parigidin-br2 5' and 3' UTRs showed the presence of 12 putative candidate sites for binding of regulatory proteins, suggesting that the flanking and intronic regions of the parigidin-br2 gene must play important roles in transcriptional rates and in the regulation of temporal and spatial gene expression. The high degree of genetic similarity and structural organization among the cyclotide genes isolated in the present study from the Brazilian Cerrado and other well-characterized plant cyclotides may contribute to a better understanding of cyclotide evolution.
Collapse
Affiliation(s)
- Nicolau Brito da Cunha
- Centro de Analises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916 Módulo B Avenida W5, Brasília, DF, 70790-160, Brazil
| | | | - Renato Goulart de Almeida
- Centro de Analises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916 Módulo B Avenida W5, Brasília, DF, 70790-160, Brazil
| | - William Farias Porto
- Centro de Analises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916 Módulo B Avenida W5, Brasília, DF, 70790-160, Brazil
| | - Mariana Rocha Maximiano
- Centro de Analises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916 Módulo B Avenida W5, Brasília, DF, 70790-160, Brazil
| | - Luana Cristina Silva Álvares
- Centro de Analises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916 Módulo B Avenida W5, Brasília, DF, 70790-160, Brazil
| | - Cassia Beatriz Rodrigues Munhoz
- Departamento de Botânica, Instituto de Ciências Biológicas. Bloco D. Universidade de Brasília. Campus Darcy Ribeiro 70904-970, Asa Norte. Brasília, DF, Brazil
| | - Chesterton Ulysses Orlando Eugênio
- Centro de Analises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916 Módulo B Avenida W5, Brasília, DF, 70790-160, Brazil
| | - Antônio Américo Barbosa Viana
- Centro de Analises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916 Módulo B Avenida W5, Brasília, DF, 70790-160, Brazil
| | - Octavio Luiz Franco
- Centro de Analises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916 Módulo B Avenida W5, Brasília, DF, 70790-160, Brazil.,S-Inova Biotech, Pós Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil
| | - Simoni Campos Dias
- Centro de Analises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916 Módulo B Avenida W5, Brasília, DF, 70790-160, Brazil
| |
Collapse
|
9
|
Porto WF, Miranda VJ, Pinto MFS, Dohms SM, Franco OL. High-performance computational analysis and peptide screening from databases of cyclotides from poaceae. Biopolymers 2017; 106:109-18. [PMID: 26572696 DOI: 10.1002/bip.22771] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/21/2015] [Accepted: 11/09/2015] [Indexed: 12/22/2022]
Abstract
Cyclotides are a family of head-to-tail cyclized peptides containing three conserved disulfide bonds, in a structural scaffold also known as a cyclic cysteine knot. Due to the high degree of cysteine conservation, novel members from this peptide family can be identified in protein databases through a search through regular expression (REGEX). In this work, six novel cyclotide-like precursors from the Poaceae were identified from NCBI's non-redundant protein database by the use of REGEX. Two out of six sequences (named Zea mays L and M) showed an Asp residue in the C-terminal, which indicated that they could be cyclic. Gene expression in maize tissues was investigated, showing that the previously described cyclotide-like Z. mays J is expressed in the roots. According to molecular dynamics, the structure of Z. mays J seems to be stable, despite the putative absence of cyclization. As regards cyclotide evolution, it was hypothesized that this is an outcome from convergent evolution and/or horizontal gene transfer. The results showed that peptide screening from databases should be performed periodically in order to include novel sequences, which are deposited as the databases grow. Indeed, the advances in computational and experimental methods will together help to answer key questions and reach new horizons in defense-related peptide identification.
Collapse
Affiliation(s)
- William F Porto
- Centro De Análises Proteômicas E Bioquímicas, Pós-Graduação Em Ciências Genômicas E Biotecnologia Universidade Católica De Brasília, Brasília-DF, Brazil
| | - Vivian J Miranda
- Centro De Análises Proteômicas E Bioquímicas, Pós-Graduação Em Ciências Genômicas E Biotecnologia Universidade Católica De Brasília, Brasília-DF, Brazil
| | - Michelle F S Pinto
- Centro De Análises Proteômicas E Bioquímicas, Pós-Graduação Em Ciências Genômicas E Biotecnologia Universidade Católica De Brasília, Brasília-DF, Brazil
| | - Stephan M Dohms
- Centro De Análises Proteômicas E Bioquímicas, Pós-Graduação Em Ciências Genômicas E Biotecnologia Universidade Católica De Brasília, Brasília-DF, Brazil
| | - Octavio L Franco
- Centro De Análises Proteômicas E Bioquímicas, Pós-Graduação Em Ciências Genômicas E Biotecnologia Universidade Católica De Brasília, Brasília-DF, Brazil.,S-Inova Biotech, Pos Graduação em Biotecnologia, Universidade Catolica Dom Bosco, Campo Grande MS, Brazil
| |
Collapse
|
10
|
Nguyen PQT, Ooi JSG, Nguyen NTK, Wang S, Huang M, Liu DX, Tam JP. Antiviral Cystine Knot α-Amylase Inhibitors from Alstonia scholaris. J Biol Chem 2015; 290:31138-50. [PMID: 26546678 DOI: 10.1074/jbc.m115.654855] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Indexed: 11/06/2022] Open
Abstract
Cystine knot α-amylase inhibitors are cysteine-rich, proline-rich peptides found in the Amaranthaceae and Apocynaceae plant species. They are characterized by a pseudocyclic backbone with two to four prolines and three disulfides arranged in a knotted motif. Similar to other knottins, cystine knot α-amylase inhibitors are highly resistant to degradation by heat and protease treatments. Thus far, only the α-amylase inhibition activity has been described for members of this family. Here, we show that cystine knot α-amylase inhibitors named alstotides discovered from the Alstonia scholaris plant of the Apocynaceae family display antiviral activity. The alstotides (As1-As4) were characterized by both proteomic and genomic methods. All four alsotides are novel, heat-stable and enzyme-stable and contain 30 residues. NMR determination of As1 and As4 structures reveals their conserved structural fold and the presence of one or more cis-proline bonds, characteristics shared by other cystine knot α-amylase inhibitors. Genomic analysis showed that they contain a three-domain precursor, an arrangement common to other knottins. We also showed that alstotides are antiviral and cell-permeable to inhibit the early phase of infectious bronchitis virus and Dengue infection, in addition to their ability to inhibit α-amylase. Taken together, our results expand membership of cystine knot α-amylase inhibitors in the Apocynaceae family and their bioactivity, functional promiscuity that could be exploited as leads in developing therapeutics.
Collapse
Affiliation(s)
| | - Justin Seng Geap Ooi
- From the School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Ngan Thi Kim Nguyen
- From the School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Shujing Wang
- From the School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Mei Huang
- From the School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Ding Xiang Liu
- From the School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - James P Tam
- From the School of Biological Sciences, Nanyang Technological University, Singapore 637551
| |
Collapse
|
11
|
Phoenix DA, Harris F, Mura M, Dennison SR. The increasing role of phosphatidylethanolamine as a lipid receptor in the action of host defence peptides. Prog Lipid Res 2015; 59:26-37. [PMID: 25936689 DOI: 10.1016/j.plipres.2015.02.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 02/26/2015] [Accepted: 02/27/2015] [Indexed: 01/04/2023]
Abstract
Host defence peptides (HDPs) are antimicrobial agents produced by organisms across the prokaryotic and eukaryotic kingdoms. Many prokaryotes produce HDPs, which utilise lipid and protein receptors in the membranes of bacterial competitors to facilitate their antibacterial action and thereby survive in their niche environment. As a major example, it is well established that cinnamycin and duramycins from Streptomyces have a high affinity for phosphatidylethanolamine (PE) and exhibit activity against other Gram-positive organisms, such as Bacillus. In contrast, although eukaryotic HDPs utilise membrane interactive mechanisms to facilitate their antimicrobial activity, the prevailing view has long been that these mechanisms do not involve membrane receptors. However, this view has been recently challenged by reports that a number of eukaryotic HDPs such as plant cyclotides also use PE as a receptor to promote their antimicrobial activities. Here, we review current understanding of the mechanisms that underpin the use of PE as a receptor in the antimicrobial and other biological actions of HDPs and describe medical and biotechnical uses of these peptides, which range from tumour imaging and detection to inclusion in topical microbicidal gels to prevent the sexual transmission of HIV.
Collapse
Affiliation(s)
- David A Phoenix
- School of Applied Science, London South Bank University, 103 Borough Road, London SE1 0AA, UK.
| | - Frederick Harris
- School of Applied Science, London South Bank University, 103 Borough Road, London SE1 0AA, UK; School of Forensic and Investigative Science, University of Central Lancashire, Preston PR1 2HE, UK
| | - Manuela Mura
- School of Mathematics and Physics, College of Science, University of Lincoln, Brayford Pool, Lincoln, Lincolnshire LN6 7TS, UK
| | - Sarah R Dennison
- School of Applied Science, London South Bank University, 103 Borough Road, London SE1 0AA, UK; School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, UK
| |
Collapse
|
12
|
Fensterseifer ICM, Silva ON, Malik U, Ravipati AS, Novaes NRF, Miranda PRR, Rodrigues EA, Moreno SE, Craik DJ, Franco OL. Effects of cyclotides against cutaneous infections caused by Staphylococcus aureus. Peptides 2015; 63:38-42. [PMID: 25451333 DOI: 10.1016/j.peptides.2014.10.019] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 10/31/2014] [Accepted: 10/31/2014] [Indexed: 12/31/2022]
Abstract
The main bacterium associated with skin infection is Staphylococcus aureus, occurring especially in infections acquired via surgical wounds, commonly leading to lethal hospital-acquired infections, emphasizing the importance of identifying new antimicrobial compounds. Among them, cyclotides have gained interest due to their high stability and multifunctional properties. Here, cycloviolacin 2 (CyO2) and kalata B2 (KB2) were evaluated to determinate their anti-staphylococcal activities using a subcutaneous infection model. Anti-staphylococcal activities of 50mM for KB2 and 25mM for CyO2 were detected with no cytotoxic activities against RAW 264.7 monocytes. In the in vivo assays, both cyclotides reduced bacterial load and CyO2 demonstrated an increase in the phagocytosis index, suggesting that the CyO2 in vivo anti-staphylococcal activity may be associated with phagocytic activity, additionally to direct anti-pathogenic activity.
Collapse
Affiliation(s)
- Isabel C M Fensterseifer
- Centro de Análises, Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, 70790-160 Brazil; Molecular Pathology Post-graduate Program, University of Brasilia, Brasília 70910-900, Brazil
| | - Osmar N Silva
- Centro de Análises, Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, 70790-160 Brazil; Department of Biology, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora 36036-900, MG, Brazil
| | - Uru Malik
- Institute for Molecular Bioscience, the University of Queensland, Brisbane, Queensland, Australia
| | - Anjaneya S Ravipati
- Institute for Molecular Bioscience, the University of Queensland, Brisbane, Queensland, Australia
| | - Natasha R F Novaes
- Centro de Análises, Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, 70790-160 Brazil
| | - Paulo R R Miranda
- Centro de Análises, Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, 70790-160 Brazil
| | - Elaine A Rodrigues
- Centro de Análises, Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, 70790-160 Brazil
| | - Susana E Moreno
- Centro de Análises, Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, 70790-160 Brazil
| | - David J Craik
- Institute for Molecular Bioscience, the University of Queensland, Brisbane, Queensland, Australia
| | - Octavio L Franco
- Centro de Análises, Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, 70790-160 Brazil; Molecular Pathology Post-graduate Program, University of Brasilia, Brasília 70910-900, Brazil; Department of Biology, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora 36036-900, MG, Brazil; S-Inova, Pos-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Caampo Grande, MS, Brazil.
| |
Collapse
|
13
|
Mandal SM, Porto WF, Dey P, Maiti MK, Ghosh AK, Franco OL. The attack of the phytopathogens and the trumpet solo: Identification of a novel plant antifungal peptide with distinct fold and disulfide bond pattern. Biochimie 2013; 95:1939-48. [PMID: 23835303 DOI: 10.1016/j.biochi.2013.06.027] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 06/28/2013] [Indexed: 02/08/2023]
Abstract
Phytopathogens cause economic losses in agribusiness. Plant-derived compounds have been proposed to overcome this problem, including the antimicrobial peptides (AMPs). This paper reports the identification of Ps-AFP1, a novel AMP isolated from the Pisum sativum radicle. Ps-AFP1 was purified and evaluated against phytopathogenic fungi, showing clear effectiveness. In silico analyses were performed, suggesting an unusual fold and disulfide bond pattern. A novel fold and a novel AMP class were here proposed, the αβ-trumpet fold and αβ-trumpet peptides, respectively. The name αβ-trumpet was created due to the peptide's fold, which resembles the musical instrument. The Ps-AFP1 mechanism of action was also proposed. Microscopic analyses revealed that Ps-AFP1 could affect the fungus during the hyphal elongation from spore germination. Furthermore, confocal microscopy performed with Ps-AFP1 labeled with FITC shows that the peptide was localized at high concentration along the fungal cell surface. Due to low cellular disruption rates, it seems that the main target is the fungal cell wall. The binding thermogram and isothermal titration, molecular dynamics and docking analyses were also performed, showing that Ps-AFP1 could bind to chitin producing a stable complex. Data here reported provided novel structural-functional insights into the αβ-trumpet peptide fold.
Collapse
Affiliation(s)
- Santi M Mandal
- Central Research Facility, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | | | | | | | | | | |
Collapse
|
14
|
Silva ON, Porto WF, Migliolo L, Mandal SM, Gomes DG, Holanda HHS, Silva RSP, Dias SC, Costa MP, Costa CR, Silva MR, Rezende TMB, Franco OL. Cn-AMP1: a new promiscuous peptide with potential for microbial infections treatment. Biopolymers 2013. [PMID: 23193596 DOI: 10.1002/bip.22071] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The antimicrobial peptides (AMPs) are evolutionarily ancient molecules that act as components of the innate immune system. Recently, it was demonstrated that a single AMP can perform various functions; this ability is known as "peptide promiscuity." However, little is known about promiscuity in plant AMPs without disulfide bonds. This study was carried out to evaluate the promiscuity of Cn-AMP1: a promising disulfide-free plant peptide with reduced size and cationic and hydrophobic properties. Its activity against human pathogenic bacteria and fungal pathogens, as well as its in vitro immunostimulatory activity and effects on cancerous and healthy mammalian cell proliferation were studied here. Cn-AMP1 exerts antimicrobial effects against Gram-positive bacteria, Gram-negative bacteria, and fungi. Moreover, tumor cell viability activity in Caco-2 cells, as well as immunostimulatory activity by evaluating upregulated inflammatory-cytokine secretion by monocytes was also positively observed. Cn-AMP1 does not exhibit a well-defined conformation in aqueous solution and probably undergoes a 3(10)-helix transition in hydrophobic environments. The experimental results support the promiscuous activity of Cn-AMP1, presenting a wide range of activities, including antibacterial, antifungal, and immunostimulatory activity. In the future, Cn-AMP1 should be used in the development of novel biopharmaceuticals, mainly due to its reduced size and broad spectrum of activity.
Collapse
Affiliation(s)
- Osmar N Silva
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|