An antibacterial peptides recognition method based on BERT and Text-CNN / 生物工程学报

Antimicrobial peptides (AMPs) are small molecule peptides that are widely found in living organisms with broad-spectrum antibacterial activity and immunomodulatory effect. Due to slower emergence of resistance, excellent clinical potential and wide range of application, AMP is a strong alternative to conventional antibiotics. AMP recognition is a significant direction in the field of AMP research. The high cost, low efficiency and long period shortcomings of the wet experiment methods prevent it from meeting the need for the large-scale AMP recognition. Therefore, computer-aided identification methods are important supplements to AMP recognition approaches, and one of the key issues is how to improve the accuracy. Protein sequences could be approximated as a language composed of amino acids. Consequently, rich features may be extracted using natural language processing (NLP) techniques. In this paper, we combine the pre-trained model BERT and the fine-tuned structure Text-CNN in the field of NLP to model protein languages, develop an open-source available antimicrobial peptide recognition tool and conduct a comparison with other five published tools. The experimental results show that the optimization of the two-phase training approach brings an overall improvement in accuracy, sensitivity, specificity, and Matthew correlation coefficient, offering a novel approach for further research on AMP recognition.

Progress on the design and optimization of antimicrobial peptides / 生物医学工程学杂志

Antimicrobial peptides (AMPs) are a class of peptides widely existing in nature with broad-spectrum antimicrobial activity. It is considered as a new alternative to traditional antibiotics because of its unique mechanism of antimicrobial activity. The development and application of natural AMPs are limited due to their drawbacks such as low antimicrobial activity and unstable metabolism. Therefore, the design and optimization of derived peptides based on natural antimicrobial peptides have become recent research hotspots. In this paper, we focus on ribosomal AMPs and summarize the design and optimization strategies of some related derived peptides, which include reasonable primary structure modification, cyclization strategy and computer-aided strategy. We expect to provide ideas for the design and optimization of antimicrobial peptides and the development of anti-infective drugs through analysis and summary in this paper.

Cloning and purification of the first termicin-like peptide from the cockroach Eupolyphaga sinensis

Abstract Background Termicin is an antimicrobial peptide with six cysteines forming three disulfide bridges that was firstly isolated from the salivary glands and hemocytes of the termite Pseudacanthotermes spiniger. In contrast to many broad-spectrum antimicrobial peptides, termicin is most active against filamentous fungi. Although more than one hundred complementary DNAs (cDNAs) encoding termicin-like peptides have been reported to date, all these termicin-like peptides were obtained from Isoptera insects. Methods The cDNA was cloned by combination of cDNA library construction kit and DNA sequencing. The polypeptide was purified by gel filtration and reversed-phase high performance liquid chromatography (RP-HPLC). Its amino acid sequence was determined by Edman degradation and mass spectrometry. Antimicrobial activity was tested against several bacterial and fungal strains. The minimum inhibitory concentration (MIC) was determined by microdilution tests. Results A novel termicin-like peptide with primary structure ACDFQQCWVTCQRQYSINFISARCNGDSCVCTFRT was purified from extracts of the cockroach Eupolyphaga sinensis (Insecta: Blattodea). The cDNA encoding Es-termicin was cloned by cDNA library screening. This cDNA encoded a 60 amino acid precursor which included a 25 amino acid signal peptide. Amino acid sequence deduced from the cDNA matched well with the result of protein Edman degradation. Susceptibility test indicated that Es-termicin showed strong ability to kill fungi with a MIC of 25 μg/mL against Candida albicans ATCC 90028. It only showed limited potency to affect the growth of Gram-positive bacteria with a MIC of 200 μg/mL against Enterococcus faecalis ATCC 29212. It was inactive against gram-negative bacteria at the highest concentration tested (400 μg/mL). Es-termicin showed high sequence similarity with termicins from many species of termites (Insecta: Isoptera). Conclusions This is the first report of a termicin-like peptide isolated from E. sinensis that belongs to the insect order Blattodea. Our results demonstrate the diversity of termicin-like peptides, as well as antimicrobial peptides in insects.(AU)

Identification of three novel myeloid cathelicidin cDNAs and their predicted peptides in buffalo (Bubalus bubalis).

Antimicrobial peptides (AMPs) are broad spectrum antibiotics, which mostly act without specific receptors. Identification of AMPs is important in the current scenario of emerging multi-drug resistant bacteria. In the present study, in an attempt to identify new AMPs, myeloid cathelicidin cDNAs were synthesized from buffalo (Bubalus bubalis) bone marrow and were amplified using specific primers. Sequence analysis of cloned cDNAs revealed three novel myeloid cathelicidins. They were named based on the number of active amino acids in the C-terminal region of their predicted peptide sequences as BuMAP-28 (having an additional Gly at position 22nd), BuMAP-29 (having an additional IIe at position 27) and BuMAP-34, compared to BMAP-27, BMAP-28 and BMAP-34 of cattle. The BuMAPs showed 93%, 95% and 87% homology respectively with that of its cattle counterpart. Predicted number of amino acids of the cDNAs was 159, 155 and 157 residues, with cationic C-terminal sequences of 28, 29 and 34, respectively, which correspond to putative antimicrobial domains. Several amino acid substitutions were observed in all the three cathelicidins. The conformation of the peptides was predicted to be alpha helical, having total net positive charge and hydrophobicity, similar to that of BMAPs in cattle. Comparative analysis of the predicted peptides suggested potential antimicrobial activity and the sequence variations detected might enable the peptides to act as effective broad spectrum antimicrobial agents.

Structure-activity relationship of buffalo antibacterial hepcidin analogs.

Hepcidin is an anti-microbial peptide expressed predominantly in the liver of many species. Based on the amino acid sequence deduced from buffalo (Bubalus bubalis) hepcidin cDNA (Accession no. EU399814), six peptides Hepc1-25, Hepc6-25, Hepc7-25, Hepc9-25, Hepc11-25 and Hepc15-25 were synthesized using solid-phase fluorenylmethoxycarbonyl (Fmoc) chemistry. CD spectroscopy revealed different spectra of the peptides in different solvents and in all the cases b-structure was found to be dominant with less a-helix as predicted. Quantitation of secondary structure indicated the highest b-structure for all the six peptides in SDS solution, when used as mimetic for membrane-like environment. The CD spectra of all the peptides taken in water showed that degree of randomness decreased with increase in chain length of the peptide. Out of the six peptides, only Hepc1-25, Hepc6-25 and Hepc7-25 showed antibacterial activity against Staphylococcus aureus (Gram-positive bacteria). The peptides did not show any sensitivity toward E. coli (Gram-negative bacteria). Minimum inhibitory concentration (MIC) showed the lowest value for Hepc7-25 as an antibacterial agent, followed by Hepc6-25 and Hepc1-25. The peptides Hepc9-25, Hepc11-25 and Hepc15-25 with more random structure did not show any antimicrobial activity The study demonstrated that 5 amino acids at N-terminal in buffalo hepcidin can be truncated without loss of antimicrobial activity and further reduction of length of the analog from 20 to 19 amino acids resulted increase in the activity because of increase in -structure of the peptide shown by CD spectroscopy.

Antifungal and antitumor models of bioactive protective peptides

Peptides are remarkably reactive molecules produced by a great variety of species and able to display a number of functions in uni-and multicellular organisms as mediators, agonists and regulating substances. Some of them exert cytotoxic effects on cells other than those that produced them, and may have a role in controlling subpopulations and protecting certain species or cell types. Presently, we focus on antifungal and antitumor peptides and discuss a few models in which specific sequences and structures exerted direct inhibitory effects or stimulated a protective immune response. The killer peptide, deduced from an antiidiotypic antibody, with several antimicrobial activities and other Ig-derived peptides with cytotoxic activities including antitumor effects, are models studied in vitro and in vivo. Peptide 10 from gp43 of P. brasiliensis (P10) and the vaccine perspective against paracoccidioidomycosis is another topic illustrating the protective effect in vivo against a pathogenic fungus. The cationic antimicrobial peptides with antitumor activities are mostly reviewed here. Local treatment of murine melanoma by the peptide gomesin is another model studied at the Experimental Oncology Unit of UNIFESP.

Peptídeos são moléculas particularmente reativas produzidas por uma grande variedade de espécies, aptos a exercer um número de funções em organismos uni-e multicelulares como mediadores, agonistas e substâncias regulatórias. Alguns deles exercem efeitos citotóxicos em células outras das que os produzem, e podem ter um papel controlando subpopulações e protegendo certas espécies ou tipos celulares. No presente, focalizamos peptídeos antifúngicos e antitumorais e discutimos alguns modelos nos quais seqüências específicas e estruturas exercem efeitos inibitórios diretos ou estimulam uma resposta imune protetora. O peptídeo letal ("killer"), deduzido de um anticorpo anti-idiotípico, com várias atividades antimicrobianas bem como outros peptídeos derivados de imunoglobulinas com atividades citotóxicas incluindo efeitos antitumorais são modelos estudados in vitro e in vivo. O peptídeo P10 da gp43 de P. brasiliensis e a perspectiva de vacina contra a paracoccidioidomicose é outro tópico ilustrando o efeito protetor in vivo contra um fungo patogênico. Peptídeos antimicrobianos catiônicos com atividades antitumorais são os principais revistos aqui. O tratamento local do melanoma murino com o peptídeo gomesina é outro modelo estudado na Unidade de Oncologia Experimental (UNONEX) da UNIFESP.

Effects of salt and denaturant on structure of the amino terminal alpha-helical segment of an antibacterial peptide dermaseptin and its binding to model membranes.

The amino terminal 1-18 domain of dermaseptin s is an important determinant of its structure as well as the antibacterial activity. A thorough investigation on the structure of the 18-residue peptide (D18) and its binding to model membranes in presence of salt and denaturant guanidinium chloride has been carried out. In presence of salt, there is an increase in the fraction of peptide molecules in helical conformation. In presence of the denaturant, D18 is unordered, but addition of the structure-promoting solvent trifluoroethanol results in a transition to the helical conformation. In presence of denaturant, the peptide is unordered, but binding to lipid vesicles is not abolished. Investigation of model membrane permeabilizing ability of the peptide in solutions containing various proportions of sodium chloride and guanidinium chloride indicates that vesicle permeabilization parallels extent of binding. The peptide thus binds to lipid vesicles in an unfolded state. Since the peptide has propensity to fold into a helical conformation, lipid induced transition to a helical structure occurs, followed by membrane permeabilization as a result of pore formation.