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.
Anti-Bacterial Agents/chemistry* ; Amino Acid Sequence ; Antimicrobial Cationic Peptides/chemistry* ; Antimicrobial Peptides ; Natural Language Processing

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.
Antimicrobial Cationic Peptides/chemistry* ; Antimicrobial Peptides ; Drug Design ; Anti-Infective Agents/pharmacology* ; Anti-Bacterial Agents

Antimicrobial Cationic Peptides ; biosynthesis ; Hepacivirus ; pathogenicity ; Hepcidins ; Iron ; metabolism ; Liver ; chemistry ; metabolism ; pathology

PEGylating is an effective way for prolonging the half-time period and decreasing the immunogenicity of protein drugs. With experiments of single factor, it was proved that the optimal processes for PEGylating the fused protein of LL-37 and interferon (IFN)-α2a were: PEG molecular weight was 5,000, fused protein concentration was 0.6 mg/mL, the mole ratio of protein to mPEG₅₀₀₀-SS was 1:10, the reaction temperature was 4 °C, and the pH was 9.0, respectively. With orthogonal experiments, we proved that the influential order of 3 main factors is: the fused protein concentration > the mole ratio of protein and mPEG₅₀₀₀-SS > pH and the optimal conditions were the fused protein concentration as 0.6 mg/mL, the mole ratio of protein and mPEG₅₀₀₀-SS as 1:10, pH as 8.8. Under these optimal conditions, the average rate of PEGylated protein with 3 times parallel experiments was 86.98%. After PEGylated, the interferon activity and antimicrobial activity of fused protein could be remained higher than 58% and 97%, respectively.
Anti-Infective Agents ; chemistry ; Antimicrobial Cationic Peptides ; chemistry ; Interferon-alpha ; chemistry ; Polyethylene Glycols ; chemistry ; Recombinant Proteins ; chemistry

Animals ; Antimicrobial Cationic Peptides ; chemistry ; pharmacology ; Fluorescence Resonance Energy Transfer ; Humans ; Peptide Chain Elongation, Translational ; drug effects ; Single Molecule Imaging

Broad-spectrum antimicrobial peptides provide a new way to address the urgent growing problem of bacterial resistance. However, the limited natural resources and the high cost of extraction and purification of natural antimicrobial peptides can not meet the requirements of clinical application. In order to solve this problem, researchers have utilized two basic common structural features (amphiphilic and cationic) for designing and preparing synthetic antimicrobial macromolecular polymers. During the last decade, several kinds of amphiphilic polymers, including arylamide oligomers, phenylene ethynylenes, polymethacrylates, polynorbornenes as well as nylon-3 polymers have been synthesized. In this paper, the structures, antibacterial activities and selectivities of these polymers are reviewed, and the effects of molecular size, polarity and ratio of hydrophobic groups, positive charge density on antibacterial activity and selectivity are also summarized.
Anti-Infective Agents ; chemical synthesis ; chemistry ; Antimicrobial Cationic Peptides ; chemical synthesis ; chemistry ; Drug Design ; Inhibitory Concentration 50 ; Macromolecular Substances ; chemical synthesis ; chemistry ; Polymers ; chemical synthesis ; chemistry

Antibacterial peptides are a family of host-defense peptides most of which are gene-encoded and produced by living organisms of all types. Antibacterial peptides are small molecular proteins with broad antimicrobial spectrum against bacteria, viruses, fungi and sometimes even as anticancer peptide. SMAP-29, a cathelicidin-like peptide derived from sheep myeloid, line alpha-helical Structure, exerts a powerful broad antimicrobial activity against different pathogens including Gram-positive and Gram-negative bacteria, fungi, viruses, parasites, spirochaetes, chlamydia and antiendotoxin activity, and particular antibacterial mechanism, rapidly to permeabilize membranes of susceptible organisms. This paper summarizes the lately research progress of SMAP-29 and Variants including the characteristics of structure, structure-activity relationships, mode of action, diverse biological functions, gene recombinant and expression. We put emphasis on the necessity of molecular design, and primary and secondary structure-based modification, to provides a strong foundation for further drug development and design of SMAP-29.
Animals ; Antimicrobial Cationic Peptides ; chemistry ; genetics ; physiology ; Blood Proteins ; chemistry ; genetics ; physiology ; Cathelicidins ; chemistry ; genetics ; physiology ; Drug Design ; Recombinant Proteins ; chemistry ; genetics ; Sheep

Bactericidal/permeability-increasing protein (BPI) can bind to and specifically neutralize lipopolysaccharide (LPS) from the outer membrane of Gram-negative bacteria. In order to evaluate potent LPS-neutralizing activity of bovine BPI, the full-length coding sequence (1 449bp) or 714 bp N-terminal coding sequence (BPI714) of bovine BPI was transfected into mHEK293 cells and the expression of LPS-induced inflammatory cytokines was studied. First, we constructed the lentiviral expression vectors and generated mHEK293 cells stably expressing recombinant bovine BPI or BPI714. Then, we detected the expression of IL-8, IL-1β, TNF-α, NF-κB-1 and NF-κB-2 genes by real-time PCR at 0, 1, 3, 6, 12, 24, 36 and 48 h post of LPS induction in cells with or without recombinant bovine BPI or BPI714 ectopic expression, respectively. In response to LPS, the robust abundance of inflammatory cytokines including IL-8, IL-1β, TNF-α and NF-κB-2 was observed in wild type mHEK293 cells at eachtime point. On the contrary, mRNA abundance of IL-8, TNF-α and NF-κB-2 in transfected mHEK293 cells showed no significant changes at each indicated time point. Our results demonstrated that recombinant bovine full length BPI or BPI714 down-regulated the expression of inflammatory cytokines and revealed that either of bovine BPI or BPI714 was able to inhibit the immune respond stimulated by LPS. This study provides evidence for further investigating the mechanisms and application of BPI/LPS-neutralizing activity and also documents a reliable approach for analysis of the efficacy of antibacterial proteins.
Animals ; Antimicrobial Cationic Peptides ; chemistry ; Blood Proteins ; chemistry ; Cattle ; Cytokines ; biosynthesis ; HEK293 Cells ; Humans ; Interleukins ; biosynthesis ; Lipopolysaccharides ; chemistry ; NF-kappa B ; biosynthesis ; Transfection ; Tumor Necrosis Factor-alpha ; biosynthesis

As a key role in mussel defense system, Mytilin is an important antibacterial peptide isolated from the mussel serum. The structural and functional researches on Mytilin showed that the fragment connecting two beta-sheets in a stable beta-hairpin structure was probably required for antimicrobial activity. To elucidate the structural features and the antimicrobial activity of this fragment, we re-designed and synthesized two peptides corresponding to the main mimic structures of Mytilin-1 from Mytilus coruscus, we named these two peptides Mytilin Derived Peptide-1 and Mytilin Derived Peptide-2, respectively. Using a liquid growth inhibition assay, we evaluated their activity towards Gram-positive, Gram-negative bacteria and fungus. The results showed that both peptides can inhibit the growth of Gram-positive, Gram-negative bacteria and fungus. Besides, these two peptides showed high stability in heat water and human serum. These works laid the foundation for further research on the molecular mechanism of Mytilin and for further exploitation of antibacterial peptides with lower molecular mass and more stable structure.
Amino Acid Sequence ; Animals ; Anti-Infective Agents ; chemical synthesis ; pharmacology ; Antimicrobial Cationic Peptides ; chemical synthesis ; chemistry ; pharmacology ; Molecular Sequence Data ; Mytilus ; chemistry

Mytilin-derived-peptide-1 (MDP-1) and mytilin-derived-peptide-2 (MDP-2) are two truncated decapeptides with reversed sequence synthesized corresponding to the residues 20-29 of mytilin-1 (GenBank Accession No. FJ973154) from M. coruscus. The objective of this study is to characterize the structural basis of these two peptides for their antimicrobial activities and functional differences, and to investigate the inhibitory mechanism of MDPs on Escherichia coli and Sarcina lutea. The structures of MDP-1 and MDP-2 in solution were determined by 1H 2D NMR methods; the antibactericidal effects of MDPs on E. coli and S. lutea were observed by transmitted electron microscopy (TEM). Both MDP-1 and MDP-2 have a well-defined loop structure stabilized by two additional disulfide bridges, which resemble the-hairpin structure of mytilin-1 model. The surface profile of MDPs' structures was characterized by protruding charged residues surrounded by hydrophobic residues. TEM analysis showed that MDPs destroyed cytoplasmic membrane and cell wall of bacteria and the interface between the cell wall and membrane was blurred. Furthermore, some holes were observed in treated bacteria, which resulted in cell death. Structural comparison between MDP-1 and MDP-2 shows that the distribution of positively charged amino acids on the loop of MDPs is topologically different significantly, which might be the reason why MDP-2 has higher activity than MDP-1. Furthermore, TEM results suggested that the bactericidal mechanisms of MDPs against E. coli and S. lutea were similar. Both MDP-1 and MDP-2 could attach to the negatively charged bacterial wall by positively charged amino acid residues and destroy the bacteria membrane in a pore-forming manner, thus cause the contents of the cells to release and eventually cell death.
Animals ; Anti-Infective Agents ; chemical synthesis ; pharmacology ; Antimicrobial Cationic Peptides ; chemical synthesis ; chemistry ; pharmacology ; Cell Wall ; drug effects ; Escherichia coli ; drug effects ; Mytilus ; chemistry ; Sarcina ; drug effects