Mechanistic and structural basis of bioengineered bovine Cathelicidin-5 with optimized therapeutic activity

MA-PEP: A novel anticancer peptide prediction framework with multimodal feature fusion based on attention mechanism

AntiCancer Peptides (ACPs) have emerged as promising therapeutic agents for cancer treatment. The time-consuming and costly nature of wet-lab discriminatory methods has spurred the development of various machine learning and deep learning-based ACP classification methods. Nonetheless, current methods encountered challenges in efficiently integrating features from various peptide modalities, thereby limiting a more comprehensive understanding of ACPs and further restricting the improvement of prediction model performance. In this study, we introduce a novel ACP prediction method, MA-PEP, which leverages multiple attention mechanisms for feature enhancement and fusion to improve ACP prediction. By integrating the enhanced molecular-level chemical features and sequence information of peptides, MA-PEP demonstrates superior prediction performance across several benchmark datasets, highlighting its efficacy in ACP prediction. Moreover, the visual analysis and case studies further demonstrate MA-PEP's reliable feature extraction capability and its promise in the realm of ACP exploration. The code and datasets for MA-PEP are available at https://github.com/liangxiaodata/MA-PEP.

Lessons from a Single Amino Acid Substitution: Anticancer and Antibacterial Properties of Two Phospholipase A2-Derived Peptides

The membrane-active nature of phospholipase A₂-derived peptides makes them potential candidates for antineoplastic and antibacterial therapies. Two short 13-mer C-terminal fragments taken from snake venom Lys49-PLA₂ toxins (p-AppK and p-Acl), differing by a leucine/phenylalanine substitution, were synthesized and their bioactivity was evaluated. Their capacity to interfere with the survival of Gram-positive and Gram-negative bacteria as well as with solid and liquid tumors was assessed in vitro. Toxicity to red blood cells was investigated via in silico and in vitro techniques. The mode of action was mainly studied by molecular dynamics simulations and membrane permeabilization assays. Briefly, both peptides have dual activity, i.e., they act against both bacteria, including multidrug-resistant strains and tumor cells. All tested bacteria were susceptible to both peptides, Pseudomonas aeruginosa being the most affected. RAMOS, K562, NB4, and CEM cells were the main leukemic targets of the peptides. In general, p-Acl showed more significant activity, suggesting that phenylalanine confers advantages to the antibacterial and antitumor mechanism, particularly for osteosarcoma lines (HOS and MG63). Peptide-based treatment increased the uptake of a DNA-intercalating dye by bacteria, suggesting membrane damage. Indeed, p-AppK and p-Acl did not disrupt erythrocyte membranes, in agreement with in silico predictions. The latter revealed that the peptides deform the membrane and increase its permeability by facilitating solvent penetration. This phenomenon is expected to catalyze the permeation of solutes that otherwise could not cross the hydrophobic membrane core. In conclusion, the present study highlights the role of a single amino acid substitution present in natural sequences towards the development of dual-action agents. In other words, dissecting and fine-tuning biomembrane remodeling proteins, such as snake venom phospholipase A₂ isoforms, is again demonstrated as a valuable source of therapeutic peptides.

Significance of Endogenous Antimicrobial Peptides on the Health of Food Animals

Acquired resistance to in-feed antibiotic growth promoters continues to be an imperative problem in the livestock industries, thereby necessitating continuous pursuit for alternatives. Antimicrobial peptides (AMPs) represent a critical part of the host's innate immune system and have been documented to have immunomodulatory activity. Increasing research evidence suggests that in contrast to antibiotics, AMPs exert broad-spectrum antibacterial activity in a manner that reduces bacterial acquisition of resistance genes. This review summarizes current knowledge on the protective effects of endogenous (natural) AMPs in the gastrointestinal tract of food animals. Factors limiting the efficacy of these AMPs were also discussed and mitigating strategies were proposed.

Gadolinium Complexes as Contrast Agent for Cellular NMR Spectroscopy

Aqua Gd³⁺ and Gd-DOTA (gadolinium-1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacete) complexes were studied as a contrast agent in cellular NMR (nuclear magnetic resonance) spectroscopy for distinguishing between intracellular and extracellular spaces. The contrast agents for this purpose should provide strong paramagnetic relaxation enhancement and localize in the extracellular space without disturbing biological functions. Cell membrane permeability to Gd complexes was evaluated from the concentrations of gadolinium complexes in the inside and outside of E. coli cells measured by the ¹H-NMR relaxation. The site-specific binding of the complexes to E. coli cells was also analyzed by high-resolution solid-state ¹³C-NMR. The aqua Gd³⁺ complex did not enhance T₁ relaxation in proportion to the amount of added Gd³⁺. This Gd³⁺ concentration dependence and the ¹³C-NMR indicated that its strong cytotoxicity should be due to the binding of the paramagnetic ions to cellular components especially at the lipid membranes. In contrast, Gd-DOTA stayed in the solution states and enhanced relaxation in proportion to the added amount. This agent exhibited strong T₁ contrast between the intra- and extracellular spaces by a factor of ten at high concentrations under which the cells were viable over a long experimental time of days. These properties make Gd-DOTA suitable for selectively contrasting the living cellular space in NMR spectroscopy primarily owing to its weak interaction with cellular components.

Recent advances: peptides and self-assembled peptide-nanosystems for antimicrobial therapy and diagnosis

Bacterial infections, especially the refractory treatment of drug-resistant bacteria, are one of the greatest threats to human health. Self-assembling peptide-based strategies can specifically detect the bacteria at the site of infection in the body and kill it.

Diverse Structural Conversion and Aggregation Pathways of Alzheimer's Amyloid-β (1-40)

Complex amyloid aggregation of amyloid-β (1-40) (Aβ_1-40) in terms of monomer structures has not been fully understood. Herein, we report the microscopic mechanism and pathways of Aβ_1-40 aggregation with macroscopic viewpoints through tuning its initial structure and solubility. Partial helical structures of Aβ_1-40 induced by low solvent polarity accelerated cytotoxic Aβ_1-40 amyloid fibrillation, while predominantly helical folds did not aggregate. Changes in the solvent polarity caused a rapid formation of β-structure-rich protofibrils or oligomers via aggregation-prone helical structures. Modulation of the pH and salt concentration transformed oligomers to protofibrils, which proceeded to amyloid formation. We reveal diverse molecular mechanisms underlying Aβ_1-40 aggregation with conceptual energy diagrams and propose that aggregation-prone partial helical structures are key to inducing amyloidogenesis. We demonstrate that context-dependent protein aggregation is comprehensively understood using the macroscopic phase diagram, which provides general insights into differentiation of amyloid formation and phase separation from unfolded and folded structures.

BeStSel: a web server for accurate protein secondary structure prediction and fold recognition from the circular dichroism spectra

Circular dichroism (CD) spectroscopy is a widely used method to study the protein secondary structure. However, for decades, the general opinion was that the correct estimation of β-sheet content is challenging because of the large spectral and structural diversity of β-sheets. Recently, we showed that the orientation and twisting of β-sheets account for the observed spectral diversity, and developed a new method to estimate accurately the secondary structure (PNAS, 112, E3095). BeStSel web server provides the Beta Structure Selection method to analyze the CD spectra recorded by conventional or synchrotron radiation CD equipment. Both normalized and measured data can be uploaded to the server either as a single spectrum or series of spectra. The originality of BeStSel is that it carries out a detailed secondary structure analysis providing information on eight secondary structure components including parallel-β structure and antiparallel β-sheets with three different groups of twist. Based on these, it predicts the protein fold down to the topology/homology level of the CATH protein fold classification. The server also provides a module to analyze the structures deposited in the PDB for BeStSel secondary structure contents in relation to Dictionary of Secondary Structure of Proteins data. The BeStSel server is freely accessible at http://bestsel.elte.hu.

Structural analysis and mode of action of BMAP-27, a cathelicidin-derived antimicrobial peptide

BMAP-27, a member of cathelicidin family, plays an important role against microorganisms, including bacteria and fungi. BMAP-27 may exert antimicrobial effects through membrane integrity disruption, but the exact molecular mechanism remains unclear. To identify the structural features important for antimicrobial activity and propose a mechanism underlying antibacterial effects, we determined the nuclear magnetic resonance structure of BMAP-27 in a membrane-mimetic environment and investigated its interactions with lipid membranes. BMAP-27 exhibited a long N-terminal α-helix with faces patterned into aromatic and cationic regions, central kink, and short hydrophobic C-terminal helix. While the N-terminal 18-residue peptide (BMAP-18) exerted only antibacterial activity, BMAP-27 showed potent activity against bacteria and cancer cells. Both peptides inhibited bacterial growth, but BMAP-18 showed delayed bactericidal activity and BMAP-27 completely killed bacteria within 20 min. The differences in antimicrobial activities and microbicidal kinetics may be associated with membrane permeabilisation; BMAP-27 rapidly and largely disrupted membrane integrity, whereas BMAP-18 showed low membrane disruption activity. Thus, the N-terminal helix is sufficient to inhibit bacterial growth and the C-terminal helix is involved in membrane permeabilisation for rapid bactericidal and efficient anticancer activities. The structural and functional characterisation of BMAP-27 may encourage the development of novel antimicrobial/anticancer agents.

Arginine/Tryptophan-Rich Cyclic α/β-Antimicrobial Peptides: The Roles of Hydrogen Bonding and Hydrophobic/Hydrophilic Solvent-Accessible Surface Areas upon Activity and Membrane Selectivity

The bacterial selectivity of an amphiphilic library of small cyclic α/β-tetra-, α/β-penta-, and α/β-hexapeptides rich in arginine/tryptophan (Arg/Trp) residues, which contains asymmetric backbone configurations and differ in hydrophobicity and alternating d,l-amino acids, was investigated against Bacillus subtilis and Escherichia coli. The structural analyses showed that the peptides tend to form assemblies of different shapes. All-l-peptides, especially the most hydrophobic pentamers, were more strongly anti-B. subtilis. With the exception to cyclo(Phe-d-Trp-β³ hArg-Arg-d-Trp) (Phe=phenylalanine), the peptides had no effects on inner membrane of E. coli, but lyzed the lipopolysaccharide layer according to their activity pattern. The activities adversely changed with a decrease in the number of amide intramolecular hydrogen bonds in assemblies of diastereomeric peptides and the ratio of hydrophobic/hydrophilic solvent-accessible surface areas. The remarkable enhanced entropic contribution for the partitioning of the least conformationally constrained cyclo(Trp-d-Phe-β³ hTrp-Arg-d-Arg) sequence into the membranes supported the strong self-assembly behavior, therefore making the peptide less penetrable through the E. coli outer layer.

Host defense cathelicidins in cattle: types, production, bioactive functions and potential therapeutic and diagnostic applications

Cathelicidins are a primitive class of host defense peptides and are known for their broad-spectrum antimicrobial activity against bacteria, fungi, and enveloped viruses. These small, cationic, proteolytically-activated peptides are diverse in structure, encompassing a wide range of activities on host immune and inflammatory cell responses. The dual capacity of cathelicidins to directly control infection and regulate host defenses highlights the potential use of these peptides as alternatives to antibiotics and immunomodulators. Cathelicidins are found in many mammalian species; this review focuses on bovine cathelicidins. Eight naturally and two synthetically occurring bovine cathelicidins are described in detail, with a focus on recent advances in their expression, location and biological roles. This review also presents an overview of the bioactive functions of cathelicidins in bovine mastitis, a disease causing economic losses in cattle dairy production. Comparison of the structural, antimicrobial, cytotoxic and mechanistic properties of bovine cathelicidins advances the knowledge needed for the development of these peptides as potential identifiers of infectious diseases (e.g., bovine mastitis) and as novel therapeutic alternatives to antibiotics.