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Computational and Structural... 2023SARS-CoV-2 variants continue to spread throughout the world and cause waves of COVID-19 infections. It is important to find effective antiviral drugs to combat...
BACKGROUND
SARS-CoV-2 variants continue to spread throughout the world and cause waves of COVID-19 infections. It is important to find effective antiviral drugs to combat SARS-CoV-2 and its variants. The main protease (M) of SARS-CoV-2 is a promising therapeutic target due to its crucial role in viral replication and its conservation in all the variants. Therefore, the aim of this work was to identify an effective inhibitor of M.
METHODS
We studied around 200 antimicrobial peptides using methods including molecular docking and allergenicity and toxicity prediction. One selected antiviral peptide was studied experimentally using a Bioluminescence Resonance Energy Transfer (BRET)-based M biosensor, which reports M activity through a decrease in energy transfer.
RESULTS
Molecular docking identified one natural antimicrobial peptide, Protegrin-2, with high binding affinity and stable interactions with M allosteric residues. Furthermore, free energy calculations and molecular dynamics simulation illustrated a high affinity interaction between the two. We also determined the impact of the binding of Protegrin-2 to M using a BRET-based assay, showing that it inhibits the proteolytic cleavage activity of M.
CONCLUSIONS
Our and experimental studies identified Protegrin-2 as a potent inhibitor of M that could be pursued further towards drug development against COVID-19 infection.
PubMed: 37576748
DOI: 10.1016/j.csbj.2023.07.020 -
BioRxiv : the Preprint Server For... Sep 2023Antimicrobial peptides commonly act by disrupting bacterial membranes, but also frequently damage mammalian membranes. Deciphering the rules governing membrane...
Antimicrobial peptides commonly act by disrupting bacterial membranes, but also frequently damage mammalian membranes. Deciphering the rules governing membrane selectivity is critical to understanding their function and enabling their therapeutic use. Past attempts to decipher these rules have failed because they cannot interrogate adequate peptide sequence variation. To overcome this problem, we develop deep mutational surface localized antimicrobial display (dmSLAY), which reveals comprehensive positional residue importance and flexibility across an antimicrobial peptide sequence. We apply dmSLAY to Protegrin-1, a potent yet toxic antimicrobial peptide, and identify thousands of sequence variants that positively or negatively influence its antibacterial activity. Further analysis reveals that avoiding large aromatic residues and eliminating disulfide bound cysteine pairs while maintaining membrane bound secondary structure greatly improves Protegrin-1 bacterial specificity. Moreover, dmSLAY datasets enable machine learning to expand our analysis to include over 5.7 million sequence variants and reveal full Protegrin-1 mutational profiles driving either bacterial or mammalian membrane specificity. Our results describe an innovative, high-throughput approach for elucidating antimicrobial peptide sequence-structure-function relationships which can inform synthetic peptide-based drug design.
PubMed: 37547010
DOI: 10.1101/2023.07.28.551017 -
International Journal of Molecular... Jul 2023Antimicrobial peptides (AMPs) are promising alternatives to existing treatments for multidrug-resistant bacteria-infected wounds. Therefore, the effect of protegrin-1...
Antimicrobial peptides (AMPs) are promising alternatives to existing treatments for multidrug-resistant bacteria-infected wounds. Therefore, the effect of protegrin-1 (PG1), a potent porcine AMP with broad-spectrum activity, on wound healing was evaluated. PG1-overexpressing transgenic mice were used as an in vivo model to evaluate its healing efficiency against -infected (10 colony forming units) wounds. We analyzed the wounds under four specific conditions in the presence or absence of antibiotic treatment. We observed the resolution of bacterial infection and formation of neo-epithelium in -infected wounds of the mice, even without antibiotic treatment, whereas all wild-type mice with bacterial infection died within 8 to 10 days due to uncontrolled bacterial proliferation. Interestingly, the wound area on day 7 was smaller ( 0.01) in PG1 transgenic mice than that in the other groups, including antibiotic-treated mice, suggesting that PG1 exerts biological effects other than bactericidal effect. Additionally, we observed that the treatment of primary epidermal keratinocytes with recombinant PG1 enhanced cell migration in in vitro scratch and cell migration assays. This study contributes to the understanding of broad-spectrum endogenous cathelicidins with potent antimicrobial activities, such as PG1, on wound healing. Furthermore, our findings suggest that PG1 is a potent therapeutic candidate for wound healing.
Topics: Swine; Mice; Animals; Cathelicidins; Staphylococcus aureus; Mice, Transgenic; Antimicrobial Cationic Peptides; Anti-Bacterial Agents; Wound Infection; Staphylococcal Infections
PubMed: 37511418
DOI: 10.3390/ijms241411658 -
Archives of Animal Nutrition Jun 2023The present study aimed to compare the effects of vitamin D and vitamin D supplementation on concentrations of total and free 25(OH)D in plasma and the expression of...
Effect of supplementation of vitamin D or vitamin D on serum concentrations of free and total 25-hydroxyvitamin D and the expression of genes involved in immune function in peripheral blood mononuclear cells of weaned pigs.
The present study aimed to compare the effects of vitamin D and vitamin D supplementation on concentrations of total and free 25(OH)D in plasma and the expression of genes involved in the innate immune system in peripheral blood mononuclear cells (PBMC) in weaned pigs. Five groups of pigs (with an initial body weight of around 9 kg) received basal diets supplemented with either 500 (control group), 1000 or 2000 IU vitamin D/kg diet or 1000 or 2000 IU vitamin D/kg diet for a period of 4 weeks. Vitamin D supplementation did not influence feed intake, body weight gain, feed conversion ratio, apparent total tract digestibility of calcium and phosphorus, and serum concentrations of calcium, inorganic phosphate and parathyroid hormone. Supplementation of vitamin D led to a dose-dependent increase of the concentrations of total and free 25(OH)D in serum. In contrast, pigs supplemented with 1000 or 2000 IU vitamin D/kg diet did not have higher concentrations of total and free 25(OH)D in serum than the control group. The ratio of free/total 25(OH)D in serum was not influenced by vitamin D supplementation, whereas the group supplemented with 2000 IU vitamin D/kg diet had a higher free/total 25(OH)D ratio than the groups supplemented with 1000 or 2000 IU vitamin D/kg diet. Genes involved in vitamin D signalling (), as well as pro-inflammatory and immune regulatory genes ( and ) and genes encoding porcine protegrins (), proteins belonging to the group of antimicrobial peptides, in PBMC were not different among groups supplemented with vitamin D or vitamin D and the control group. Therefore, the study indicates that supplementation of vitamin D causes much lower levels of total 25(OH)D than supplementation of vitamin D and that supplementation of vitamins D or D at moderate levels does not have an impact on the innate immune function in healthy pigs.
Topics: Swine; Animals; Cholecalciferol; Leukocytes, Mononuclear; Calcium; Diet; Animal Feed; Vitamin D; Calcifediol; Dietary Supplements; Body Weight; Immunity
PubMed: 37335004
DOI: 10.1080/1745039X.2023.2219176 -
Acta Naturae 2023Bacterial infections caused by antibiotic-resistant pathogens pose an extremely serious and elusive problem in healthcare. The discovery and targeted creation of new...
Bacterial infections caused by antibiotic-resistant pathogens pose an extremely serious and elusive problem in healthcare. The discovery and targeted creation of new antibiotics are today among the most important public health issues. Antibiotics based on antimicrobial peptides (AMPs) are of particular interest due to their genetically encoded nature. A distinct advantage of most AMPs is their direct mechanism of action that is mediated by their membranolytic properties. The low rate of emergence of antibiotic resistance associated with the killing mechanism of action of AMPs attracts heightened attention to this field. Recombinant technologies enable the creation of genetically programmable AMP producers for large-scale generation of recombinant AMPs (rAMPs) or the creation of rAMP-producing biocontrol agents. The methylotrophic yeast Pichia pastoris was genetically modified for the secreted production of rAMP. Constitutive expression of the sequence encoding the mature AMP protegrin-1 provided the yeast strain that effectively inhibits the growth of target gram-positive and gram-negative bacteria. An antimicrobial effect was also observed in the microculture when a yeast rAMP producer and a reporter bacterium were co-encapsulated in droplets of microfluidic double emulsion. The heterologous production of rAMPs opens up new avenues for creating effective biocontrol agents and screening antimicrobial activity using ultrahigh-throughput technologies.
PubMed: 37153506
DOI: 10.32607/actanaturae.11878 -
Plant Disease Oct 2023Optimizing synthetic antimicrobial peptides for safe and enhanced activity against fungal and bacterial pathogens is useful for genetic engineering of plants for...
Optimizing synthetic antimicrobial peptides for safe and enhanced activity against fungal and bacterial pathogens is useful for genetic engineering of plants for resistance to plant pathogens and their associated mycotoxins. Nine synthetic peptides modeled after lytic peptides tachyplesin 1, D4E1 from cecropin A, and protegrin 1 were added to germinated spores of fungal species , , f. sp. , , , , , and and bacterial cultures of pv. and pv. at different doses and inhibitory dose response curves, and were modeled to assess antimicrobial activity. Peptides GV185 and GV187, modified from tachyplesin 1, had superior abilities to inhibit fungal and bacterial growth (50% inhibitory concentrations [IC] ranging from 0.1 to 8.7 µM). (IC = 8.1 µM), (IC = 3.1 µM), and (IC = 2.2 µM) were less inhibited by GV185 and GV187 than all the remaining fungi (IC = 1.4 µM) and bacteria (IC = 0.1 µM). Of the remaining peptides, GV193, GV195, and GV196 (IC range of 0.9 to 6.6 µM) inhibited fungal growth of , , and less than GV185 and GV187 (IC range of 0.8 to 3.9 µM), followed by GV197 (IC range of 0.8 to 9.1 µM), whereas GV190 and GV192 inhibited poorly (IC range of 28.2 to 36.6 µM and 15.5 to 19.4 µM, respectively) and GV198 stimulated growth. GV185 and GV187 had slightly weaker hydrophobic and cationic residues than other tachyplesin 1 modified peptides but still had unexpectedly high lytic activity. Germinated fungal spores of and exposed to these two peptides and D4E1 and AGM182 appeared wrinkled, with perforations near potential cytoplasmic leakage, which provided evidence of plasma membrane and cell wall lysis. We conclude that peptides GV185 and GV187 are promising candidates for genetic engineering of crops for resistance to plant-pathogenic bacteria and fungi, including and aflatoxin contamination.
Topics: Antifungal Agents; Aspergillus flavus; Spores, Fungal; Aflatoxins; Crops, Agricultural
PubMed: 36947838
DOI: 10.1094/PDIS-11-22-2572-RE -
ACS Applied Bio Materials Mar 2023Current antimicrobial challenges in hospitals, pharmaceutical production units, and food packaging have motivated the development of antimicrobial agents, among them the...
Current antimicrobial challenges in hospitals, pharmaceutical production units, and food packaging have motivated the development of antimicrobial agents, among them the antimicrobial compounds based on cellulose and peptides. Herein, we develop molecular dynamics (MD) models to dissect and characterize the adsorption process of antimicrobial peptides (AMPs) such as protegrin 1, magainin 2, and cyclic indolicidin on various surfaces of cellulose including [-1-10], [1-10], [-100], [100], [-110], and [110]. Our results suggest that the magainin 2 antimicrobial peptide loses most of its initial helix form, spreads on the cellulose surface, and makes the most rigid structure with [110] surface. The cyclic indolicidin peptide has the lowest affinity to adsorb on the cellulose surfaces, and the protegrin 1 peptide successfully adsorbs on all the proposed cellulose surfaces. Our MD simulations confirmed that cellulose can improve the corresponding peptides' structural stability and change their secondary structures during adsorption. The [-1-10] and [100] surfaces of cellulose show considerable affinity against the AMPs, exhibiting greater interactions with and adsorption to the peptides. Our data imply that the stronger adsorptions are caused by a set of H-bonds, van der Waals, and electrostatic interactions, where van der Waals interactions play a prominent role in the stability of the AMP-cellulose structures. Our energy analysis results suggest that glutamic acid and arginine amino acids have key roles in the stability of AMPs on cellulose surfaces due largely to stronger interactions with the cellulose surfaces as compared with other residues. Our results can provide useful insight at the molecular level that can help design better antimicrobial biomaterials based on cellulose.
Topics: Antimicrobial Peptides; Adsorption; Magainins; Cellulose; Anti-Infective Agents
PubMed: 36935640
DOI: 10.1021/acsabm.2c00905 -
Experimental and Therapeutic Medicine Jan 2023[This corrects the article DOI: 10.3892/etm.2015.2202.].
[This corrects the article DOI: 10.3892/etm.2015.2202.].
PubMed: 36569443
DOI: 10.3892/etm.2022.11713 -
Antibiotics (Basel, Switzerland) Dec 2022Tuberculosis is a highly contagious disease caused by the Mycobacterium tuberculosis complex (MTBC). Although TB is treatable, multidrug-resistant, extensively...
Tuberculosis is a highly contagious disease caused by the Mycobacterium tuberculosis complex (MTBC). Although TB is treatable, multidrug-resistant, extensively drug-resistant, and totally drug-resistant forms of M. tuberculosis have become a new life-threatening concern. New anti-TB drugs that are capable of curing these drug-resistant strains are urgently needed. The purpose of this study is to determine the antimycobacterial activity of D-enantiomer human lactoferricin 1-11 (D-hLF 1-11) against mycobacteria in vitro using a 3-(4,5-dimethylthiazol-2-yl)-2,5-dephenyltetrazolium bromide colorimetric assay, resazurin microplate assay, and microscopic observation drug susceptibility assay. Three previously described antimicrobial peptides, protegrin-1, AK 15-6, and melittin, with potent anti-TB activity, were included in this study. The findings suggest that D-hLF 1-11 can inhibit the growth of M. tuberculosis with a minimum inhibitory concentration of 100−200 µg/mL in susceptible, isoniazid (INH)-monoresistant, rifampicin (RF)-monoresistant, and MDR strains. The peptide can also inhibit some nontuberculous mycobacteria and other MTBC in similar concentrations. The antibiofilm activity of D-hLF 1-11 against the biofilm-forming M. abscessus was determined by crystal violet staining, and no significant difference is observed between the treated and untreated biofilm control. The checkerboard assay was subsequently carried out with M. tuberculosis H37Rv and the results indicate that D-hLF 1-11 displays an additive effect when combined with INH and a synergistic effect when combined with RF, with fractional inhibitory concentration indices of 0.730 and 0.312, respectively. The red blood cell hemolytic assay was initially applied for the toxicity determination of D-hLF 1-11, and negligible hemolysis (<1%) was observed, despite a concentration of up to 4 mg/mL being evaluated. Overall, D-hLF 1-11 has potential as a novel antimycobacterial agent for the future treatment of drug-sensitive and drug-resistant M. tuberculosis infections.
PubMed: 36551443
DOI: 10.3390/antibiotics11121785 -
Communications Biology Nov 2022Antimicrobial peptides (AMPs) are cationic antibiotics that can kill multidrug-resistant bacteria via membrane insertion. However, their weak activity limits their...
Antimicrobial peptides (AMPs) are cationic antibiotics that can kill multidrug-resistant bacteria via membrane insertion. However, their weak activity limits their clinical use. Ironically, the cationic charge of AMPs is essential for membrane binding, but it obstructs membrane insertion. In this study, we postulate that this problem can be overcome by locating cationic amino acids at the energetically preferred membrane surface. All amino acids have an energetically preferred or less preferred membrane position profile, and this profile is strongly related to membrane insertion. However, most AMPs do not follow this profile. One exception is protegrin-1, a powerful but neglected AMP. In the present study, we found that a potent AMP, WCopW5, strongly resembles protegrin-1 and that the match between its sequence and the preferred position profile closely correlates with its antimicrobial activity. One of its derivatives, WCopW43, has antimicrobial activity comparable to that of the most effective AMPs in clinical use.
Topics: Amino Acids; Anti-Bacterial Agents; Antimicrobial Peptides; Cations
PubMed: 36347951
DOI: 10.1038/s42003-022-04164-4