In silico designing of some agonists of toll-like receptor 5 as a novel vaccine adjuvant candidates

Investigate the binding of pesticides with the TLR4 receptor protein found in mammals and zebrafish using molecular docking and molecular dynamics simulations

The widespread use of pesticides poses significant threats to both environmental and human health, primarily due to their potential toxic effects. The study investigated the cardiovascular toxicity of selected pesticides, focusing on their interactions with Toll-like receptor 4 (TLR4), an important part of the innate immune system. Using computational tools such as molecular docking, molecular dynamics (MD) simulations, principal component analysis (PCA), density functional theory (DFT) calculations, and ADME analysis, this study identified C160 as having the lowest binding affinity (-8.2 kcal/mol), followed by C107 and C165 (-8.0 kcal/mol). RMSD, RMSF, Rg, and hydrogen bond metrics indicated the formation of stable complexes between specific pesticides and TLR4. PCA revealed significant structural changes upon ligand binding, affecting stability and flexibility, while DFT calculations provided information about the stability, reactivity, and polarity of the compounds. ADME studies highlighted the solubility, permeability, and metabolic stability of C107, C160, and C165, suggesting their potential for bioavailability and impact on cardiovascular toxicity. C107 and C165 exhibit higher bioactivity scores, indicating favourable absorption, metabolism, and distribution properties. C165 also violated rule where molecular weight is greater than 500 g/mol. Further, DFT and NCI analysis of post MD conformations confirmed the binding of ligands at the binding pocket. The analysis shed light on the molecular mechanisms of pesticide-induced cardiovascular toxicity, aiding in the development of strategies to mitigate their harmful effects on human health.

The novel anti-cancer feature of Brazzein through activating of hTLR5 by integration of biological evaluation: molecular docking and molecular dynamics simulation

Many of plant proteins exhibit the properties similar to the antitumor proteins although the anticancer activity of Brazzein on modulating the autophagy signaling pathway has not been determined so far. The present study aimed to develop a simplified system to enable the rational design of the activating extracellular domain of human Toll-like receptor 5 (hTLR5). To identify the anticancer effect of Brazzein, HADDOCK program and molecular dynamics (MD) simulation were applied to examine the binding of the wild type (WT) and p.A19K mutant of Brazzein to the TLR5. The expression of MAP1S and TNF-α genes was estimated based on real-time PCR. The results clearly confirmed that the WT of Brazzein activated hTLR5 in the MCF-7 cell line since the genes were more and significantly less expressed in the cells treated with the WT and p.A19K mutant than the control, respectively. The snapshots of MD simulation exhibit the consistent close interactions of hTLR5 with the two helices of Brazzein on its lateral side. The results of per residue-free energy decomposition analysis substantiate those of intermolecular contact analysis perfectly one. We propose that the WT of Brazzein can act as an antitumor drug candidate.

A Novel Design of Multi-epitope Peptide Vaccine Against Pseudomonas aeruginosa

Background:

As an opportunistic pathogen, Pseudomonas aeruginosa causes many different hazardous infections. The high mortality rate resulting from infection with this antibiotic-resistant pathogen has made it a major challenge in clinical treatment; it has been listed as the most harmful bacterium to humans by the WHO. So far, no vaccine has been approved for P. aeruginosa.

Objective:

Infections performed by bacterial attachment and colonization with type IV pili (T4P), known as the most essential adhesive vital for adhesion, while pilQ is necessary for the biogenesis of T4P, also outer membrane proteins of a pathogen is also effective in stimulating the immune system; in this regard, pilQ, OprF, and OprI, are excellent candidate antigens for production of an effective vaccine against P. aeruginosa.

Methods:

In this research, various bioinformatics methods were employed in order to design a new multiepitope peptide vaccine versus P. aeruginosa. Since T CD4+ cell immunity is important in eradicating P. aeruginosa, OprF, OprI, and pilQ antigens were analyzed to determine Helper T cell Lymphocyte (HTL) epitopes by many different immunoinformatics servers. One of the receptor agonists 2 (TLR2), a segment of the Por B protein from Neisseria meningitides was used as an adjuvant in order to stimulate an effective cellular immune response, and suitable linkers were used to connect all the above mentioned parts. In the vaccine construct, linear B cell epitopes were also identified.

Results:

Conforming the bioinformatics forecasts, the designed vaccine possesses high antigenicity and is not allergen.

Conclusion:

In this regard, the designed vaccine candidate is strongly believed to possess the potential of inducing cellular and humoral immunity against P. aeruginosa.

Comparison of the efficacy of HIV-1 Nef-Tat-Gp160-p24 polyepitope vaccine candidate with Nef protein in different immunization strategies

OBJECTIVES

One of the promising strategies for effective HIV-1 vaccine design involves finding the polyepitope immunogens using T cell epitopes.

METHODS

Herein, an HIV-1 polyepitope construct (i.e., Nef-Tat-Gp160-P24) comprising of several epitopes from Nef, Tat, Gp160, and P24 proteins was designed. To improve its immunogenicity in BALB/c mice, cell-penetrating peptides (HR9 & MPG for DNA delivery, and LDP-NLS & CyLoP-1 for protein transfer), Montanide adjuvant, and heterologous DNA prime/polypeptide boost strategy were used. To compare the immunogenicity, Nef was utilized as a vaccine candidate. The levels of total IgG and its subclasses, cytokines, and Granzyme B were assessed using ELISA.

RESULTS

Immunological studies showed that heterologous prime-boost regimens for both antigens could considerably augment the levels of IgG2a, IgG2b, IFN-γ, and Granzyme B directed toward Th1 and CTL immune responses in comparison with homologous prime-boost strategies. The levels of IFN-γ, IL-10, total IgG, IgG1, and IgG2b were drastically higher in groups immunized with Nef-Tat-Gp160-P24 in heterologous prime-boost regimens than those in groups immunized with Nef.

CONCLUSIONS

The use of the Nef-Tat-Gp160-P24 polyepitope immunogen in heterologous prime-boost strategy could generate the mixture of Th1 and Th2 responses directed further toward Th1 response as a hopeful method for improvement of HIV-1 vaccine.

Virtual screening for potential inhibitors of β(1,3)-D-glucan synthase as drug candidates against fungal cell wall

Background

To enhance the outcome in patients with invasive candidiasis, initiation of an efficient antifungal treatment in a suitable dosage is necessary. Echinocandins (e.g. caspofungin) inhibit the enzyme β(1,3)-D-glucan synthase of the fungal cell wall. Compared to azoles and other antifungal agents, echinocandins have lower adverse effects and toxicity in humans. Echinocandins are available in injectable (intravenous) form.

Methods

In this study, to identify the novel oral drug-like compounds that affect the fungal cell wall, downloaded oral drug-like compounds from the ZINC database were processed with a virtual screening procedure. The docking free energies were calculated and compared with the known inhibitor caspofungin. Four molecules were selected as the most potent ligands and subjected to hydrogen bonds analysis.

Results

Considering the hydrogen bond analysis, two compounds (ZINC71336662 and ZINC40910772) were predicted to better interact with the active site of β(1,3)-D-glucan synthase compared with caspofungin.

Conclusion

The introduced compound in this study may be valuable to analyze experimentally as a novel oral drug candidate targeting fungal cell walls.

Exploring T & B-cell epitopes and designing multi-epitope subunit vaccine targeting integration step of HIV-1 lifecycle using immunoinformatics approach

Till now, AIDS, caused by the human immunodeficiency virus (HIV) is still a severe health problem worldwide. It weakens the immune system by targeting the T-helper cells. Specifically, the severity of the pandemic HIV-1 makes the emergence of an enduring effective vaccine against HIV-1. Therefore, we have applied a series of immunoinformatics approaches to the four conserved domains of HIV-1 integrase (IN) proteins to design an effective multi-epitope based subunit vaccine which might induce a competent immunity against HIV-1. Therefore, we have selected three peptide fragments that contained all overlapping epitopes (35 CD4⁺, 8 CD8⁺ T-cell epitopes, and 3 B-cell epitopes) where the epitopes had a high conservancy score. The cumulative population coverage for combined CD8⁺ and CD4⁺ T-cell epitopes and their respective HLA-alleles were found as 98.03% in the world which is also followed by East Asia (96.24%), South Asia (96.31%), North Africa (96.14%), North America (98.99%), and Europe (98.80%). The proposed vaccine composed by an adjuvant (β-defensin) at the N-terminal site of the vaccine constructs and three peptide fragments where the adjuvant was fused by EAAAK linker and the peptide fragments were fused by GPGPG linker. The designed final vaccine construct (length: 159 amino acid) was found to be antigenic and non-allergic, which indicates its safety. The vaccine construct was found as good antigenic, stable, higher thermostable, and hydrophilic in nature. The codon adaptation and in silico cloning ensured the high expression rate of the vaccine constructs in E. coli K12 with CAI value of 1.0. Finally, the binding affinity of the vaccine constructs with the immune receptor TLR3 was confirmed by the lowest energy score of -1026.8 evaluated by molecular docking. However, the proposed in silico vaccine construct needs experimental validation for assuring the safety and immunogenicity profile which will ensure an active immunity against HIV-1.

Virtual Screening for Potential Inhibitors of CTX-M-15 Protein of Klebsiella pneumoniae

The Gram-negative bacterium Klebsiella pneumoniae, responsible for a wide variety of nosocomial infections in immuno-deficient patients, involves the respiratory, urinary and gastrointestinal tract infections and septicemia. Extended spectrum β-lactamases (ESBL) belong to β-lactamases capable of conferring antibiotic resistance in Gram-negative bacteria. CTX-M-15, a prevalent ESBL reported from Enterobacteriaceae including K. pneumoniae, was selected as a potent anti-bacterial target. To identify the novel drug-like compounds, structure-based screening procedure was employed against downloaded drug-like compounds from ZINC database. An acronym for "ZINC" is not commercial. The docking free energy values were investigated and compared to the known inhibitor Avibactam. Six best novel drug-like compounds were selected and their hydrogen bindings with the receptor were determined. Based on the binding efficiency mode, three among these six identified most potential inhibitors, ZINC21811621, ZINC93091917 and ZINC19488569, were predicted as potential competitive inhibitors against CTX-M-15 compared to Avibactam. These three inhibitors may provide a framework for the experimental studies to develop anti-Klebsiella novel drug candidates targeting CTX-M-15.