In-depth computational analysis of calcium-dependent protein kinase 3 of Toxoplasma gondii provides promising targets for vaccination

Toxoplasma calcium-dependent protein kinases 3 mediates M1 macrophage polarization by targeting host Arginase-1

BACKGROUND

Toxoplasma gondii, an obligate intracellular parasite, has developed sophisticated ways to manipulate host immunity, resulting in long-lasting infection and causing serious public health problems in humans and animals. T. gondii type II is the type most frequently associated with human diseases, but the mechanism remains unclear. Toxoplasma calcium-dependent protein kinase 3(CDPK3), a protein located on the T. gondii parasite periphery, is highly expressed in type II strains. Although TgCDPK3 regulates parasite egress from host cells, calcium-based infiltration, and development of tissue cysts, the host target proteins that it modulates are still unclear.

METHODS

Firstly, mass spectrometry was used to analyze proteins that selectively bind to TgCDPK3. Subsequently, GST (glutathione-s-transferase) pull-down, immunoprecipitation, and immunofluorescence assay were used to confirm the interaction and colocalization between TgCDPK3 and Arginase-1. Western blotting and Argininaseactivity assays were performed to detect the relative levels of endogenous Arginase-1 and inducible nitric oxide synthase (iNOS) in a murine microglial cell line. Fluorescence activated cell sorting (FACS) assays and enzyme-linked immunosorbent assay (ELISA) analysis were performed to confirm the association of interaction between TgCDPK3 and Arginase-1 within an M1/M2-polarized macrophage. Intracellular multiplication assays and plaque assays were performed to test whether the interaction between TgCDPK3 and Arginase-1 affected intercellular parasite growth.

RESULTS

The interaction between TgCDPK3 and Arginase-1 is functionally correlated and leads to a reduction in Arginase-1 activity, ultimately, contributing to the M1-biased phenotype of the host macrophages, which is related to restraining the proliferation of parasites.

CONCLUSIONS

Our data showed that CDPK3 mediates M1 macrophage polarization by targeting host Arginase-1, which is beneficial to understanding the mechanism for long term latency establishment of less virulent strains of Toxoplasma.

Preliminary In silico Analysis of Echinococcus granulosus Calreticulin for Enhanced Vaccine Design against Cystic Echinococcosis

BACKGROUND

A neglected zoonosis, Cystic Echinococcosis (CE), is most common in developing nations worldwide. Vaccination is, therefore, helpful in preventing this disease.

OBJECTIVE

Predicting the main biochemical properties of E. granulosus Calreticulin (CRT) and its possible B-cell and T-cell-binding epitopes as a valuable candidate for immunization was the goal of the current study.

METHODS

Predictions were made to determine biochemical, antigenic, structural, and subcellular characteristics, along with the immunogenic epitopes, using several online servers.

RESULTS

The extracellular 48.15 KDa protein exhibited no allergenicity, while possessing hydrophilicity (GRAVY: -0.785), stability (instability: 33.88), tolerance to a wide range of temperatures (aliphatic: 62.45), and 59 post-translational modification sites. The secondary structure mostly comprised random coils and extended strands. The 3D model was generated using the Robetta server (confidence: 0.72), and was rehashed and confirmed subsequently. Common B-cell epitopes were discovered by three servers and screened for antigenic, allergenic, and solubility traits. Moreover, MHC-associated epitopes for mice and humans were predicted in E. granulosus CRT with subsequent screening.

CONCLUSION

This work offers a foundation for further investigation in order to design an effective vaccination against CE. Further empirical research on the examined protein solely or in combination with other antigens is needed.

Investigation of bioremediation for glyphosate and its metabolite in soil using arbuscular mycorrhizal GmHsp60 protein: a molecular docking and molecular dynamics simulations approach

The widespread use of glyphosate and the high dependence of the agricultural industry on this herbicide cause environmental pollution and pose a threat to living organisms. One of the appropriate solutions in sustainable agriculture to deal with pollution caused by glyphosate and its metabolites is creating a symbiotic relationship between plants and mycorrhizal fungi. Glomalin-related soil protein is a key protein for the bioremediation of glyphosate and its metabolite aminomethyl phosphonic acid in soil. This study uses homology modeling, molecular docking, and molecular dynamic simulation approaches to investigate the binding mechanism of glomalin-related soil protein from arbuscular mycorrhiza (GmHsp60) with glyphosate and its metabolite and the role of soil protein in the removal and sequestering of common agricultural soil pollutants. GmHsp60 protein structure was predicted by homology modeling, and the quality of the generated model was assessed. Then, the interaction between glyphosate and aminomethyl phosphonic acid and the modeled GmHsp60 protein was explored by molecular docking. Based on docking results, GmHsp60 has an efficient role in the bioremediation of glyphosate and aminomethyl phosphonic acid (-6.03 and -5.34 kcal/mol). Glyphosate forms three hydrogen bonds with Lys258, Gly262, and Glu58 of GmHsp60, and aminomethyl phosphonic acid forms three hydrogen bonds with Lys258, Gly261, and Gly262 of GmHsp60. In addition, the glyphosate's and its metabolite's stability was confirmed by molecular docking simulations and binding free energy calculations using MM/PBSA analysis. This study provides a molecular-level understanding of GmHsp60 expression and function for glyphosate bioremediation.

Immunoinformatic Analysis of Leishmania Major gp46 Protein and Potential Targets for Vaccination against Leishmaniasis

BACKGROUND

Cutaneous leishmaniasis (CL) is a parasitic disease with a significant burden in the Old World countries.

OBJECTIVE

In the current study, some of the primary biochemical properties and IFN-γ inducing epitopes with specific binding capacity to human and mouse MHC alleles were predicted for Leishmania major gp46 antigenic protein.

METHODS

Several online servers were used to predict physico-chemical traits, allergenicity, antigenicity, transmembrane domain and signal peptide, subcellular localization, post-translational modifications (PTMs), secondary and tertiary structures, tertiary model refining with validations. Also, IEDB web server was used to predict mouse/human cytotoxic T-lymphocyte (CTL) and helper T-lymphocyte (HTL) epitopes.

RESULTS

The 33.25 kDa protein was stable, hydrophilic, antigenic, while non-allergenic, with enhanced thermotolerance and 45 PTM sites. The secondary structure encompassed a random coil, followed by extended strands and helices. Ramachandran-based analysis of the refined model showed 73.1%, 21.6%, 3.4% and 1.9% of residues in the most favored, additional allowed, generously-allowed and disallowed regions, respectively. Epitope screening demonstrated 4 HTL epitopes against seemingly protective HLA alleles, 5 HTL epitopes against the HLA reference set, 3 human CTL epitopes and a number of mouse MHC-restricted epitopes.

CONCLUSION

This paper provides insights into the bioinformatics characteristics of the L. major gp46 protein as a promising vaccine candidate.

Toxoplasmosis vaccines: what we have and where to go?

Despite recent major advances in developing effective vaccines against toxoplasmosis, finding new protective vaccination strategies remains a challenging and elusive goal as it is critical to prevent the disease. Over the past few years, various experimental approaches have shown that developing an effective vaccine against T. gondii is achievable. However, more remains unknown due to its complicated life cycle, difficulties in clinical translation, and lack of a standardized platform. This minireview summarizes the recent advances in the development of T. gondii vaccines and the main obstacles to developing a safe, effective and durable T. gondii vaccine. The successes and failures in developing and testing vaccine candidates for the T. gondii vaccine are also discussed, which may facilitate the future development of T. gondii vaccines.

Protective Effect Against Toxoplasmosis in BALB/c Mice Vaccinated With Recombinant Toxoplasma gondii MIF, CDPK3, and 14-3-3 Protein Cocktail Vaccine

Toxoplasma gondii can infect almost all endotherm organisms including humans and cause life-threatening toxoplasmosis in immunocompromised individuals, which leads to serious public health problems. Developing an excellent vaccine against this disease is impending. In present study, we formulated a cocktail protein vaccine including the TgMIF, TgCDPK3, and Tg14-3-3 proteins, which play critical roles in T. gondii infection. The recombinant protein vaccines were constructed and assessed by vaccination in BALB/c mice. We organized the mice in various protein combination groups of vaccines, and all mice were immunized with corresponding proteins at 0, 2, and 4 weeks. The specific protective effects of the vaccines on mice against T. gondii were analyzed by the mensuration of cytokines, serum antibodies, splenocyte proliferation assay, survival time, and parasite cyst burden of mice after the challenge. The study indicated that mice immunized with all three multicomponent proteins vaccine triggered a strong immune response with highest levels of IFN-γ production and IgG antibody compared with the other two protein combinations and controls. Moreover, there was an increase in IL-4 production and antigen-specific lymphocyte proliferation. The parasite cysts were significantly reduced (resulting in an 82.7% reduction), and survival time was longer in immunized mice with three multicomponent proteins compared with the other groups of mice. The enhanced humoral and cell-mediated immunity indicated that the protein cocktail vaccine containing three antigens provided effective protection for mice. These results indicated that recombinant TgMIF, TgCDPK3, and Tg14-3-3 multicomponent proteins were potential candidates for vaccine against toxoplasmosis.

Toxoplasma gondii Tyrosine-Rich Oocyst Wall Protein: A Closer Look through an In Silico Prism

Toxoplasmosis is a global threat with significant zoonotic concern. The present in silico study was aimed at determination of bioinformatics features and immunogenic epitopes of a tyrosine-rich oocyst wall protein (TrOWP) of Toxoplasma gondii. After retrieving the amino acid sequence from UniProt database, several parameters were predicted including antigenicity, allergenicity, solubility and physico-chemical features, signal peptide, transmembrane domain, and posttranslational modifications. Following secondary and tertiary structure prediction, the 3D model was refined, and immunogenic epitopes were forecasted. It was a 25.57 kDa hydrophilic molecule with 236 residues, a signal peptide, and significant antigenicity scores. Moreover, several linear and conformational B-cell epitopes were present. Also, potential mouse and human cytotoxic T-lymphocyte (CTL) and helper T-lymphocyte (HTL) epitopes were predicted in the sequence. The findings of the present in silico study are promising as they render beneficial characteristics of TrOWP to be included in future vaccination experiments.

Immunoinformatic Analysis of Calcium-Dependent Protein Kinase 7 (CDPK7) Showed Potential Targets for Toxoplasma gondii Vaccine

Apicomplexan parasites, including Toxoplasma gondii (T. gondii), express different types of calcium-dependent protein kinases (CDPKs), which perform a variety of functions, including attacking and exiting the host cells. In the current bioinformatics study, we have used several web servers to predict the basic features and specifications of the CDPK7 protein. The findings showed that CDPK7 protein has 2133 amino acid residues with an average molecular weight (MW) of 219085.79 D. The aliphatic index with 68.78 and grand average of hydropathicity (GRAVY) with -0.331 score were estimated. The outcomes of current research showed that the CDPK7 protein included 502 alpha-helix, 1311 random coils, and 320 extended strands with GOR4 method. Considering the Ramachandran plot, the favored region contains more than 92% of the amino acid residues. In addition, evaluation of antigenicity and allergenicity showed that CDPK7 protein has immunogenic and nonallergenic nature. The present research provides key data for more animal-model study on the CDPK7 protein to design an efficient vaccine against toxoplasmosis in the future.

The main post-translational modifications and related regulatory pathways in the malaria parasite Plasmodium falciparum: An update

There are important challenges when investigating individual post-translational modifications (PTMs) or protein interaction network and delineating if PTMs or their changes and cross-talks are involved during infection, disease initiation or as a result of disease progression. Proteomics and in silico approaches now offer the possibility to complement each other to further understand the regulatory involvement of these modifications in parasites and infection biology. Accordingly, the current review highlights key expressed or altered proteins and PTMs are invisible switches that turn on and off the function of most of the proteins. PTMs include phosphorylation, glycosylation, ubiquitylation, palmitoylation, myristoylation, prenylation, acetylation, methylation, and epigenetic PTMs in P. falciparum which have been recently identified. But also other low-abundant or overlooked PTMs that might be important for the parasite's survival, infectivity, antigenicity, immunomodulation and pathogenesis. We here emphasize the PTMs as regulatory pathways playing major roles in the biology, pathogenicity, metabolic pathways, survival, host-parasite interactions and the life cycle of P. falciparum. Further validations and functional characterizations of such proteins might confirm the discovery of therapeutic targets and might most likely provide valuable data for the treatment of P. falciparum, the main cause of severe malaria in human.

Bioinformatics analysis of calcium-dependent protein kinase 4 (CDPK4) as Toxoplasma gondii vaccine target

OBJECTIVES

Toxoplasma gondii (T. gondii), an obligate intracellular apicomplexan parasite, could affect numerous warm-blooded animals, such as humans. Calcium-dependent protein kinases (CDPKs) are essential Ca²⁺ signaling mediators and participate in parasite host cell egress, outer membrane motility, invasion, and cell division.

RESULTS

Several bioinformatics online servers were employed to analyze and predict the important properties of CDPK4 protein. The findings revealed that CDPK4 peptide has 1158 amino acid residues with average molecular weight (MW) of 126.331 KDa. The aliphatic index and GRAVY for this protein were estimated at 66.82 and - 0.650, respectively. The findings revealed that the CDPK4 protein comprised 30.14% and 34.97% alpha-helix, 59.84% and 53.54% random coils, and 10.02% and 11.49% extended strand with SOPMA and GOR4 tools, respectively. Ramachandran plot output showed 87.87%, 8.40%, and 3.73% of amino acid residues in the favored, allowed, and outlier regions, respectively. Also, several potential B and T-cell epitopes were predicted for CDPK4 protein through different bioinformatics tools. Also, antigenicity and allergenicity evaluation demonstrated that this protein has immunogenic and non-allergenic nature. This paper presents a basis for further studies, thereby provides a fundamental basis for the development of an effective vaccine against T. gondii infection.

Immunoinformatic analysis of immunogenic B- and T-cell epitopes of MIC4 protein to designing a vaccine candidate against Toxoplasma gondii through an in-silico approach

Purpose

Toxoplasmosis, transmitted by Toxoplasma gondii, is a worldwide parasitic disease that affects approximately one-third of the world's inhabitants. Today, there are no appropriate drugs to deter tissue cysts from developing in infected hosts. So, developing an effective vaccine would be valuable to avoid from toxoplasmosis. Considering the role of microneme antigens such as microneme protein 4 (MIC4) in T. gondii pathogenesis, it can be used as potential candidates for vaccine against T. gondii.

Materials and Methods

In this study several bioinformatics methods were used to assess the different aspects of MIC4 protein such as secondary and tertiary structure, physicochemical characteristics, the transmembrane domains, subcellular localization, B-cell, helper-T lymphocyte, cytotoxic-T lymphocyte epitopes, and other notable characteristic of this protein design a suitable vaccine against T. gondii.

Results

The studies revealed that MIC4 protein includes 59 potential post-translational modification sites without any transmembrane domains. Moreover, several probable epitopes of B- and T-cells were detected for MIC4. The secondary structure comprised 55.69% random coil, 5.86% beta-turn, 19.31% extended strand, and 19.14% alpha helix. According to the Ramachandran plot results, 87.42% of the amino acid residues were located in the favored, 9.44% in allowed, and 3.14% in outlier regions. The protein allergenicity and antigenicity revealed that it was non-allergenic and antigenic.

Conclusion

This study gives vital basic on MIC4 protein for further research and also established an effective vaccine with different techniques against acute and chronic toxoplasmosis.