In silico homology modelling and prediction of novel epitopic peptides from P24 protein of Haemonchus contortus

Potential Disrupting Effects of Wastewater-Derived Disinfection Byproducts on Chinese Rare Minnow (Gobiocypris rarus) Transthyretin: An In Vitro and In Silico Study

The available information about whether wastewater-derived disinfection byproducts (DBPs) could elicit potential endocrine-related detrimental effects on aquatic organisms was scarce. Herein, the potential disrupting effects and underlying binding mechanism of 14 wastewater-derived aliphatic and aromatic DBPs and 12 other substances on Chinese rare minnow (Gobiocypris rarus) transthyretin (CrmTTR) were tested and revealed by in vitro and in silico methods. The amino acid sequences of CrmTTR were determined, and the recombinant CrmTTR with a molecular mass of 66.3 kDa was expressed and purified. In vitro assay results indicated that eight selected aromatic DBPs exhibited detectable CrmTTR disrupting ability. Meanwhile, six aliphatic DBPs were not CrmTTR binders. Molecular modeling results implied that hydrophobic hydrogen bonds and/or ionic pair interactions were non-negligible. Four binary classification models with high classification performance were constructed. A significant positive linear relationship was observed for the binding affinity data from CrmTTR and human TTR (n = 18, r = 0.922, p < 0.0001). However, the binding affinity for 13 out of 18 tested compounds with CrmTTR was higher than that with human TTR. All the results highlighted that some wastewater-derived DBPs may be potential disruptors on the aquatic organism endocrine system, and interspecies variation should not be neglected in future determination of the potential endocrine disrupting effects of wastewater-derived DBPs.

The Advantage of Using Immunoinformatic Tools on Vaccine Design and Development for Coronavirus

After the outbreak of SARS-CoV-2 by the end of 2019, the vaccine development strategies became a worldwide priority. Furthermore, the appearances of novel SARS-CoV-2 variants challenge researchers to develop new pharmacological or preventive strategies. However, vaccines still represent an efficient way to control the SARS-CoV-2 pandemic worldwide. This review describes the importance of bioinformatic and immunoinformatic tools (in silico) for guide vaccine design. In silico strategies permit the identification of epitopes (immunogenic peptides) which could be used as potential vaccines, as well as nonacarriers such as: vector viral based vaccines, RNA-based vaccines and dendrimers through immunoinformatics. Currently, nucleic acid and protein sequential as well structural analyses through bioinformatic tools allow us to get immunogenic epitopes which can induce immune response alone or in complex with nanocarriers. One of the advantages of in silico techniques is that they facilitate the identification of epitopes, while accelerating the process and helping to economize some stages of the development of safe vaccines.

Hepatocellular carcinoma-associated antigen 59 and ADP-ribosylation factor 1 with poly (lactic-co-glycolic acid): A promising candidate as nanovaccine against haemonchosis

Haemonchus contortus (H. contortus) ADP-ribosylation factor 1 (Hc-ARF1) and Hepatocellular carcinoma-associated antigen 59 (Hc-HCA59) are recognized to largely regulate the immune responses of host cells. However, studies about the protective efficacy of the two molecules are poorly unknown. In this research, combinations of recombinant Hc-HCA59 (rHc-HCA59) and Hc-ARF1 (rHc-ARF1) proteins were amalgamated with poly (lactic-co-glycolic acid) (PLGA) nanoparticles adjuvant in order to investigate their protection potential against H. contortus in goats. The results demonstrated that the levels of IgG, IgA, IgE, and IL-4 were noticeably enhanced in the rHc-HCA59 and rHc-ARF1 (rHc-HCA59+rHc-ARF1) group before H. contortus third-stage larvae (L3) challenge. After the L3 challenge, the levels of IL-17, IL-9, and TGF-β were considerably upregulated in the rHc-HCA59+rHc-ARF1 group. In the meantime, the abomasal worm burdens and the fecal eggs were reduced by 63.2% and 69.4% respectively in the rHc-HCA59+rHc-ARF1 group. According to the studies, PLGA nanoparticles immobilized with rHc-HCA59 and rHc-ARF1 proteins conferred partial protection and were expected to be a potential candidate for developing nano vaccines to combat goat haemonchosis.

Designing of a Chimeric Vaccine Using EIS (Rv2416c) Protein Against Mycobacterium tuberculosis H37Rv: an Immunoinformatics Approach

Mycobacterium tuberculosis (Mtb) is a respiratory pathogen that causes tuberculosis (TB). There are a large number of proteins that are involved in the pathogenesis of TB. Stimulating the immune response against TB is very important to clear the pathogens from host. In the present study, an immunoinformatics conduit is used for designing an epitope based chimeric vaccine against TB. Enhanced intracellular survival (EIS) protein from Mtb is used for designing the chimeric vaccine. One B cell epitope, 8 cytotoxic T lymphocyte (CTL), and 6 helper T lymphocyte (HTL) epitopes were predicted based on the MHC allele binding, immunogenicity, antigenicity, allergenicity, toxicity and IFN epitopes. The selected epitopes were used for chimeric vaccine designing. Furthermore, 3D structure elucidation, structural refinement and validation of the designed chimeric vaccine were carried out. The 3D structure was used for protein-protein docking studies with Toll-like receptor 4 (TLR-4), followed by molecular dynamic simulation (MDS) and the interaction between the chimeric vaccine and TLR-4 complex was verified.

De novo pathway is an active metabolic pathway of cysteine synthesis in Haemonchus contortus

Haemonchus contortus, commonly known as Barber's pole worm, is an economically important gastrointestinal nematode of sheep and goats especially in tropical and sub-tropical regions of the world. Cysteine synthesis is a very important metabolic pathway for the parasite, however the functional aspects of cysteine synthesis in parasite are largely unknown. The key question which we have investigated in the study is; whether the parasite uses a de novo pathway of cysteine synthesis, which is unknown in multicellular organisms of the animal kingdom and known to be absent in mammals. Directional cloning of the cysteine synthase (CS) gene was done in pET303 champion vector using restriction sites XbaI and XhoI. The CS gene of the H.contortus was closely related to CS-A protein of Oesophagostomum dentatum and a hypothetical protein of Ancylostoma ceylanicum. Recombinant protein of the H contortus CS (rHC-CS) gene was expressed using pET303 vector in pLysS BL21 strain of E.coli and subsequently purified by Ni-NTA affinity chromatography. Western blot using anti-His tag antibody confirmed the presence of rHC-CS. Biochemical assay, FTIR and enzyme kinetics studies revealed that rHC-CS used O-acetyl serine as substrate to produce cysteine using de novo pathway and CS activity was also confirmed with the homogenate of H.contortus. Upregulation of CS transcripts in the adult and its downregulation in the L3 larval stage suggests that de novo pathway contributes to the cysteine requirement of mature H.contortus. It is concluded that de novo pathway is an active metabolic pathway in H.contortus.

Downregulation of G3BP2 reduces atherosclerotic lesions in ApoE-/- mice

BACKGROUND AND AIMS

Atherosclerosis is mainly caused by stress in arterial microenvironments, which results in the formation of stress granules as a consequence of the stress response. As the core protein of stress granules, GTPase-activating protein (SH3 domain)-binding protein 2 (G3BP2) is known to play pivotal roles in tumour initiation, viral infection and Alzheimer's disease, but the role of G3BP2 in atherosclerosis development is poorly understood. Previous studies have shown that vaccination with epitopes from self-antigens could reduce atherosclerotic lesions. Here, we investigated the effect of immunizing ApoE^-/- mice with G3BP2 peptides, and whether this immunization exerted an anti-atherogenic effect.

METHODS AND RESULTS

In our study, ApoE^-/- mice were fed a high-fat diet for 12 weeks from 8 to 20 weeks of age. Then, using a repetitive multiple site strategy, the mice were immunized with a Keyhole limpet haemocyanin (KLH) conjugated G3BP2 peptide for 2 weeks from weeks 16 to 18. High levels of G3BP2 antibodies were detectable before sacrifice. Histological analyses showed that the number of atherosclerotic lesions in ApoE^-/- mice was significantly reduced following G3BP2 immunotherapy. The levels of pro-inflammatory cytokines and macrophages were also greatly decreased, while the collagen content of the plaques showed significant increase. Furthermore, knocking down G3BP2 in ApoE^-/- mice reduced the number of lesions compared to ApoE^-/- mice fed a high-fat diet for eight weeks. In vitro studies demonstrated that G3BP2 regulated ox-LDL-induced inflammation in HUVECs via controlling the localization of IκBα.

CONCLUSIONS

Immunization with the G3BP2 peptide antigen or knocking down of G3BP2 significantly decreased early atherosclerotic plaques in the ApoE^-/- mouse model of atherosclerosis. G3BP2 is a promising potential target for atherosclerosis therapy.

Structural Dynamics Behind Clinical Mutants of PncA-Asp12Ala, Pro54Leu, and His57Pro of Mycobacterium tuberculosis Associated With Pyrazinamide Resistance

Pyrazinamide (PZA) is one of the main FDA approved drugs to be used as the first line of defense against Mycobacterium Tuberculosis (MTB). It is activated into pyrazinoic acid (POA) via MTB's pncA gene-encoded pyrazinamidase (PZase). Mutations are most commonly responsible for PZA-resistance in nearly 70% of the resistant samples. In the present work, MTB positive samples were chosen for PZA drug susceptibility testing (DST) against critical concentration (100 ug/ml) of PZA. The resistant samples were subjected to pncA sequencing. As a result, 36 various mutations have been observed in the PZA resistant samples, uploaded to the NCBI (GeneBank accession no. MH461111). Here we report the mechanism of PZA resistance behind the three mutants (MTs), Asp12Ala, Pro54Leu, and His57Pro in comparison with the wild type (WT) through molecular dynamics simulation to unveil how these mutations affect the overall conformational stability. The post-simulation analyses revealed notable deviations as compared to the WT structure. Molecular docking studies of PZA with MTs and WT, pocket volume inspection and overall shape complementarity analysis confirmed the deleterious nature of these mutations and gave an insight into the mechanism behind PZA-resistance. These analyses provide vital information regarding MTB drug resistance and could be extremely useful in therapy management and overcoming its global burden.

Model Optimization and In Silico Analysis of Potential Dipeptidyl Peptidase IV Antagonists from GC-MS Identified Compounds in Nauclea latifolia Leaf Extracts

Dipeptidyl peptidase IV (DPP-IV) is a pharmacotherapeutic target in type 2 diabetes. Inhibitors of this enzyme constitute a new class of drugs used in the treatment and management of type 2 diabetes. In this study, phytocompounds in Nauclea latifolia (NL) leaf extracts, identified using gas chromatography–mass spectroscopy (GC-MS), were tested for potential antagonists of DPP-IV via in silico techniques. Phytocompounds present in N. latifolia aqueous (NLA) and ethanol (NLE) leaf extracts were identified using GC–MS. DPP-IV model optimization and molecular docking of the identified compounds/standard inhibitors in the binding pocket was simulated. Drug-likeness, pharmacokinetic and pharmacodynamic properties of promising docked leads were also predicted. Results showed the presence of 50 phytocompounds in NL extracts of which only 2-O-p-methylphenyl-1-thio-β-d-glucoside, 3-tosylsedoheptulose, 4-benzyloxy-6-hydroxymethyl-tetrahydropyran-2,3,5-triol and vitamin E exhibited comparable or better binding iGEMDOCK and AutoDock Vina scores than the clinically prescribed standards. These four compounds exhibited promising drug-likeness as well as absorption, distribution, metabolism, excretion and toxicity (ADMET) properties suggesting their candidature as novel leads for developing DPP-IV inhibitors.