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All for a game
When fourth-grader Jon Gummyshoes is framed for stealing a video game from the principal's office he needs to use his detective skills to expose who framed him--and why.
Book
SARS-CoV-2 Spike-Heat Shock Protein A5 (GRP78) Recognition may be Related to the Immersed Human Coronaviruses
The human coronavirus (HCoV), SARS-CoV-2, caused more than 34 M confirmed infections from which more than 1 M deaths are reported until now (the WHO situation report-154). The current pandemic causes severe socio-economic burden. Due to the importance of understanding of the mode of recognition and viral entry, spike protein shed drug designers as the first look protein target with the first released solved structure on 26 February 2020 (PDB ID: 6VSB). It is proposed that the recognition site for GRP78 is found in SARS-CoV-2 and the immersed human coronaviruses but experimental validation is still required.
Journal Article
The Extraction and Impact of Essential Oils on Bioactive Films and Food Preservation, with Emphasis on Antioxidant and Antibacterial Activities—A Review
Essential oils, consisting of volatile compounds, are derived from various plant parts and possess antibacterial and antioxidant properties. Certain essential oils are utilized for medicinal purposes and can serve as natural preservatives in food products, replacing synthetic ones. This review describes how essential oils can promote the performance of bioactive films and preserve food through their antioxidant and antibacterial properties. Further, this article emphasizes the antibacterial efficacy of essential oil composite films for food preservation and analyzes their manufacturing processes. These films could be an attractive delivery strategy for improving phenolic stability in foods and the shelf-life of consumable food items. Moreover, this article presents an overview of current knowledge of the extraction of essential oils, their effects on bioactive films and food preservation, as well as the benefits and drawbacks of using them to preserve food products.
Journal Article
Computational characterization of GRP78 binding sites on mitochondrial GPX4: implications for targeting ferroptosis in triple-negative breast cancer
About 20% of breast cancer cases are triple-negative breast cancer (TNBC), a highly aggressive subtype with limited therapeutic options. Emerging evidence suggests that ferroptosis — a form of regulated cell death — and stress-response pathways play critical roles in TNBC progression. We investigated the interaction between glucose-regulated protein 78 (GRP78), a central stress-response chaperone, and mitochondrial glutathione peroxidase 4 (mGPX4), a key regulator of ferroptosis resistance. Using a combined computational approach — including protein–protein docking, molecular dynamics (MD) simulations, and MM/GBSA free-energy calculations — we identified stable complexes between GRP78’s SBDβ domain and several regions of mGPX4. Docking with PRODIGY revealed binding affinities ranging from − 7.7 ± 0.5 to − 10.5 ± 0.6 kcal/mol, surpassing that of Pep42 (–6.9 ± 0.1 kcal/mol), with region III (the mitochondrial import sequence) showing the strongest binding (–10.5 ± 0.6 kcal/mol). HADDOCK scoring further highlighted region II as particularly favorable (–72.0 ± 5.4). After 100 ns of MD, MM/GBSA analysis estimated binding free energies from − 45.20 to − 86.39 kcal/mol, with the region-II complex exhibiting the highest affinity (–86.4 kcal/mol), driven predominantly by electrostatic and van der Waals interactions. This interaction could serve as a promising therapeutic target to undermine cancer cell survival by sensitizing TNBC cells to ferroptosis-inducing strategies.
Journal Article
Ebola virus glycoprotein GP1—host cell-surface HSPA5 binding site prediction
Ebola virus (EBOV) infection is a widespread infection that has created a bad memory in Africa. In the 2014 and 2015 outbreak, more than 28,000 infections were reported by the World Health Organization, with about 11,300 deaths in Guinea, Liberia, and Sierra Leone. Heat shock protein A5 (HSPA5), termed also GRP78, is a host cell chaperone protein responsible for the unfolded protein response in the endoplasmic reticulum. Under stress, HSPA5 is upregulated and becomes cell-surface exposed. Recent studies report the association of cell-surface HSPA5 with EBOV glycoproteins GP1 and GP2. In this study, structural and sequence analysis and molecular docking are used to predict the possible binding site between the cell-surface HSPA5 and EBOV GP1. The results show a promising binding site that supports the hypothesis of HSPA5 selectivity for binding to a specific peptide sequence (pep42). This study paves the way to suggest possible inhibitors to stop viral association with cell-surface receptors and subsequently reduce viral infection.
Journal Article
Synthesis, characterization of Mg doped CuFe2O4 nanoparticles for potential anticancer applications
Ferrite nanoparticles (NPs) have emerged as promising candidates for cancer therapy. In this study, Mg-doped copper ferrite NPs, MgₓCu₁₋ₓFe
2
O
4
(x = 0.0, 0.5, and 1.0), were synthesized via a citrate–nitrate combustion method and evaluated for their anticancer potential. Structural and morphological characteristics were analyzed using powder X-ray diffraction, field-emission scanning electron microscopy, and energy-dispersive X-ray spectroscopy. Cytotoxicity against human cancer cell lines was assessed using MTT and flow cytometry assays, along with analyses of reactive oxygen species (ROS) generation and apoptosis. Among the compositions studied, Cu
0.5
Mg
0.5
Fe
2
O
4
demonstrated the highest cytotoxic efficacy, with IC₅₀ values of 17.2 ± 0.15 µg/mL (PC-3) and 25.04 ± 0.28 µg/mL (Caco-2). Flow cytometric analysis revealed increased total apoptosis of 42.08% and 34.95% in PC-3 and Caco-2 cells, respectively. Gene expression analysis revealed downregulation of Bcl-2 and Cyclin D and upregulation of BAX, P53, and Caspase-3, indicating ROS-mediated mitochondria-dependent apoptosis. The enhanced anticancer activity of Cu
0.5
Mg
0.5
Fe
2
O
4
is attributed to its optimized size, surface charge, and composition, which promote cellular uptake, ROS generation, DNA damage, and interactions with cellular components. These findings highlight the potential of mixed-metal ferrite nanoparticles as effective nanomaterial-based cancer therapeutics.
Journal Article
Clean Grinding Technique: A Facile Synthesis and In Silico Antiviral Activity of Hydrazones, Pyrazoles, and Pyrazines Bearing Thiazole Moiety against SARS-CoV-2 Main Protease (Mpro)
A novel series of some hydrazones bearing thiazole moiety were generated via solvent-drop grinding of thiazole carbohydrazide 2 with various carbonyl compounds. Also, dehydrative-cyclocondensation of 2 with active methylene compounds or anhydrides gave the respective pyarzole or pyrazine derivatives. The structures of the newly synthesized compounds were established based on spectroscopic evidences and their alternative syntheses. Additionally, the anti-viral activity of all the products was tested against SARS-CoV-2 main protease (Mpro) using molecular docking combined with molecular dynamics simulation (MDS). The average binding affinities of the compounds 3a, 3b, and 3c (−8.1 ± 0.33 kcal/mol, −8.0 ± 0.35 kcal/mol, and −8.2 ± 0.21 kcal/mol, respectively) are better than that of the positive control Nelfinavir (−6.9 ± 0.51 kcal/mol). This shows the possibility of these three compounds to effectively bind to SARS-CoV-2 Mpro and hence, contradict the virus lifecycle.
Journal Article
New progresses on cell surface protein HSPA5/BiP/GRP78 in cancers and COVID-19
Heat-shock-protein family A (Hsp70) member 5 (HSPA5), aliases GRP78 or BiP, is a protein encoded with 654 amino acids by the HSPA5 gene located on human chromosome 9q33.3. When the endoplasmic reticulum (ER) was stressed, HSPA5 translocated to the cell surface, the mitochondria, and the nucleus complexed with other proteins to execute its functions. On the cell surface, HSPA5/BiP/GRP78 can play diverse functional roles in cell viability, proliferation, apoptosis, attachments, and innate and adaptive immunity regulations, which lead to various diseases, including cancers and coronavirus disease 2019 (COVID-19). COVID-19 is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, which caused the pandemic since the first outbreak in late December 2019. HSPA5, highly expressed in the malignant tumors, likely plays a critical role in SARS-CoV-2 invasion/attack in cancer patients via tumor tissues. In the current study, we review the newest research progresses on cell surface protein HSPA5 expressions, functions, and mechanisms for cancers and SARS-CoV-2 invasion. The therapeutic and prognostic significances and prospects in cancers and COVID-19 disease by targeting HSPA5 are also discussed. Targeting HSPA5 expression by natural products may imply the significance in clinical for both anti-COVID-19 and anti-cancers in the future.
Journal Article
In silico prediction of GRP78-CRIPTO binding sites to improve therapeutic targeting in glioblastoma
Glioblastoma multiforme (GBM) is one of the most malignant tumors in central nervous system (CNS) tumors. The glucose-regulated protein 78 (GRP78) and CRIPTO (Cripto-1), a protein that belongs to the EGF-CFC (epidermal growth factor cripto-1 FRL-1 cryptic) family, are overexpressed in GBM. A complex between GRP78 SBDβ (substrate binding domain beta) and CRIPTO CFC domain was reported in previous studies. This complex activates MAPK/AKT signaling, Src/PI3K/AKT, and Smad2/3 pathways which is a reason for tumor proliferation. In this work, we study how the two proteins form the complex figuring out binding sites between GRP78 and CRIPTO utilizing computational biophysics and bioinformatics tools, such as protein–protein docking, molecular dynamics simulation and MMGBSA calculations. Haddock web server results of 4 regions from the CFC domain (region1 (− 70.4), region2 (− 78.7), region3 (− 74.2), region4 (− 86.8)) with selected residues of the SBDβ are then simulated for 100 ns MDS then MMGBSA were calculated for the four complexes. The results reveal the stability of the complexes with binding free energy (complex1 (− 15.07 kcal/mol), complex2 (− 59.78 kcal/mol), complex3 (− 81.92 kcal/mol), complex4 (− 126.26 kcal/mol). All these findings ensure that GRP78 SBDβ associates with the CRIPTO CFC domain, and the binding sites suggested make stable interactions between the proteins.
Journal Article
Bacteriorhodopsin of purple membrane reverses anisotropy outside the pH range of proton pumping based on logic gate realization
The bacteriorhodopsin of purple membrane is the first discovered light-sensing protein among ion transporting microbial rhodopsins, some of which (e.g. Archaerhodopsin 3) could be broadly used as tools in optogenetics having wide potential of medical applications. Since its discovery as early as in 1971, bacteriorhodopsin has attracted wide interests in nano-biotechnology, particularly in optoelectronics devices. Therefore, the present work has been motivated due to two topics; firstly, anisotropy demand became indispensible in bioelectronics; secondly, the stationary level of electric response in bacteriorhodopsin within the pH range of proton pumping (pH 3 – pH 10) implies, in turn, raising here a question about whether the electric anisotropy is implicated for reducing (or switching off) such level beyond such pH range. Noteworthy is that the purple membrane converts to blue form upon acidification, while to reddish purple form upon alkalization. In the present study, the acidic and alkaline forms of bacteriorhodopsin have exhibited most probable state of reversal for the dielectric anisotropy around pH 2.5 and pH 10.5, respectively. This is underscored by proposing a correlation seemingly found between disassembly of the crystalline structure of bacteriorhodopsin and the reversal of dielectric anisotropy, at such acidic and alkaline reversal pH’s, in terms of the essence of the crystalline lattice. Most importantly, the results have substantiated dual frequency characteristics and logic gate-based dielectric anisotropy reversal to bacteriorhodopsin, which may implicate it for potential applications in bioelectronics.
Journal Article