Human antigen R: Exploring its inflammatory response impact and significance in cardiometabolic disorders.

RNA-binding proteins (RBPs) play a crucial role in the regulation of posttranscriptional RNA networks, which can undergo dysregulation in many pathological conditions. Human antigen R (HuR) is a highly researched RBP that plays a crucial role as a posttranscriptional regulator. HuR plays a crucial role in the amplification of inflammatory signals by stabilizing the messenger RNA of diverse inflammatory mediators and key molecular players. The noteworthy correlations between HuR and its target molecules, coupled with the remarkable impacts reported on the pathogenesis and advancement of multiple diseases, position HuR as a promising candidate for therapeutic intervention in diverse inflammatory conditions. This review article examines the significance of HuR as a member of the RBP family, its regulatory mechanisms, and its implications in the pathophysiology of inflammation and cardiometabolic illnesses. Our objective is to illuminate potential directions for future research and drug development by conducting a comprehensive analysis of the existing body of research on HuR.

Structural vaccinology, molecular simulation and immune simulation approaches to design multi-epitopes vaccine against John Cunningham virus.

The JCV (John Cunningham Virus) is known to cause progressive multifocal leukoencephalopathy, a condition that results in the formation of tumors. Symptoms of this condition such as sensory defects, cognitive dysfunction, muscle weakness, homonosapobia, difficulties with coordination, and aphasia. To date, there is no specific and effective treatment to completely cure or prevent John Cunningham polyomavirus infections. Since the best way to control the disease is vaccination. In this study, the immunoinformatic tools were used to predict the high immunogenic and non-allergenic B cells, helper T cells (HTL), and cytotoxic T cells (CTL) epitopes from capsid, major capsid, and T antigen proteins of JC virus to design the highly efficient subunit vaccines. The specific immunogenic linkers were used to link together the predicted epitopes and subjected to 3D modeling by using the Robetta server. MD simulation was used to confirm that the newly constructed vaccines are stable and properly fold. Additionally, the molecular docking approach revealed that the vaccines have a strong binding affinity with human TLR-7. The codon adaptation index (CAI) and GC content values verified that the constructed vaccines would be highly expressed in E. coli pET28a (+) plasmid. The immune simulation analysis indicated that the human immune system would have a strong response to the vaccines, with a high titer of IgM and IgG antibodies being produced. In conclusion, this study will provide a pre-clinical concept to construct an effective, highly antigenic, non-allergenic, and thermostable vaccine to combat the infection of the John Cunningham virus.

Unraveling the genetic variations underlying virulence disparities among SARS-CoV-2 strains across global regions: insights from Pakistan.

Over the course of the COVID-19 pandemic, several SARS-CoV-2 variants have emerged that may exhibit different etiological effects such as enhanced transmissibility and infectivity. However, genetic variations that reduce virulence and deteriorate viral fitness have not yet been thoroughly investigated. The present study sought to evaluate the effects of viral genetic makeup on COVID-19 epidemiology in Pakistan, where the infectivity and mortality rate was comparatively lower than other countries during the first pandemic wave. For this purpose, we focused on the comparative analyses of 7096 amino-acid long polyprotein pp1ab. Comparative sequence analysis of 203 SARS-CoV-2 genomes, sampled from Pakistan during the first wave of the pandemic revealed 179 amino acid substitutions in pp1ab. Within this set, 38 substitutions were identified within the Nsp3 region of the pp1ab polyprotein. Structural and biophysical analysis of proteins revealed that amino acid variations within Nsp3's macrodomains induced conformational changes and modified protein-ligand interactions, consequently diminishing the virulence and fitness of SARS-CoV-2. Additionally, the epistatic effects resulting from evolutionary substitutions in SARS-CoV-2 proteins may have unnoticed implications for reducing disease burden. In light of these findings, further characterization of such deleterious SARS-CoV-2 mutations will not only aid in identifying potential therapeutic targets but will also provide a roadmap for maintaining vigilance against the genetic variability of diverse SARS-CoV-2 strains circulating globally. Furthermore, these insights empower us to more effectively manage and respond to potential viral-based pandemic outbreaks of a similar nature in the future.

Designing State-of-the-Art Gas Sensors: From Fundamentals to Applications.

Gas sensors are crucial in environmental monitoring, industrial safety, and medical diagnostics. Due to the rising demand for precise and reliable gas detection, there is a rising demand for cutting-edge gas sensors that possess exceptional sensitivity, selectivity, and stability. Due to their tunable electrical properties, high-density surface-active sites, and significant surface-to-volume ratio, nanomaterials have been extensively investigated in this regard. The traditional gas sensors utilize homogeneous material for sensing where the adsorbed surface oxygen species play a vital role in their sensing activity. However, their performance for selective gas sensing is still unsatisfactory because the employed high temperature leads to the poor stability. The heterostructures nanomaterials can easily tune sensing performance and their different energy band structures, work functions, charge carrier concentration and polarity, and interfacial band alignments can be precisely designed for high-performance selective gas sensing at low temperature. In this review article, we discuss in detail the fundamentals of semiconductor gas sensing along with their mechanisms. Further, we highlight the existed challenges in semiconductor gas sensing. In addition, we review the recent advancements in semiconductor gas sensor design for applications from different perspective. Finally, the conclusion and future perspectives for improvement of the gas sensing performance are discussed.

Improving the substrate binding of acetyl-CoA carboxylase (AccB) from Streptomyces antibioticus through computational enzyme engineering.

Malonyl-CoA serves as the main building block for the biosynthesis of many important polyketides, as well as fatty acid-derived compounds, such as biofuel. Escherichia coli, Corynebacterium gultamicum, and Saccharomyces cerevisiae have recently been engineered for the biosynthesis of such compounds. However, the developed processes and strains often have insufficient productivity. In the current study, we used enzyme-engineering approach to improve the binding of acetyl-CoA with ACC. We generated different mutations, and the impact was calculated, which reported that three mutations, that is, S343A, T347W, and S350W, significantly improve the substrate binding. Molecular docking investigation revealed an altered binding network compared to the wild type. In mutants, additional interactions stabilize the binding of the inner tail of acetyl-CoA. Using molecular simulation, the stability, compactness, hydrogen bonding, and protein motions were estimated, revealing different dynamic properties owned by the mutants only but not by the wild type. The findings were further validated by using the binding-free energy (BFE) method, which revealed these mutations as favorable substitutions. The total BFE was reported to be -52.66 ± 0.11 kcal/mol for the wild type, -55.87 ± 0.16 kcal/mol for the S343A mutant, -60.52 ± 0.25 kcal/mol for T347W mutant, and -59.64 ± 0.25 kcal/mol for the S350W mutant. This shows that the binding of the substrate is increased due to the induced mutations and strongly corroborates with the docking results. In sum, this study provides information regarding the essential hotspot residues for the substrate binding and can be used for application in industrial processes.

Role of Functional Groups in Tuning Luminescence Signature of Solution-Processed Graphene Quantum Dots: Experimental and Theoretical Insights.

Zero-dimensional graphene quantum dots (GQDs) present unique optoelectronic properties in the large-spectrum range from UV to visible. However, the origin of luminescence in GQDs is still a debatable question. Therefore, the present work investigates the features of trap-mediated and edge-state-functionalized group-associated luminescence enhancement of GQDs. The attached functional groups' involvement in the upsurge of photoluminescence has been discussed theoretically as well as experimentally. In addition, the role of the aromatic ring, the functional group attached, and their positions of attachment to the aromatic ring to tune the emission wavelength and Raman modes have been elucidated theoretically as well as experimentally. We found that in the case of the -OH group attached outside of the aromatic ring, the long-range π hybridization dominates, which suggests that the emission from this model can be dictated by long-range π hybridization. In particular, we found that oxygen-containing functional groups attached outside of the aromatic ring are the main source of the luminescence signature in GQDs. Furthermore, density functional theory (DFT) indicates that the -OH functional group attached outside of the aromatic ring perfectly matched with our experimental results, as the experimental bandgap (2.407 eV) is comparable with the theoretical simulated bandgap (2.399 eV) of the -OH group attached outside of the aromatic ring.

Association of podoplanin expression to histopathological grades of oral epithelial dysplasia and oral squamous cell carcinoma.

Objective: To determine the expression of podoplanin, and to correlate it with histopathological grades in oral epithelial dysplasia and oral squamous cell carcinoma cases. METHODS: The retrospective, analytical, cross-sectional study was conducted at the City Laboratory, Peshawar, Pakistan, and comprised specimen block data of histologically diagnosed cases of oral benign lesions, dysplastic lesions and oral squamous cell carcinoma from January 2017 to August 2021. Two sections (4um) were cut from each specimen block for Haematoxylin and Eosin staining and immunohistochemistry. The slides were re-evaluated by two pathologists for confirmation of the diagnosis, and podoplanin marker was applied to cases selected using immunohistochemistry. Data was analysed using SPSS 22. RESULTS: Of the 80 cases identified, 68(85%) were analysed. There were 20(29.4%) benign cases; 11(55%) females and 9(45%) males with mean age 39.90±16.23 years, 20(29.4%) oral dysplastic cases; 14(70%) males and 6(30%) females with mean age 57.75±12.02 years, and 28(41.2%) oral squamous cell carcinoma cases; 17(61%) males and 11(39%) females with mean age 50.55±14.80 years. Podoplanin expression in oral epithelial dysplasia cases was significant (p=0.028), while it was not significant in the other 2 groups (p>0.05). CONCLUSIONS: Podoplanin when used along with histopathological evaluation could aid as an adjuvant technique in the diagnosis and grading of oral epithelial dysplasia.

WGX50 mitigates doxorubicin-induced cardiotoxicity through inhibition of mitochondrial ROS and ferroptosis.

BACKGROUND: Doxorubicin (DOX)-induced cardiotoxicity (DIC) is a major impediment to its clinical application. It is indispensable to explore alternative treatment molecules or drugs for mitigating DIC. WGX50, an organic extract derived from Zanthoxylum bungeanum Maxim, has anti-inflammatory and antioxidant biological activity, however, its function and mechanism in DIC remain unclear. METHODS: We established DOX-induced cardiotoxicity models both in vitro and in vivo. Echocardiography and histological analyses were used to determine the severity of cardiac injury in mice. The myocardial damage markers cTnT, CK-MB, ANP, BNP, and ferroptosis associated indicators Fe2+, MDA, and GPX4 were measured using ELISA, RT-qPCR, and western blot assays. The morphology of mitochondria was investigated with a transmission electron microscope. The levels of mitochondrial membrane potential, mitochondrial ROS, and lipid ROS were detected using JC-1, MitoSOX™, and C11-BODIPY 581/591 probes. RESULTS: Our findings demonstrate that WGX50 protects DOX-induced cardiotoxicity via restraining mitochondrial ROS and ferroptosis. In vivo, WGX50 effectively relieves doxorubicin-induced cardiac dysfunction, cardiac injury, fibrosis, mitochondrial damage, and redox imbalance. In vitro, WGX50 preserves mitochondrial function by reducing the level of mitochondrial membrane potential and increasing mitochondrial ATP production. Furthermore, WGX50 reduces iron accumulation and mitochondrial ROS, increases GPX4 expression, and regulates lipid metabolism to inhibit DOX-induced ferroptosis. CONCLUSION: Taken together, WGX50 protects DOX-induced cardiotoxicity via mitochondrial ROS and the ferroptosis pathway, which provides novel insights for WGX50 as a promising drug candidate for cardioprotection.

Discovery of Isojacareubin as a covalent inhibitor of SARS-CoV-2 main protease using structural and experimental approaches.

The ongoing pandemic with the emergence of immune evasion potential and, particularly, the current omicron subvariants intensified the situation further. Although vaccines are available, the immune evasion capabilities of the recent variants demand further efficient therapeutic choices to control the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. Hence, considering the necessity of the small molecule inhibitor, we target the main protease (3CLpro), which is an appealing target for the development of antiviral drugs against SARS-CoV-2. High-throughput molecular in silico screening of South African natural compounds database reported Isojacareubin and Glabranin as the potential inhibitors for the main protease. The calculated docking scores were reported to be -8.47 and -8.03 kcal/mol, respectively. Moreover, the structural dynamic assessment reported that Isojacareubin in complex with 3CLpro exhibit a more stable dynamic behavior than Glabranin. Inhibition assay indicated that Isojacareubin could inhibit SARS-CoV-2 3CLpro in a time- and dose-dependent manner, with half maximal inhibitory concentration values of 16.00 ± 1.35 µM (60 min incubation). Next, the covalent binding sites of Isojacareubin on SARS-CoV-2 3CLpro was identified by biomass spectrometry, which reported that Isojacareubin can covalently bind to thiols or Cysteine through Michael addition. To evaluate the inactivation potency of Isojacareubin, the inactivation kinetics was further investigated. The inactivation kinetic curves were plotted according to various concentrations with gradient-ascending incubation times. The KI value of Isojacareubin was determined as 30.71 µM, whereas the Kinact value was calculated as 0.054 min-1 . These results suggest that Isojacareubin is a covalent inhibitor of SARS-CoV-2 3CLpro .

Comparative binding analysis of WGX50 and Alpha-M with APP family proteins APLP1 and APLP2 using structural-dynamics and free energy calculation approaches.

A.D. is a common disease among other neurodegenerative disorders primarily developing due to amyloid-ß (Aß) neurotoxicity derived from the amyloid-ß protein precursor (AßPP). The amyloid precursor-like proteins 1 and 2 (APP1 and APLP2) biochemically behave similarly in many aspects to AßPP. We, therefore, proposed to test WGX-50 and Alpha-M for their interaction mechanism with APLP1 and APLP2 because both these drug candidate compounds previously showed inhibition of Aß aggregation. We employed a comparative atomic investigation on Alpha-M and WGX-50 in complex with novel targets, i.e., APLP1 and APLP2, using biophysical and molecular simulation methods. The docking score was -6.83 kcal mol-1 for Alpha-M-APLP1, -8.41 kcal mol-1 for WGX-50-APLP1, -7.02 kcal mol-1 for Alpha-M-APLP2 and -8.25 kcal mol-1 for the WGX-50-APLP2 complex. Our results also elaborate that in the case of their interaction with both APLP1 and APLP2, the WGX-50 complex exhibits better stability than the APLP1/2-Alpha-M complexes during simulation. Furthermore, WGX50 in both APLP1 and APLP2 stabilized the internal flexibility upon binding in contrast to the Alpha-M complexes. The data showed that the BFE for Alpha-M-APLP1 was calculated to be -27.38 ± 0.93 kcal mol-1, for WGX-50-APLP1 -39.65 ± 0.95 kcal mol-1, for Alpha-M-APLP2 -24.80 ± 0.63 kcal mol-1 while for WGX-50-APLP2 the BFE was -57.16 ± 1.03 kcal mol-1 respectively. These results highlight that APLP2-WGX50 has greater binding energies in all four systems. PCA and FEL analysis further revealed variations in the dynamic behavior of these complexes. Overall, our findings demonstrate that WGX50 potentially acts as a more potent inhibitor for APLP1 and APLP2 than Alpha-M and thus shows the diverse pharmacological potential of WGX50. Due to its stable binding interaction, WGX50 might be a suitable candidate drug compound for targeting these precursors under pathological conditions.

Repositioning of experimentally validated anti-breast cancer peptides to target FAK-PAX complex to halt the breast cancer progression: a biomolecular simulation approach.

FAK (focal adhesin kinase), a tyrosine kinase, plays an imperative role in cell-cell communication, particularly in cell signaling systems. It is a multi-functional signaling protein, which integrates and transduces signals into cancer cells through growth factor receptors or integrin and its interaction with Paxillin (PAX). The molecular processes by which FAK promotes the development and progression of cancer have progressively established the possible relationship between FAK-PAX complex in many types of cancer. The interaction of FAX and PAX is very important in breast cancer and thus acts as an essential biomarker for drugs, vaccines or peptide inhibitor designing. In this regard, computational approaches, particularly peptide designing to target the binding interface of the interacting partners, would greatly assist the design of peptide inhibitors against various cancer. Accordingly, in this present study, we screened 236 experimentally validated anti-breast cancer peptides using computational drugs repositioning approach to design peptides targeting the FAK-PAX complex. Using protein-peptide docking the binding site for the HP1 was confirmed and a total of 236 anti-breast cancer peptides were screened. Among the 236, only 12 peptides reported a docking score better than the control. From these 12, Magainin with the docking score - 103.8 ± 10.3 kcal/mol, NRC-07 with the docking score - 100.8 ± 16.5 kcal/mol, and Indolicidin with the docking score - 101.7 ± 3.9 kcal/mol, peptides potentially inhibit the FAX-PAX binding. Calculation of protein's motion and FEL revealed the binding and inhibitory behavior. Moreover, binding free energy (MM/GBSA) confirmed that Magainin exhibited the total binding energy - 53.28 kcal/mol, NRC-07 possessed the TBE - 44.16 kcal/mol, and Indolicidin reported the TBE of - 40.48 kcal/mol, thus explaining the inhibitory potential of these peptides. In conclusion, these peptides exhibit strong inhibitory potential and could abrogate the FAK-PAX complex in in vitro models and thus may relieve the burden of breast cancer.

Web architecture, behavior, and predatory potential of Larinia chloris from rice fields (Araneae: Araneidae).

Present study was carried out to investigate the variation in web architecture of Larinia chloris (Audouin 1826) in relation to seasonal differences and the biotic factors of the environment. In addition, relative abundance, behavior, and predatory potential of L. chloris were also recorded. For this purpose, 100 orb-webs of L. chloris were observed in rice fields (August-October, 2022) from 3 districts of Punjab (Lahore, Sheikhupura, and Kasur). Percent abundance of L. chloriswas found to be highest in rice fields from Barki road, Lahore (39.53%). All the webs of L. chloris were vertical at height equal to the height of vegetation (115.2 ±â€…9.7 cm). Time required to complete the web was 45 ±â€…5 min. There was positive correlation between web architecture and vegetation height. Web capture area and average mesh height of L. chloris also showed positive correlation with carapace length. There was a significant difference in various web parameters (number of spirals, number of radii, capture area, average mesh height, upper radii, lower radii, left radii, and right radii) among different trapping months. A total of 1,326 insects were recorded from the 100 webs of L. chloris. The prey abundance was found to be highest in the fields from Barki Road, Lahore. The majority of the prey collected from webs of L. chloris belonged to order Diptera, Hemiptera, Coleoptera, and Lepidoptera. However, prey items recorded during different growth stages (from vegetative to ripening) varied significantly. This is the first ever report describing the ecology of L. chloris in rice fields from Punjab, Pakistan.

Thermo-Chemical Modification of Cellulose for the Adsorptive Removal of Titan Yellow from Wastewater.

This research work focuses on the isolation and thermo-chemical modification of cellulose and its application as an adsorbent for the removal of organic pollutants. The used cellulose was collected from a locally available plant (Olive Europa) commonly called Zaitoon. The stem branches of Zaitoon were collected and then kept in water for 40-45 days at room temperature to extract the cellulose fibers. These cellulose fibers were then kept in the Soxhlet apparatus for washing in n-hexane for 72 h. The purified cellulose was divided into three parts: one part was subjected to thermal activation (TAC), the second was modified chemically (CMC) with Benzyl Chloride, while the last one remained un-functionalized (UFC). All the three forms of cellulose were characterized via FTIR and SEM, then utilized for the removal of Titan Yellow (TY) dye from aqueous media via adsorption process by varying the contact time, temperature, concentration of dye and type, and dose of adsorbent. The adsorption efficiencies of all adsorbents were compared under different experimental variables. Thermally activated cellulose showed the best results for the removal of TY compared with other materials. The calculated removal percentage of TY was found to be 97.69, 94.83, 94.83, and 98% under equilibrium conditions of contact time, temperature, adsorbent dose, and TY concentration. Similarly, the uptake capacities of TAC under optimal experimental conditions were found to be 19.56, 18.96, 18.52, and 18.75 mg/g. Thermodynamic studies of TAC, CMC, and UFC showed that the values of ΔG are negative, while those of ΔH and ΔS are positive in all cases and at all temperatures. This indicates that the TY elimination process is endothermic and spontaneous with an entropy-driven nature. The obtained results indicate that the as-fabricated low-cost biomaterials can effectively remove dyes from wastewater through physicochemical interactions. The removal process was influenced by the nature of the adsorbent and the operating variables.

Exploring the medicinal potential of Dark Chemical Matters (DCM) to design promising inhibitors for PLpro of SARS-CoV-2 using molecular screening and simulation approaches.

The growing concerns and cases of COVID-19 with the appearance of novel variants i.e., BA.2.75. BA.5 and XBB have prompted demand for more effective treatment options that could overcome the risk of immune evasion. For this purpose, discovering novel small molecules to inhibit druggable proteins such as PLpro required for viral pathogenesis, replication, survival, and spread is the best choice. Compounds from the Dark chemical matter (DCM) database is consistently active in various screening tests and offer intriguing possibilities for finding drugs that are extremely selective or active against uncommon targets. Considering the essential role of PLpro, the current study uses DCMdatabase for the identification of potential hits using in silico virtual molecular screening and simulation approaches to inhibit the current and emerging variants of SARS-CoV-2. Our results revealed the 10 best compounds with docking scores between -7.99 to -7.03 kcal/mol better than the control drug (GRL0617) among which DC 5977-0726, DC 6623-2024, DC C879-0379 and DC D135-0154 were observed as the best hits. Structural-dynamics properties such as dynamic stability, protein packing, and residue flexibility demonstrated the pharmacologically favorable properties of these top hits in contrast to GRL0617. The hydrogen bonding half-life revealed that Asp164, Arg166, Tyr264, and Tyr268 have major contributions to the hydrogen bonding during the simulation. However, some of the important hydrogen bonds were missing in the control drug (GRL0617). Finally, the total binding free energy was reported to be -34.41 kcal/mol for GRL0617 (control), -41.03 kcal/mol for the DC5977-0726-PLpro, for the DC6623-2024-Plpro complex the TBE was -48.87 kcal/mol, for the for DCC879-0379-Plpro complex the TBE was -45.66 kcal/mol while for the DCD135-0154-PLpro complex the TBE was calculated to be -40.09 kcal/mol respectively, which shows the stronger potency of these compounds against PLpro and further in in vivo and in vitro test are required for the possible usage as potential drug against SARS-CoV-2.

Towards specie-specific ensemble vaccine candidates against mammarenaviruses using optimized structural vaccinology pipeline and molecular modelling approaches.

Mammarena viruses are emerging pathogenic agents and cause hemorrhagic fevers in humans. These viruses accomplish host immune system evasion to replicate and spread in the host. There are only few available therapeutic options developed for Mammarena Virus (also called MMV). Currently, only a single candidate vaccine called Candid#1 is available against Junin virus. Similarly, the effective treatment Ribavirin is used only in Lassa fever treatments. Herein, immune-informatics pipeline has been used to annotate whole proteome of the seven human infecting Mammarena strains. The extensive immune based analysis reveals specie specific epitopes with a crucial role in immune response induction. This was achieved by construction of immunogenic epitopes (CTL "Cytotoxic T-Lymphocytes", HTL "Helper T-Lymphocytes", and B cell "B-Lymphocytes") based vaccine designs against seven different Mammarena virus species. Furthermore, validation of the vaccine constructs through exploring physiochemical properties was performed to confirm experimental feasibility. Additionally, in-silico cloning and receptor based immune simulation was performed to ensure induction of primary and secondary immune response. This was confirmed through expression of immune factors such as IL, cytokines, and antibodies. The current study provides with novel vaccine designs which needs further demonstrations through potential processing against MMVs. Future studies may be directed towards advanced evaluations to determine the efficacy and safety of the designed vaccines through further experimental procedures.

Characterization of proteome wide antigenic epitopes to design proteins specific and proteome-wide ensemble vaccines against heartland virus using structural vaccinology and immune simulation approaches.

Heartland virus is a single-stranded negative-sense RNA virus that infects humans and causes lethargy, myalgia, headaches, nausea, diarrhea, weight loss, arthralgia, loss of appetite, leukopenia, and easy bruising due thrombocytopenia. The unavailability of antiviral drugs for HRTV infection is a major obstacle to treat this infection, therefore supportive care management is adopted in the case of a severe ailment. In this scientific study, proteins specific and proteome-wide Helper T-cell (HTL), linear B cell, and cytotoxic T-cell (CTL) epitopes mapping joined together with suitable linkers to design multi-epitopes subunit vaccine (MEVC). The constructed four vaccines from nucleocapsid protein, replicase, glycoprotein and finally whole proteome-wide constructs demonstrated stronger antigenic and non-allergenic behavior. Physiochemical properties evaluation also reported easy and efficient expression and downstream analysis of the constructs. Molecular docking of these constructs with toll-like receptor 7 (TLR7) revealed good binding and further validation based on MM/GBSA also demonstrated stronger interaction between the vaccine constructs and TLR7. Moreover, in silico cloning reported CAI value of 0.96 for each construct and excellent GC contents percentage required for experimental analysis. Furthermore, immune simulation-based immune response surveillance revealed that upon the injection of antigen the primary and secondary antibodies were produced between 5 and 15 days, and a more robust neutralization of the antigen by the proteome-wide vaccine construct was observed. This research could pave the way for the development of dynamic and efficient vaccines that contain a unique mix of numerous HRTV derived antigenic peptides to control HRTV infection.

Virulence and biofilm inhibition of 3-methoxycinnamic acid against Agrobacterium tumefaciens.

AIMS: In the current study the anti-virulence and anti-biofilm activities of the cinnamic acid derivative, 3-methoxycinnamic acid, was investigated against Agrobacterium tumefaciens. METHODS AND RESULTS: Based on the disc diffusion test and ß-galactosidase activity assay, 3-methoxycinnamic acid was shown to interfere with the quorum sensing (QS) system of A. tumefaciens. Crystal violet staining assay, phenol-sulfuric acid method, Bradford protein assay and confocal laser scanning microscopy (CLSM) revealed that the biofilm formation of A. tumefaciens was inhibited after the treatment of 3-methoxycinnamic acid. Employing high-performance liquid chromatography (HPLC) analysis of culture supernatant revealed that the production of 3-oxo-octanoylhomoserine lactone (3-oxo-C8-HSL) decreased concentration-dependently after treatment with 3-methoxycinnamic acid. Swimming and chemotaxis assays also indicated that 3-methoxycinnamic acid had a good effect on reducing the motility and chemotaxis of A. tumefaciens. In addition, the RT-qPCR, molecular docking and simulations further demonstrated that 3-methoxycinnamic acid could competitively inhibit the binding of 3-oxo-C8-HSL to TraR and down-regulate virulence-related genes. CONCLUSIONS: 3-Methoxycinnamic acid is proved to have good anti-virulence and anti-biofilm activities against A. tumefaciens. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first study that investigates the anti-virulence and anti-biofilm activities of 3-methoxycinnamic acid against A. tumefaciens. With its potential QS-related virulence and biofilm inhibitory activities, 3-methoxycinnamic acid is expected to be developed as a potent pesticide or adjuvant for the prevention and treatment of crown gall caused by A. tumefaciens.

Computational prediction of the effect of mutations in the receptor-binding domain on the interaction between SARS-CoV-2 and human ACE2.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing COVID-19 continues to mutate. Numerous studies have indicated that this viral mutation, particularly in the receptor-binding domain area, may increase the viral affinity for human angiotensin-converting enzyme 2 (hACE2), the receptor for viral entry into host cells, thereby increasing viral virulence and transmission. In this study, we investigated the binding affinity of SARS-CoV-2 variants (Delta plus, Iota, Kappa, Mu, Lambda, and C.1.2) on hACE2 using computational modeling with a protein-protein docking approach. The simulation results indicated that there were differences in the interactions between the RBD and hACE2, including hydrogen bonding, salt bridge interactions, non-bonded interactions, and binding free energy differences among these variants. Molecular dynamics simulations revealed that mutations in the RBD increase the stability of the hACE2-spike protein complex relative to the wild type, following the global stability trend and increasing the binding affinity. The value of binding-free energy calculated using molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) indicated that all mutations in the spike protein increased the contagiousness of SARS-CoV-2 variants. The findings of this study provide a foundation for developing effective interventions against these variants. Computational modeling elucidates that the spike protein of SARS-CoV-2 variants binds considerably stronger than the wild-type to hACE2.

Prospect of Anterior Gradient 2 homodimer inhibition via repurposing FDA-approved drugs using structure-based virtual screening.

Anterior Gradient 2 (AGR2) has recently been reported as a tumor biomarker in various cancers, i.e., breast, prostate and lung cancer. Predominantly, AGR2 exists as a homodimer via a dimerization domain (E60-K64); after it is self-dimerized, it helps FGF2 and VEGF to homo-dimerize and promotes the angiogenesis and the invasion of vascular endothelial cells and fibroblasts. Up till now, no small molecule has been discovered to inhibit the AGR2-AGR2 homodimer. Therefore, the present study was performed to prepare a validated 3D structure of AGR2 by homology modeling and discover a small molecule by screening the FDA-approved drugs library on AGR2 homodimer as a target protein. Thirteen different homology models of AGR2 were generated based on different templates which were narrowed down to 5 quality models sorted by their overall Z-scores. The top homology model based on PDB ID = 3PH9 was selected having the best Z-score and was further assessed by Verify-3D, ERRAT and RAMPAGE analysis. Structure-based virtual screening narrowed down the large library of FDA-approved drugs to ten potential AGR2-AGR2 homodimer inhibitors having FRED score lower than - 7.8 kcal/mol in which the top 5 drugs' binding stability was counter-validated by molecular dynamic simulation. To sum up, the present study prepared a validated 3D structure of AGR2 and, for the first time reported the discovery of 5 FDA-approved drugs to inhibit AGR2-AGR2 homodimer by using structure-based virtual screening. Moreover, the binding of the top 5 hits with AGR2 was also validated by molecular dynamic simulation. A validated 3D structure of Anterior Gradient 2 (AGR2) was prepared by homology modeling, which was used in virtual screening of FDA-approved drugs library for the discovery of prospective inhibitors of AGR2-AGR2 homodimer.

Photo-Assisted Removal of Rhodamine B and Nile Blue Dyes from Water Using CuO-SiO2 Composite.

Wastewater from the textile industries contaminates the natural water and affects the aquatic environment, soil fertility and biological ecosystem through discharge of different hazardous effluents. Therefore, it is essential to remove such dissolved toxic materials from water by applying more efficient techniques. We performed a comparative study on the removal of rhodamine B (RhB) and Nile blue (NB) from water through a catalytic/photocatalytic approach while using a CuO-SiO2 based nanocomposite. The CuO-SiO2 nanocomposite was synthesized through a sol-gel process using copper nitrate dihydrate and tetraethylorthosilicate as CuO and SiO2 precursors, respectively, with ammonia solution as the precipitating agent. The synthesized nanocomposites were characterized, for their structure, morphology, crystallinity, stability, surface area, pore size and pore volume, by using a scanning electron microscope (SEM), transmission electron microscope (TEM), energy dispersive X-ray spectroscopy (EDX), X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR) and Brunauer-Emmett-Teller (BET) techniques. The CuO-SiO2 nanocomposite was used for potential environmental applications in the terms of its catalytic and photocatalytic activities toward the degradation of rhodamine B (RhB) and Nile blue (NB) dyes, in the presence and absence of light, while monitoring the degradation process of dyes by UV-Visible spectroscopy. The catalytic efficiency of the same composite was studied and discussed in terms of changes in the chemical structures of dyes and other experimental conditions, such as the presence and absence of light. Moreover, the composite showed 85% and 90% efficiency towards the removal of rhodamine B and Nile blue dyes respectively. Thus, the CuO-SiO2 nanocomposite showed better efficiency toward removal of Nile blue as compared to rhodamine B dye while keeping other experimental variables constant. This can be attributed to the structure-property relationships and compatibility of a catalyst with the molecular structures of dyes.