Subtractive proteomics assisted therapeutic targets mining and designing ensemble vaccine against Candida auris for immune response induction

The emergence of variants and the reports of co-infection caused by Candida auris in COVID-19 patients adds a further complication to the global pandemic situation. To date, no effective therapy is available for C. auris infections. Thus, characterization of therapeutic targets and designing effective vaccine candidates using subtractive proteomics and immune-informatics approaches is useful tool in controlling the emerging infections associated with SARS-CoV-2. In the current study, subtractive proteomics-assisted annotation of the vaccine targets was performed, which revealed seven vaccine targets. An immunoinformatic-driven approach was then employed to map protein-specific and proteome-wide immunogenic peptides (CTL, B cell, and HTL) for the design of multi-epitope vaccine candidates (MEVCs). The results demonstrated that the vaccine candidates possess strong antigenic features (>0.4 threshold score) and are classified as non-allergenic. Validation of the designed MEVCs through molecular docking, in-silico cloning, and immune simulation further demonstrated the efficacy of the vaccines by producing immune factor titers (ranging from 2500 to 16000 au/mL) i.e., IgM, IgG, IL-6, and Interferon-α. In conclusion, the current study provides a strong impetus in designing anti-fungal strategies against Candida auris.

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 5-15 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.

Idiopathic Pleuroparenchymal Fibroelastosis

Idiopathic pleuroparenchymal fibroelastosis (IPPFE) is a rare form of idiopathic interstitial pneumonia. The disease is characterized by fibrosis of the pleura and subpleural lung parenchyma predominantly affecting the upper lobes. Various triggers have been proposed as inciting factors in the development of the disease. Diagnosis is made clinically in conjunction with radiographic findings and histopathology when available. There are no known effective treatment options and several cases of lung transplantation have been reported. We report a case of an 86-year-old female who presented to the emergency department with worsening dyspnea and hypoxia. She had a history of unexplained pneumomediastinum and a 20 - 25 pounds unintentional weight loss over 10 months. Computed tomography (CT) of the chest without contrast revealed radiographic evidence of IPPFE. Despite symptomatic management with antibiotics, diuretics, and steroids, her condition continued to deteriorate. Unfortunately, our patient was not a candidate for a lung transplant. She was transitioned to hospice care and succumbed to her disease. IPPFE is a rare disease with an unknown prevalence. It has a median survival rate of 2 years. Usually, there is an overlap with interstitial lung diseases, making it challenging to diagnose. There are only a few cases reported in the literature, and there are currently no guidelines available on the appropriate management of this debilitating disease. We recommend more cases be reported, and further research is done to establish better criteria for diagnosis and management.

Potential Immunogenic Activity of Computationally Designed mRNA- and Peptide-Based Prophylactic Vaccines against MERS, SARS-CoV, and SARS-CoV-2: A Reverse Vaccinology Approach

The continued emergence of human coronaviruses (hCoVs) in the last few decades has posed an alarming situation and requires advanced cross-protective strategies against these pandemic viruses. Among these, Middle East Respiratory Syndrome coronavirus (MERS-CoV), Severe Acute Respiratory Syndrome coronavirus (SARS-CoV), and Severe Acute Respiratory Syndrome coronavirus-2 (SARS-CoV-2) have been highly associated with lethality in humans. Despite the challenges posed by these viruses, it is imperative to develop effective antiviral therapeutics and vaccines for these human-infecting viruses. The proteomic similarity between the receptor-binding domains (RBDs) among the three viral species offers a potential target for advanced cross-protective vaccine designs. In this study, putative immunogenic epitopes including Cytotoxic T Lymphocytes (CTLs), Helper T Lymphocytes (HTLs), and Beta-cells (B-cells) were predicted for each RBD-containing region of the three highly pathogenic hCoVs. This was followed by the structural organization of peptide- and mRNA-based prophylactic vaccine designs. The validated 3D structures of these epitope-based vaccine designs were subjected to molecular docking with human TLR4. Furthermore, the CTL and HTL epitopes were processed for binding with respective human Lymphocytes Antigens (HLAs). In silico cloning designs were obtained for the prophylactic vaccine designs and may be useful in further experimental designs. Additionally, the epitope-based vaccine designs were evaluated for immunogenic activity through immune simulation. Further studies may clarify the safety and efficacy of these prophylactic vaccine designs through experimental testing against these human-pathogenic coronaviruses.

Crystal structure of Acetyl-CoA carboxylase (AccB) from Streptomyces antibioticus and insights into the substrate-binding through in silico mutagenesis and biophysical investigations

Acetyl-CoA carboxylase (ACC) is crucial for polyketides biosynthesis and acts as an essential metabolic checkpoint. It is also an attractive drug target against obesity, cancer, microbial infections, and diabetes. However, the lack of knowledge, particularly sequence-structure function relationship to narrate ligand-enzyme binding, has hindered the progress of ACC-specific therapeutics and unnatural "natural" polyketides. Structural characterization of such enzymes will boost the opportunity to understand the substrate binding, designing new inhibitors and information regarding the molecular rules which control the substrate specificity of ACCs. To understand the substrate specificity, we determined the crystal structure of AccB (Carboxyl-transferase, CT) from Streptomyces antibioticus with a resolution of 2.3 Å and molecular modeling approaches were employed to unveil the molecular mechanism of acetyl-CoA recognition and processing. The CT domain of S. antibioticus shares a similar structural organization with the previous structures and the two steps reaction was confirmed by enzymatic assay. Furthermore, to reveal the key hotspots required for the substrate recognition and processing, in silico mutagenesis validated only three key residues (V223, Q346, and Q514) that help in the fixation of the substrate. Moreover, we also presented atomic level knowledge on the mechanism of the substrate binding, which unveiled the terminal loop (500-514) function as an opening and closing switch and pushes the substrate inside the cavity for stable binding. A significant decline in the hydrogen bonding half-life was observed upon the alanine substitution. Consequently, the presented structural data highlighted the potential key interacting residues for substrate recognition and will also help to re-design ACCs active site for proficient substrate specificity to produce diverse polyketides.

Blocking key mutated hotspot residues in the RBD of the omicron variant (B.1.1.529) with medicinal compounds to disrupt the RBD-hACE2 complex using molecular screening and simulation approaches

A new variant of SARS-CoV-2 known as the omicron variant (B.1.1.529) reported in South Africa with 30 mutations in the whole spike protein, among which 15 mutations are in the receptor-binding domain, is continuously spreading exponentially around the world. The omicron variant is reported to be highly contagious with antibody-escaping activity. The emergence of antibody-escaping variants is alarming, and thus the quick discovery of small molecule inhibitors is needed. Hence, the current study uses computational drug screening and molecular dynamics simulation approaches (replicated) to identify novel drugs that can inhibit the binding of the receptor-binding domain (RBD) with hACE2. Screening of the North African, East African and North-East African medicinal compound databases by employing a multi-step screening approach revealed four compounds, namely (-)-pipoxide (C1), 2-(p-hydroxybenzyl) benzofuran-6-ol (C2), 1-(4-hydroxy-3-methoxyphenyl)-2-{4-[(E)-3-hydroxy-1-propenyl]-2-methoxyphenoxy}-1,3-propanediol (C3), and Rhein (C4), with excellent anti-viral properties against the RBD of the omicron variant. Investigation of the dynamics demonstrates stable behavior, good residue flexibility profiles, and structural compactness. Validation of the top hits using computational bioactivity analysis, binding free energy calculations and dissociation constant (K D) analysis also indicated the anti-viral properties of these compounds. In conclusion, this study will help in the design and discovery of novel drug therapeutics, which may be used against the emerging omicron variant of SARS-CoV-2.

The Omicron (B.1.1.529) variant of SARS-CoV-2 binds to the hACE2 receptor more strongly and escapes the antibody response: Insights from structural and simulation data

As SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) continues to inflict chaos globally, a new variant officially known as B.1.1.529 was reported in South Africa and was found to harbor 30 mutations in the spike protein. It is too early to speculate on transmission and hospitalizations. Hence, more analyses are required, particularly to connect the genomic patterns to the phenotypic attributes to reveal the binding differences and antibody response for this variant, which can then be used for therapeutic interventions. Given the urgency of the required analysis and data on the B.1.1.529 variant, we have performed a detailed investigation to provide an understanding of the impact of these novel mutations on the structure, function, and binding of RBD to hACE2 and mAb to the NTD of the spike protein. The differences in the binding pattern between the wild type and B.1.1.529 variant complexes revealed that the key substitutions Asn417, Ser446, Arg493, and Arg498 in the B.1.1.529 RBD caused additional interactions with hACE2 and the loss of key residues in the B.1.1.529 NTD resulted in decreased interactions with three CDR regions (1-3) in the mAb. Further investigation revealed that B.1.1.529 displayed a stable dynamic that follows a global stability trend. In addition, the dissociation constant (K_D), hydrogen bonding analysis, and binding free energy calculations further validated the findings. Hydrogen bonding analysis demonstrated that significant hydrogen bonding reprogramming took place, which revealed key differences in the binding. The total binding free energy using MM/GBSA and MM/PBSA further validated the docking results and demonstrated significant variations in the binding. This study is the first to provide a basis for the higher infectivity of the new SARS-CoV-2 variants and provides a strong impetus for the development of novel drugs against them.

Prevalence of gastrointestinal parasitic infection in cows and buffaloes in Lower Dir, Khyber Pakhtunkhwa, Pakistan

Gastrointestinal (GI) Parasitic infection is a hot issue for cattle management. There is variation of GI parasites effects in sex, age of cattle, drinking water condition, nutrition, and severity of infection. Studies on prevalence of GI parasites among cattle population in Dir Lower are lacking. A total of 40 farms were selected randomly in six tehsil namely Tehsil Adenzai, Tehsil Timergara, Tehsil Balambat, Tehsil Munda ,Tehsil Lalqala, Tehsil Khall. Freshly cattle fecal samples were collected randomly from the selected farms during March 2018 till December 2018. Out of 314 buffaloes and cattle examined 58.59% (184/314) were positive for eggs, cyst/oocyst of one or more species of GI Parasites. The prevalence of parasitic infection was higher in Buffaloes 63.55% (75/118) as compared to Cow 55.61% (109/196) but the difference was not significant (p>0.05) Entamoeba,spp, Moniezia spp, Haemonchus spp and Coccidian spp were found in this study. The non-treated animals indicated the highest percentage of infection in cow 57.71% (101/175) and buffalo 68.13% (62/91).GI parasite prevalence in female animal were higher female cow 62.58% (87/139) and female buffalo 77.33% (58/75) as compared to male. But the difference is non-significant (p> 0.05) Yearling calves had the lower rate of GI parasitic infection than adults. Future investigations are necessary to evaluate the economic loss due to GI parasites in cattle's.

Evaluation of the Whole Proteome of Achromobacter xylosoxidans to Identify Vaccine Targets for mRNA and Peptides-Based Vaccine Designing Against the Emerging Respiratory and Lung Cancer-Causing Bacteria

Achromobacter xylosoxidans is a rod-shaped Gram-negative bacterium linked with causing several infections which mostly includes hematological malignancies. It has been recently reported to be associated with the development and progression of lung cancer and is an emerging respiratory disease-causing bacterium. The treatment of individuals infected with A. xylosoxidans bacteremia is difficult due to the fact that this pathogen has both intrinsic and acquired resistance mechanisms, typically resulting in a phenotype of multidrug resistance (MDR). Efforts are needed to design effective therapeutic strategies to curtail the emergence of this bacterium. Computational vaccine designing has proven its effectiveness, specificity, safety, and stability compared to conventional approaches of vaccine development. Therefore, the whole proteome of A. xylosoxidans was screened for the characterization of potential vaccine targets through subtractive proteomics pipeline for therapeutics design. Annotation of the whole proteome confirmed the three immunogenic vaccine targets, such as (E3HHR6), (E3HH04), and (E3HWA2), which were used to map the putative immune epitopes. The shortlisted epitopes, specific against Cytotoxic T Lymphocytes, Helper T-cell Lymphocytes, and linear B-Cell, were used to design the mRNA and multi-epitopes vaccine (MEVC). Initial validations confirmed the antigenic and non-allergenic properties of these constructs, followed by docking with the immune receptor, TLR-5, which resulted in robust interactions. The interaction pattern that followed in the docking complex included formation of 5 hydrogen bonds, 2 salt bridges, and 165 non-bonded contacts. This stronger binding affinity was also assessed through using the mmGBSA approach, showing a total of free binding energy of -34.64 kcal/mol. Further validations based on in silico cloning revealed a CAI score of 0.98 and an optimal percentage of GC contents (54.4%) indicated a putatively higher expression of the vaccine construct in Escherichia coli. Moreover, immune simulation revealed strong antibodies production upon the injection of the designed MEVC that resulted in the highest peaks of IgM+ IgG production (>3,500) between 10 and 15 days. In conclusion the current study provide basis for vaccine designing against the emerging A. xylosoxidans, which demands further experimental studies for in vitro and in vivo validations.

Seven Day Safety Net Service

A seven day safety net telephone service was developed in an acute medical unit at a university hospital in London. The service attempts to provide all patients discharged from acute medicine with patient activated access to a member of the acute medical team. This allows patients to flag deterioration triggering further review in the ambulatory clinic or to ask for advice on symptoms or medication. Here we evaluate the first sixteen months of the service and report on its benefits and limitations.

Rapid deployment technology versus conventional sutured bioprostheses in aortic valve replacement

Objectives

Despite the benefits of rapid deployment aortic valve prostheses (RDAVR), conventional sutured valves (cAVR) are more commonly used in the treatment for aortic stenosis. Given the paucity of randomized studies, this study aimed to synthesize available data to compare both treatment options.

Methods

A systematic search of Pubmed, OVID, and MEDLINE was conducted to retrieve comparative studies for RDAVR versus cAVR in the treatment of aortic stenosis. Out of 1773 returned titles, 35 papers were used in the final analysis, including 1 randomized study, 1 registry study, 6 propensity‐matched studies, and 28 observational studies, incorporating a total of 10,381 participants (RDAVR n = 3686; cAVR n = 6310).

Results

Random‐effects meta‐analysis found no difference between the two treatment groups in terms of operative mortality, stroke, or bleeding (p > .05). The RDAVR group had reduced cardiopulmonary bypass (standardized mean difference [SMD]: −1.28, 95% confidence interval [CI]: [−1.35, −1.20], p < .001) and cross‐clamp times (SMD: −1.05, 95% CI: [−1.12, −0.98], p < .001). Length of stay in the intensive care unit was also shorter in the RDAVR group (SMD: −0.385, 95% CI: [−0.679, −0.092], p = .010). The risk of pacemaker insertion was higher for RDAVR (odds ratio [OR]: 2.41, 95% CI: [1.92, 3.01], p < .001) as was the risk of paravalvular leak (PVL) at midterm follow‐up (OR: 2.52, 95% CI: [1.32, 4.79], p = .005). Effective orifice area and transvalvular gradient were more favorable in RDAVR patients (p > .05).

Conclusions

Despite the benefits of RDAVR in terms of reduced operative time and enhanced recovery, the risk of pacemaker insertion and midterm PVL remains a significant cause for concern.

Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study

The spike protein of SARS-CoV-2 and the host ACE2 receptor plays a vital role in the entry to the cell. Among which the hotspot residue 501 is continuously subjected to positive selection pressure and induces unusual virulence. Keeping in view the importance of the hot spot residue 501, we predicted the potentially emerging structural variants of 501 residue. We analyzed the binding pattern of wild type and mutants (Spike RBD) to the ACE2 receptor by deciphering variations in the amino acids’ interaction networks by graph kernels along with evolutionary, network metrics, and energetic information. Our analysis revealed that N501I, N501T, and N501V increase the binding affinity and alter the intra and inter-residue bonding networks. The N501T has shown strong positive selection and fitness in other animals. Docking results and repeated simulations (three times) confirmed the structural stability and tighter binding of these three variants, correlated with the previous results following the global stability trend. Consequently, we reported three variants N501I, N501T, and N501V could worsen the situation further if they emerged. The relations between the viral fitness and binding affinity is a complicated game thus the emergence of high affinity mutations in the SARS-CoV-2 RBD brings up the question of whether or not positive selection favours these mutations or not?

Phytochemical and biological attributes of Bauhinia variegata L. (Caesalpiniaceae)

Abstract Bauhinia variegata plant is a very popular and traditionally potent ethnomedicine. Therefore, it is need of hour to study ameliorative characteristics of B. variegata for novel secondary metabolites. The current study was designed to explore antiproliferative potential of B. variegata due to scant reports on this aspect. Extracts of various parts (flowers, leaves, bark, stem, and roots) were prepared by successive maceration using organic solvents in increasing order of polarity (n-hexane, ethyl acetate, methanol, and water). The determination of polyphenolic contents was done by using colorimetric methods while antioxidant potential was measured using reducing power assay. Brine shrimp lethality assay was performed for determining preliminary cytotoxicity and antiproliferative activity against breast cancer MCF-7 cell line using MTT protocols. Moreover, antimicrobial activities were detected by using disc diffusion assay. The alpha-amylase assay was performed to monitor the antidiabetic potential of the plant. In case of phytochemical analysis methanolic extract of leaves and bark showed highest phenolic and flavonoids contents. n-Hexane and ethyl acetate extracts of stem and roots exhibited more than 90% mortality with LD50 ranges between 1-25 µg/mL when studied by brine shrimp lethality assay. n-Hexane and ethyl acetate extracts of roots and stem also showed antiproliferative activity against human breast cancer MCF-7 cell line with IC50 values ranges between 12.10-14.20 µg/mL. Most of the extracts displayed moderately high antibacterial and antifungal activities. The n-hexane extract of roots showed antidiabetic activity with 60.80 ± 0.20% inhibition of alpha-amylase. In sum, these preliminary results will be useful for further compound isolation from selected plant parts for the discovery of antibacterial, antidiabetic, and anticancer lead candidates.

Empyema Versus Lung Abscess: A Case Report

Lung abscesses and empyemas are 2 forms of pulmonary infection that can present with similar clinical features. However, empyemas are associated with higher morbidity and mortality, necessitating the need to distinguish one from the other. Plain radiographs can sometimes provide clues to help differentiate the 2 pathologies but more often than not, a computed tomography scan is required to confirm the diagnosis. Correct diagnosis is essential, as the goal standard therapeutic intervention for empyemas may be contraindicated in patients with lung abscesses. Empyemas require percutaneous or surgical drainage in combination with antibiotics, while lung abscesses are generally treated with antibiotics alone as drainage can be associated with various complications. We present a case of a 65-year-old man with parapneumonic empyema diagnosed with characteristic findings on chest computed tomography and treated with surgical drainage and antibiotics. We hope to improve patient outcomes by highlighting the classical radiographic findings that help distinguish empyema and abscess.

Core-Proteomics-Based Annotation of Antigenic Targets and Reverse-Vaccinology-Assisted Design of Ensemble Immunogen against the Emerging Nosocomial Infection-Causing Bacterium Elizabethkingia meningoseptica

Elizabethkingia meningoseptica is a ubiquitous Gram-negative emerging pathogen that causes hospital-acquired infection in both immunocompromised and immunocompetent patients. It is a multi-drug-resistant bacterium; therefore, an effective subunit immunogenic candidate is of great interest to encounter the pathogenesis of this pathogen. A protein-wide annotation of immunogenic targets was performed to fast-track the vaccine development against this pathogen, and structural-vaccinology-assisted epitopes were predicted. Among the total proteins, only three, A0A1T3FLU2, A0A1T3INK9, and A0A1V3U124, were shortlisted, which are the essential vaccine targets and were subjected to immune epitope mapping. The linkers EAAK, AAY, and GPGPG were used to link CTL, HTL, and B-cell epitopes and an adjuvant was also added at the N-terminal to design a multi-epitope immunogenic construct (MEIC). The computationally predicted physiochemical properties of the ensemble immunogen reported a highly antigenic nature and produced multiple interactions with immune receptors. In addition, the molecular dynamics simulation confirmed stable binding and good dynamic properties. Furthermore, the computationally modeled immune response proposed that the immunogen triggered a strong immune response after several doses at different intervals. Neutralization of the antigen was observed on the 3rd day of injection. Conclusively, the immunogenic construct produces protection against Elizabethkingia meningoseptica; however, further immunological testing is needed to unveil its real efficacy.

Evaluation of indigenous plants' extracts for mosquitocidal activity against different stages of Culex quinquefasciatus say (Diptera: Culicidae)

Being vector of West Nile Virus and falariasis the control of Culex quinquefasciatus is likely to be essential. Synthetic insecticide treatment is looking most effective for vectors mosquito control. However, these products are toxic to the environment and non-target organisms. Consequently, ecofriendly control of vectors mosquito is needed. In this regard botanical insecticide is looking more fruitful. Therefore, the present research aimed to investigate the effectiveness of methanolic extract and various fractions, including, n-hexane, ethyl-acetate, chloroform, and aqueous fraction, obtained from methanolic extract of Ailanthus altissima, Artemisia scoparia, and Justicia adhatoda using separating funnel against larval, pupal, and adult stages of Culex quinquefasciatus. The larvae and pupae of Culex quinquefasciatus were exposed to various concentrations (31.25-1000 ppm) of methanolic extract and its fractions for 24 hours of exposure period. For knock-down bioassay (filter paper impregnation bioassay) different concentration of the methanolic extract and its various fractions (i.e. 0.0625, 0.125, 0.25, 0.5 and 1mg/mL) were applied for 1 hour exposure period. The results were statistically analysed using standard deviation, probit analysis, and linear regression. The R2 values of larvae, pupae, and adult range from 0.4 to 0.99. The values of LC50 (concentration causing 50% mortality) for late 3rd instar larvae after 24 hours exposure period range from 93-1856.7 ppm, while LC90 values range from 424 -7635.5ppm. The values of LC50for pupae range form 1326.7-6818.4ppm and and values of LC90 range from 3667.3-17427.9ppm, respectively. The KDT50 range from 0.30 to 2.8% and KDT90 values range from1.2 to 110.8%, respectively. In conclusion, Justicia adhatoda may be effective for controlling populations of vector mosquito.

Copper oxide (CuO) and manganese oxide (MnO) nanoparticles induced biomass accumulation, antioxidants biosynthesis and abiotic elicitation of bioactive compounds in callus cultures of Ocimum basilicum (Thai basil)

Nano-elicitation is one among the prioritised strategies considered globally for sustainable and uniform production of industrially important medicinal compounds. Ocimum basilicum (Thai basil), a renowned medicinal species is a reservoir of commercially vital metabolites and proved for its health assuring effects in cancer, diabetes, microbial and cardiovascular diseases. However, its consumption and industrial demand raised intent to divert towards better alternates for ensuring sustainable production of medicinal compounds. Herein, we investigated the comparative potential of metal oxide [copper oxide (CuO) and manganese oxide (MnO)] nanoparticles to elicit the biosynthesis of bioactive metabolites and antioxidative capacity of O.basilicum callus cultures. Results showed that callus grown on MS media supplemented with 10 mg/L CuO-NPs resulted in the highest biomass accumulation (FW: 172.8 g/L, DW: 16.7 g/L), phenolic contents (TPC: 27.5 mg/g DW), and flavonoid contents (TFC: 9.1 mg/g DW) along with antioxidant activities (DPPH: 94%, ABTS: 881 μM TEAC, FRAP: 386 μM TEAC) compared with MnO-NPs and control. Likewise, the Superoxide dismutase (SOD: 1.28 nM/min/mg FW) and Peroxidase (POD: 0.48 nM/min/mg FW) activities were also recorded maximum in CuO-NPs elicited cultures than MnO-NPs and control. Moreover, the HPLC results showed that rosmarinic acid (11.4 mg/g DW), chicoric acid (16.6 mg/g DW), eugenol (0.21 mg/g DW) was found optimum in cultures at 10 mg/L CuO-NPs. Overall, it can be concluded that CuO nanoparticles can be effectively used as a elicitor for biosynthesis of metabolites in callus cultures of O. basilicum (Thai basil). The study is indeed a contribution to the field that will help decoding the mechanism of action of CuO NPs. However, further molecular investigations are needed to fully develop understanding about the metabolic potential of O. bascillicum and scalling up this protocol for bulkup production of bioactive compounds.

Structural-Dynamics and Binding Analysis of RBD from SARS-CoV-2 Variants of Concern (VOCs) and GRP78 Receptor Revealed Basis for Higher Infectivity

Glucose-regulated protein 78 (GRP78) might be a receptor for SARS-CoV-2 to bind and enter the host cell. Recently reported mutations in the spike glycoprotein unique to the receptor-binding domain (RBD) of different variants might increase the binding and pathogenesis. However, it is still not known how these mutations affect the binding of RBD to GRP78. The current study provides a structural basis for the binding of GRP78 to the different variants, i.e., B.1.1.7, B.1.351, B.1.617, and P.1 (spike RBD), of SARS-CoV-2 using a biomolecular simulation approach. Docking results showed that the new variants bound stronger than the wild-type, which was further confirmed through the free energy calculation results. All-atom simulation confirmed structural stability, which was consistent with previous results by following the global stability trend. We concluded that the increased binding affinity of the B.1.1.7, B.1.351, and P.1 variants was due to a variation in the bonding network that helped the virus induce a higher infectivity and disease severity. Consequently, we reported that the aforementioned new variants use GRP78 as an alternate receptor to enhance their seriousness.

MMV-db: vaccinomics and RNA-based therapeutics database for infectious hemorrhagic fever-causing mammarenaviruses

The recent viral outbreaks and the current pandemic situation urges us to timely address any emerging viral infections by designing therapeutic strategies. Multi-omics and therapeutic data are of great interest to develop early remedial interventions. This work provides a therapeutic data platform (Mammarenavirus (MMV)-db) for pathogenic mammarenaviruses with potential catastrophic effects on human health around the world. The database integrates vaccinomics and RNA-based therapeutics data for seven human pathogenic MMVs associated with severe viral hemorrhagic fever and lethality in humans. Protein-specific cytotoxic T lymphocytes, B lymphocytes, helper T-cell and interferon-inducing epitopes were mapped using a cluster of immune-omics-based algorithms and tools for the seven human pathogenic viral species. Furthermore, the physiochemical and antigenic properties were also explored to guide protein-specific multi-epitope subunit vaccine for each species. Moreover, highly efficacious RNAs (small Interfering RNA (siRNA), microRNA and single guide RNA (sgRNA)) after extensive genome-based analysis with therapeutic relevance were explored. All the therapeutic RNAs were further classified and listed on the basis of predicted higher efficacy. The online platform (http://www.mmvdb.dqweilab-sjtu.com/index.php) contains easily accessible data sets and vaccine designs with potential utility in further computational and experimental work. Conclusively, the current study provides a baseline data platform to secure better future therapeutic interventions against the hemorrhagic fever causing mammarenaviruses. Database URL: http://www.mmvdb.dqweilab-sjtu.com/index.php.