In silico designing of multiepitope-based-peptide (MBP) vaccine against MAPK protein express for Alzheimer's disease in Zebrafish.

Understanding the role of the mitogen-activated protein kinases (MAPKs) signalling pathway is essential in advancing treatments for neurodegenerative disorders like Alzheimer's. In this study, we investigate in-silico techniques involving computer-based methods to extract the MAPK1 sequence. Our applied methods enable us to analyze the protein's structure, evaluate its properties, establish its evolutionary relationships, and assess its prevalence in populations. We also predict epitopes, assess their ability to trigger immune responses, and check for allergenicity using advanced computational tools to understand their immunological properties comprehensively. We apply virtual screening, docking, and structure modelling to identify promising drug candidates, analyze their interactions, and enhance drug design processes. We identified a total of 30 cell-targeting molecules against the MAPK1 protein, where we selected top 10 CTL epitopes (PAGGGPNPG, GGGPNPGSG, SAPAGGGPN, AVSAPAGGG, AGGGPNPGS, ATAAVSAPA, TAAVSAPAG, ENIIGINDI, INDIIRTPT, and NDIIRTPTI) for further evaluation to determine their potential efficacy, safety, and suitability for vaccine design based on strong binding potential. The potential to cover a large portion of the world's population with these vaccines is substantial-88.5 % for one type and 99.99 % for another. In exploring the molecular docking analyses, we examined a library of compounds from the ZINC database. Among them, we identified twelve compounds with the lowest binding energy. Critical residues in the MAPK1 protein, such as VAL48, LYS63, CYS175, ASP176, LYS160, ALA61, LEU165, TYR45, SER162, ARG33, PRO365, PHE363, ILE40, ASN163, and GLU42, are pivotal for interactions with these compounds. Our result suggests that these compounds could influence the protein's behaviour. Moreover, our docking analyses revealed that the predicted peptides have a strong affinity for the MAPK1 protein. These peptides form stable complexes, indicating their potential as potent inhibitors. This study contributes to the identification of new drug compounds and the screening of their desired properties. These compounds could potentially help reduce the excessive activity of MAPK1, which is linked to Alzheimer's disease.

Recent Trends in Computer-aided Drug Design for Anti-cancer Drug Discovery.

Cancer is considered one of the deadliest diseases globally, and continuous research is being carried out to find novel potential therapies for myriad cancer types that affect the human body. Researchers are hunting for innovative remedies to minimize the toxic effects of conventional therapies being driven by cancer, which is emerging as pivotal causes of mortality worldwide. Cancer progression steers the formation of heterogeneous behavior, including self-sustaining proliferation, malignancy, and evasion of apoptosis, tissue invasion, and metastasis of cells inside the tumor with distinct molecular features. The complexity of cancer therapeutics demands advanced approaches to comprehend the underlying mechanisms and potential therapies. Precision medicine and cancer therapies both rely on drug discovery. In vitro drug screening and in vivo animal trials are the mainstays of traditional approaches for drug development; however, both techniques are laborious and expensive. Omics data explosion in the last decade has made it possible to discover efficient anti-cancer drugs via computational drug discovery approaches. Computational techniques such as computer-aided drug design have become an essential drug discovery tool and a keystone for novel drug development methods. In this review, we seek to provide an overview of computational drug discovery procedures comprising the target sites prediction, drug discovery based on structure and ligand-based design, quantitative structure-activity relationship (QSAR), molecular docking calculations, and molecular dynamics simulations with a focus on cancer therapeutics. The applications of artificial intelligence, databases, and computational tools in drug discovery procedures, as well as successfully computationally designed drugs, have been discussed to highlight the significance and recent trends in drug discovery against cancer. The current review describes the advanced computer-aided drug design methods that would be helpful in the designing of novel cancer therapies.

Genetic insights into obesity: in silico identification of pathogenic SNPs in MBOAT4 gene and their structural molecular dynamics consequences.

Membrane Bound O-Acyltransferase Domain-Containing 4 (MBOAT4) protein catalyzes ghrelin acylation, leading to prominent ghrelin activity, hence characterizing its role as an anti-obesity target. We extracted 625 exonic SNPs from the ENSEMBL database and one phenotype-based missense mutation associated with obesity (A46T) from the HGMD (Human Gene Mutation Database). These were differentiated on deleterious missense SNPs of the MBOAT4 gene through MAF (minor allele frequency: <0.01) cut-off criteria in relation to some bioinformatics-based supervised machine learning tools. We found 8 rare-coding and harmful missense SNPs. The consensus classifier (PredictSNP) tool predicted that the SNP (G57S, C: rs561065025) was the most pathogenic. Several trained in silico algorithms have predicted decreased protein stability [ΔΔG (kcal/mol)] function in the presence of these rare-coding pathogenic mutations in the MBOAT4 gene. Then, a stereochemical quality check (i.e. validation and assessment) of the 3D model was performed, followed by a blind cavity docking approach, used to search for druggable cavities and molecular interactions with citrus flavonoids of the Rutaceae family, ranked with energetic estimations. Significant interactions with Phloretin 3',5'-Di-C-Glucoside were also observed at R304, W306, N307, A311, L314 and H338 with (iGEMDOCK: -95.82 kcal/mol and AutoDock: -7.80 kcal/mol). The RMSD values and other variables of MD simulation analyses on this protein further validated its significant interactions with the above flavonoids. The MBOAT4 gene and its molecular interactions could serve as an interventional future anti-obesity target. The current study's findings will benefit future prospects for large population-based studies and drug development, particularly for generating personalized medicine.Communicated by Ramaswamy H. Sarma.

Elucidation of novel compounds and epitope-based peptide vaccine design against C30 endopeptidase regions of SARS-CoV-2 using immunoinformatics approaches.

There has been progressive improvement in immunoinformatics approaches for epitope-based peptide design. Computational-based immune-informatics approaches were applied to identify the epitopes of SARS-CoV-2 to develop vaccines. The accessibility of the SARS-CoV-2 protein surface was analyzed, and hexa-peptide sequences (KTPKYK) were observed having a maximum score of 8.254, located between amino acids 97 and 102, whereas the FSVLAC at amino acids 112 to 117 showed the lowest score of 0.114. The surface flexibility of the target protein ranged from 0.864 to 1.099 having amino acid ranges of 159 to 165 and 118 to 124, respectively, harboring the FCYMHHM and YNGSPSG hepta-peptide sequences. The surface flexibility was predicted, and a 0.864 score was observed from amino acids 159 to 165 with the hepta-peptide (FCYMHHM) sequence. Moreover, the highest score of 1.099 was observed between amino acids 118 and 124 against YNGSPSG. B-cell epitopes and cytotoxic T-lymphocyte (CTL) epitopes were also identified against SARS-CoV-2. In molecular docking analyses, -0.54 to -26.21 kcal/mol global energy was observed against the selected CTL epitopes, exhibiting binding solid energies of -3.33 to -26.36 kcal/mol. Based on optimization, eight epitopes (SEDMLNPNY, GSVGFNIDY, LLEDEFTPF, DYDCVSFCY, GTDLEGNFY, QTFSVLACY, TVNVLAWLY, and TANPKTPKY) showed reliable findings. The study calculated the associated HLA alleles with MHC-I and MHC-II and found that MHC-I epitopes had higher population coverage (0.9019% and 0.5639%) than MHC-II epitopes, which ranged from 58.49% to 34.71% in Italy and China, respectively. The CTL epitopes were docked with antigenic sites and analyzed with MHC-I HLA protein. In addition, virtual screening was conducted using the ZINC database library, which contained 3,447 compounds. The 10 top-ranked scrutinized molecules (ZINC222731806, ZINC077293241, ZINC014880001, ZINC003830427, ZINC030731133, ZINC003932831, ZINC003816514, ZINC004245650, ZINC000057255, and ZINC011592639) exhibited the least binding energy (-8.8 to -7.5 kcal/mol). The molecular dynamics (MD) and immune simulation data suggest that these epitopes could be used to design an effective SARS-CoV-2 vaccine in the form of a peptide-based vaccine. Our identified CTL epitopes have the potential to inhibit SARS-CoV-2 replication.

Comprehensive in silico analyses of flavonoids elucidating the drug properties against kidney disease by targeting AIM2.

Kidney disorders are among the most common diseases and there is a scarcity of effective treatments for chronic kidney disease. There has been a progressive improvement in specific flavonoids for protective effects against kidney diseases. Flavonoids inhibit the regulatory enzymes to control inflammation-related diseases. In the present study, a hybrid approach of molecular docking analyses and molecular dynamic simulation was followed by principal component analyses and a dynamics cross-correlation matrix. In the present study, the top-ranked five flavonoids were reported, and the maximum binding affinity was observed against AIM2. Molecular docking analyses revealed that Glu_186, Phe_187, Lys_245, Glu_248, Ile_263, and Asn_265 are potent residues against AIM2 for ligand-receptor interactions. Extensive in silico analyses suggested that procyanidin is a potential molecule against AIM2. Moreover, the site-directed mutagenesis for the reported interacting residues of AIM2 could be important for further in vitro analyses. The observed novel results based on extensive computational analyses may be significant for potential drug design against renal disorders by targeting AIM2.

In silico elucidation of potential drug targets against oxygenase domain of Human eNOS Dysfunction.

Nitric Oxide (NO) signaling pathway plays a vital role in various physiological and pathophysiological processes including vasodilation, neurogenesis, inflammation, translation and protein regulation. NO signaling pathway is associated with various diseases such as cardiovascular diseases, vision impairment, hypertension and Alzheimer's disease. Human Endothelial Nitric Oxide Synthase (eNOS) bound with calcium regulatory protein (calmodulin (CaM)) to produce NO which initiates cGMP pathway. The current study employs to screen the novel compounds against human eNOS independent of calcium regulatory protein (CaM). The current effort emphasized that the deficiency of CaM leads to dysfunction of cGMP signaling pathway. In this work, a hybrid approach of high-throughput virtual screening and comparative molecular docking studies followed by molecular dynamic simulation analyses were applied. The screening of top ranked two novel compounds against eNOS were reported that showed effective binding affinity, retrieved through the DrugBank and ZINC database libraries. Comparative molecular docking analyses revealed that Val-104, Phe-105, Gln-247, Arg-250, Ala-266, Trp-330, Tyr-331, Pro-334, Ala-335, Val-336, Tyr-357, Met-358, Thr-360, Glu-361, Ile-362, Arg-365, Asn-366, Asp-369, Arg-372, Trp-447 and Tyr-475 are potent residues for interactional studies. High-throughput virtual screening approach coupled with molecular dynamic simulation and drug likeness rules depicted that ZINC59677432 and DB00456 are potent compounds to target eNOS. In conclusion, the proposed compounds are potent against eNOS based on extensive in silico analyses. Overall, the findings of this study may be helpful to design therapeutic targets against eNOS.

Pharmacological Progress of Mitophagy Regulation.

With the advancement in novel drug discovery, biologically active compounds are considered pharmacological tools to understand complex biological mechanisms and the identification of potent therapeutic agents. Mitochondria boast a central role in different integral biological processes and mitochondrial dysfunction is associated with multiple pathologies. It is, therefore, prudent to target mitochondrial quality control mechanisms by using pharmacological approaches. However, there is a scarcity of biologically active molecules, which can interact with mitochondria directly. Currently, the chemical compounds used to induce mitophagy include oligomycin and antimycin A for impaired respiration and acute dissipation of mitochondrial membrane potential by using CCCP/FCCP, the mitochondrial uncouplers. These chemical probes alter the homeostasis of the mitochondria and limit our understanding of the energy regulatory mechanisms. Efforts are underway to find molecules that can bring about selective removal of defective mitochondria without compromising normal mitochondrial respiration. In this report, we have tried to summarize and status of the recently reported modulators of mitophagy.

Synthesis and characterization of copper oxide nanoparticles: its influence on corn (Z. mays) and wheat (Triticum aestivum) plants by inoculation of Bacillus subtilis.

Nanotechnology is now playing an emerging role in green synthesis in agriculture as nanoparticles (NPs) are used for various applications in plant growth and development. Copper is a plant micronutrient; the amount of copper oxide nanoparticles (CuONPs) in the soil determines whether it has positive or adverse effects. CuONPs can be used to grow corn and wheat plants by combining Bacillus subtilis. In this research, CuONPs were synthesized by precipitation method using different precursors such as sodium hydroxide (0.1 M) and copper nitrate (Cu(NO3)2) having 0.1 M concentration with a post-annealing method. The NPs were characterized through X-ray diffraction (XRD), scanning electron microscope (SEM), and ultraviolet (UV) visible spectroscopy. Bacillus subtilis is used as a potential growth promoter for microbial inoculation due to its prototrophic nature. The JAR experiment was conducted, and the growth parameter of corn (Z. mays) and wheat (Triticum aestivum) was recorded after 5 days. The lab assay evaluated the germination in JARs with and without microbial inoculation under CuONP stress at different concentrations (25 and 50 mg). The present study aimed to synthesize CuONPs and systematically investigate the particle size effects of copper (II) oxide (CuONPs) (< 50 nm) on Triticum aestivum and Z. mays. In our results, the XRD pattern of CuONPs at 500 °C calcination temperature with monoclinic phase is observed, with XRD peak intensity slightly increasing. The XRD patterns showed that the prepared CuONPs were extremely natural, crystal-like, and nano-shaped. We used Scherrer's formula to calculate the average size of the particle, indicated as 23 nm. The X-ray diffraction spectrum of synthesized materials and SEM analysis show that the particles of CuONPs were spherical in nature. The results revealed that the synthesized CuONPs combined with Bacillus subtilis used in a field study provided an excellent result, where growth parameters of Z. Mays and Triticum aestivum such as root length, shoot length, and plant biomass was improved as compared to the control group.

Epidemiological studies of sleep disorder in educational community of Pakistani population, its major risk factors and associated diseases.

Sleep is one of the most important functions of the life. The disturbance in sleep or quality of sleep leads to several dysfunctions of the human body. This study aimed to investigate the prevalence of sleep disorders, their possible risk factors and their association with other health problems. The data was collected from the educational community of the Pakistani population. The Insomnia Severity Index (ISI) was used to evaluate the insomnia and the sleep apnea was evaluated through a simple questionnaire method. The blood samples were collected to perform significant blood tests for clinical investigations. Current research revealed that the individuals in the educational community had poor sleep quality. A total of 1998 individuals from the educational community were surveyed, 1584 (79.28%) of whom had a sleep disorders, including insomnia (45.20%) and sleep apnea (34.08%). The measured onset of age for males and females was 30.35 years and 31.07 years respectively. The Clinical investigations showed that the sleep had significant impact on the hematology of the patients. Higher levels of serum uric acid and blood sugar were recorded with a sleep disorder. The individuals of the educational community were using the sleeping pills. The other associated diseases were mild tension, headaches, migraines, depression, diabetes, obesity, and myopia. The use of beverage, bad mood, medical condition, mental stress, disturbed circadian rhythms, workload and extra use of smartphone were major risk factors of sleep disorders. It was concluded that the insomnia was more prevalent than the sleep apnea. Furthermore, life changes events were directly linked with disturbance of sleep. Tension, depression, headaches, and migraine were more associated with sleep disorders than all other health issues.

Epitope-based peptide vaccine design and elucidation of novel compounds against 3C like protein of SARS-CoV-2.

Coronaviruses (CoVs) are positive-stranded RNA viruses with short clubs on their edges. CoVs are pathogenic viruses that infect several animals and plant organisms, as well as humans (lethal respiratory dysfunctions). A noval strain of CoV has been reported and named as SARS-CoV-2. Numerous COVID-19 cases were being reported all over the World. COVID-19 and has a high mortality rate. In the present study, immunoinformatics techniques were utilized to predict the antigenic epitopes against 3C like protein. B-cell epitopes and Cytotoxic T-lymphocyte (CTL) were designed computationally against SARS-CoV-2. Multiple Sequence Alignment (MSA) of seven complete strains (HCoV-229E, HCoV-NL63, HCoV-OC43, HCoV-HKU1, SARS-CoV, MERS-CoV, and SARS-CoV-2) was performed to elucidate the binding domain and interacting residues. MHC-I binding epitopes were evaluated by analyzing the binding affinity of the top-ranked peptides having HLA molecule. By utilizing the docked complexes of CTL epitopes with antigenic sites, the binding relationship and affinity of top-ranked predicted peptides with the MHC-I HLA protein were investigated. The molecular docking analyses were conducted on the ZINC database library and twelve compounds having least binding energy were scrutinized. In conclusion, twelve CTL epitopes (GTDLEGNFY, TVNVLAWLY, GSVGFNIDY, SEDMLNPNY, LSQTGIAV, VLDMCASLK, LTQDHVDIL, TTLNDFNLV, CTSEDMLNP, TTITVNVLA, YNGSPSGVY, and SMQNCVLKL) were identified against SARS-CoV-2.

The multifaceted regulation of mitophagy by endogenous metabolites.

Owing to the dominant functions of mitochondria in multiple cellular metabolisms and distinct types of regulated cell death, maintaining a functional mitochondrial network is fundamental for the cellular homeostasis and body fitness in response to physiological adaptations and stressed conditions. The process of mitophagy, in which the dysfunctional or superfluous mitochondria are selectively engulfed by autophagosome and subsequently degraded in lysosome, has been well formulated as one of the major mechanisms for mitochondrial quality control. To date, the PINK1-PRKN-dependent and receptors (including proteins and lipids)-dependent pathways have been characterized to determine the mitophagy in mammalian cells. The mitophagy is highly responsive to the dynamics of endogenous metabolites, including iron-, calcium-, glycolysis-TCA-, NAD+-, amino acids-, fatty acids-, and cAMP-associated metabolites. Herein, we summarize the recent advances toward the molecular details of mitophagy regulation in mammalian cells. We also highlight the key regulations of mammalian mitophagy by endogenous metabolites, shed new light on the bidirectional interplay between mitophagy and cellular metabolisms, with attempting to provide a perspective insight into the nutritional intervention of metabolic disorders with mitophagy deficit.Abbreviations: acetyl-CoA: acetyl-coenzyme A; ACO1: aconitase 1; ADCYs: adenylate cyclases; AMPK: AMP-activated protein kinase; ATM: ATM serine/threonine kinase; BCL2L1: BCL2 like 1; BCL2L13: BCL2 like 13; BNIP3: BCL2 interacting protein 3; BNIP3L: BCL2 interacting protein 3 like; Ca2+: calcium ion; CALCOCO2: calcium binding and coiled-coil domain 2; CANX: calnexin; CO: carbon monoxide; CYCS: cytochrome c, somatic; DFP: deferiprone; DNM1L: dynamin 1 like; ER: endoplasmic reticulum; FKBP8: FKBP prolyl isomerase 8; FOXO3: forkhead box O3; FTMT: ferritin mitochondrial; FUNDC1: FUN14 domain containing 1; GABA: γ-aminobutyric acid; GSH: glutathione; HIF1A: hypoxia inducible factor 1 subunit alpha; IMMT: inner membrane mitochondrial protein; IRP1: iron regulatory protein 1; ISC: iron-sulfur cluster; ITPR2: inositol 1,4,5-trisphosphate type 2 receptor; KMO: kynurenine 3-monooxygenase; LIR: LC3 interacting region; MAM: mitochondria-associated membrane; MAP1LC3: microtubule associated protein 1 light chain 3; MFNs: mitofusins; mitophagy: mitochondrial autophagy; mPTP: mitochondrial permeability transition pore; MTOR: mechanistic target of rapamycin kinase; NAD+: nicotinamide adenine dinucleotide; NAM: nicotinamide; NMN: nicotinamide mononucleotide; NO: nitric oxide; NPA: Niemann-Pick type A; NR: nicotinamide riboside; NR4A1: nuclear receptor subfamily 4 group A member 1; NRF1: nuclear respiratory factor 1; OPA1: OPA1 mitochondrial dynamin like GTPase; OPTN: optineurin; PARL: presenilin associated rhomboid like; PARPs: poly(ADP-ribose) polymerases; PC: phosphatidylcholine; PHB2: prohibitin 2; PINK1: PTEN induced kinase 1; PPARG: peroxisome proliferator activated receptor gamma; PPARGC1A: PPARG coactivator 1 alpha; PRKA: protein kinase AMP-activated; PRKDC: protein kinase, DNA-activated, catalytic subunit; PRKN: parkin RBR E3 ubiquitin protein ligase; RHOT: ras homolog family member T; ROS: reactive oxygen species; SIRTs: sirtuins; STK11: serine/threonine kinase 11; TCA: tricarboxylic acid; TP53: tumor protein p53; ULK1: unc-51 like autophagy activating kinase 1; VDAC1: voltage dependent anion channel 1.

The Life Cycle and in silico Elucidation of Non-structural Replicating Proteins of HCV Through a Pharmacoinformatics Approach.

BACKGROUND: Hepatitis C virus (HCV) is an enveloped and positive-stranded RNA virus that is a major causative agent of chronic liver diseases worldwide. HCV has become the main cause of liver transplantations and there is no effective drug for all hepatitis genotypes. Elucidation of the life cycle and non-structural proteins of HCV, involved in viral replication, are attractive targets for the development of antiviral drugs.. METHODS: In this work, pharmacoinformatics approaches coupled with docking analyses were applied on HCV non-structural proteins to identify the novel potential hits and HCV drugs. Molecular docking analyses were carried out on HCV-approved drugs, followed by the ligandbased pharmacophore generation to screen the antiviral libraries for novel potential hits. RESULTS: Virtual screening technique has top-ranked five novel compounds (ZINC00607900, ZINC03635748, ZINC03875543, ZINC04097464, and ZINC12503102) along with their least binding energies (-8.0 kcal/mol, -6.1 kcal/mol, -7.5 kcal/mol, -7.4 kcal/mol, and -7.3 kcal/mol, respectively) and stability with the non-structural proteins target. CONCLUSION: These promising hits exhibited better absorption and ADMET properties as compared to the selected drug molecules. These potential compounds extracted from in silico approach may be significant in drug design and development against Hepatitis and other liver diseases.

Anti-aging Natural Compounds and their Role in the Regulation of Metabolic Pathways Leading to Longevity.

Aging is an unavoidable process, leading to cell senescence due to physiochemical changes in an organism. Anti-aging remedies have always been of great interest since ancient times. The purpose of anti-aging activities is to increase the life span and the quality of life. Anti-aging activities are primarily involved in the therapies of age-related disorders such as Parkinson's Disease (PD), Alzheimer's Disease (AD), cardiovascular diseases, cancer, and chronic obstructive pulmonary diseases. These diseases are triggered by multiple factors that are involved in numerous molecular pathways including telomere shortening, NF-κB pathway, adiponectin receptor pathway, insulin, and IGF signaling pathway, AMPK, mTOR, and mitochondria dysfunction. Natural products are known as effective molecules to delay the aging process through influencing metabolic pathways and thus ensure an extended lifespan. These natural compounds are being utilized in drug design and development through computational and high throughput techniques for effective pro-longevity drugs. A comprehensive study on natural compounds demonstrating their anti-aging activities along with databases of natural products for drug designing was executed and summarized in this review article.

Immunoinformatics and Molecular Docking Studies Predicted Potential Multiepitope-Based Peptide Vaccine and Novel Compounds against Novel SARS-CoV-2 through Virtual Screening.

BACKGROUND: Coronaviruses (CoVs) are enveloped positive-strand RNA viruses which have club-like spikes at the surface with a unique replication process. Coronaviruses are categorized as major pathogenic viruses causing a variety of diseases in birds and mammals including humans (lethal respiratory dysfunctions). Nowadays, a new strain of coronaviruses is identified and named as SARS-CoV-2. Multiple cases of SARS-CoV-2 attacks are being reported all over the world. SARS-CoV-2 showed high death rate; however, no specific treatment is available against SARS-CoV-2. METHODS: In the current study, immunoinformatics approaches were employed to predict the antigenic epitopes against SARS-CoV-2 for the development of the coronavirus vaccine. Cytotoxic T-lymphocyte and B-cell epitopes were predicted for SARS-CoV-2 coronavirus protein. Multiple sequence alignment of three genomes (SARS-CoV, MERS-CoV, and SARS-CoV-2) was used to conserved binding domain analysis. RESULTS: The docking complexes of 4 CTL epitopes with antigenic sites were analyzed followed by binding affinity and binding interaction analyses of top-ranked predicted peptides with MHC-I HLA molecule. The molecular docking (Food and Drug Regulatory Authority library) was performed, and four compounds exhibiting least binding energy were identified. The designed epitopes lead to the molecular docking against MHC-I, and interactional analyses of the selected docked complexes were investigated. In conclusion, four CTL epitopes (GTDLEGNFY, TVNVLAWLY, GSVGFNIDY, and QTFSVLACY) and four FDA-scrutinized compounds exhibited potential targets as peptide vaccines and potential biomolecules against deadly SARS-CoV-2, respectively. A multiepitope vaccine was also designed from different epitopes of coronavirus proteins joined by linkers and led by an adjuvant. CONCLUSION: Our investigations predicted epitopes and the reported molecules that may have the potential to inhibit the SARS-CoV-2 virus. These findings can be a step towards the development of a peptide-based vaccine or natural compound drug target against SARS-CoV-2.

Determine the Potential Epitope Based Peptide Vaccine Against Novel SARS-CoV-2 Targeting Structural Proteins Using Immunoinformatics Approaches.

Coronaviruses (CoVs) belong to the Coronaviridae-family. The genus Beta-coronaviruses, are enveloped positive strand RNA viruses with club-like spikes at the surface with a unique replication process and a large RNA genome (∼25 kb). CoVs are known as one of the major pathogenic viruses causing a variety of diseases in birds and mammals including humans (lethal respiratory dysfunctions). Recently, a new strain of coronavirus has been identified and named as SARS-CoV-2. A large number of COVID-19 (disease caused by SARS-CoV-2) cases are being diagnosed all over the World especially in China (Wuhan). COVID-19 showed high mortality rate exponentially, however, not even a single effective cure is being introduced yet against COVID-19. In the current study, immunoinformatics approaches were employed to predict the antigenic epitopes against COVID-19 for the development of a coronavirus peptide vaccine. Cytotoxic T-lymphocyte (CTL) and B-cell epitopes were predicted for SARS-CoV-2 coronavirus structural proteins (Spikes, Membrane, Envelope, and Nucleocapsid). The docking complexes of the top 10 epitopes having antigenic sites were analyzed led by binding affinity and binding interactional analyses of top ranked predicted peptides with the MHC-I HLA molecule. The predicted peptides may have potential to be used as peptide vaccine against COVID-19.

Defective mitochondrial ISCs biogenesis switches on IRP1 to fine tune selective mitophagy.

Both iron metabolism and mitophagy, a selective mitochondrial degradation process via autolysosomal pathway, are fundamental for the cellular well-being. Mitochondria are the major site for iron metabolism, especially the biogenesis of iron-sulfur clusters (ISCs) via the mitochondria-localized ISCs assembly machinery. Here we report that mitochondrial ISCs biogenesis is coupled with receptor-mediated mitophagy in mammalian cells. Perturbation of mitochondrial ISCs biogenesis, either by depleting iron with the iron chelator or by knocking down the core components of the mitochondrial ISCs assembly machinery, triggers FUNDC1-dependent mitophagy. IRP1, one of the cellular iron sensors to maintain iron homeostasis, is crucial for iron stresses induced mitophagy. Knockdown of IRP1 disturbed iron stresses induced mitophagy. Furthermore, IRP1 could bind to a newly characterized IRE in the 5' untranslated region of the Bcl-xL mRNA and suppress its translation. Bcl-xL is an intrinsic inhibitory protein of the mitochondrial phosphatase PGAM5, which catalyzes the dephosphorylation of FUNDC1 for mitophagy activation. Alterations of the IRP1/Bcl-xL axis navigate iron stresses induced mitophagy. We conclude that ISCs serve as physiological signals for mitophagy activation, thus coupling mitophagy with iron metabolism.

Molecular docking analyses of CYP450 monooxygenases of Tribolium castaneum (Herbst) reveal synergism of quercetin with paraoxon and tetraethyl pyrophosphate: in vivo and in silico studies.

Pest management in stored grain industry is a global issue due to the development of insecticide resistance in stored grain insect pests. Excessive use of insecticides at higher doses poses a serious threat of food contamination and residual toxicity for grain consumers. Since the development of new pesticide incurs heavy costs, identifying an effective synergist can provide a ready and economical tool for controlling resistant pest populations. Therefore, the synergistic property of quercetin with paraoxon and tetraethyl pyrophosphate has been evaluated against the larvae and adults of Tribolium castaneum (Herbst). Comparative molecular docking analyses were carried out to further identify the possible mechanism of synergism. It was observed that quercetin has no insecticidal when applied at the rate of 1.5 and 3.0 mg/g; however, a considerable synergism was observed when applied in combination with paraoxon. The comparative molecular docking analyses of CYP450 monooxygenase (CYP15A1, CYP6BR1, CYP6BK2, CYP6BK3) family were performed with quercetin, paraoxon and tetraethyl pyrophosphate which revealed considerable molecular interactions, predicting the inhibition of CYP450 isoenzyme by all three ligands. The study concludes that quercetin may be an effective synergist for organophosphate pesticides depending upon the dose and type of the compound. In addition, in silico analyses of the structurally diversified organophosphates can effectively differentiate the organophosphates which are synergistic with quercetin.

In Silico identification of angiotensin-converting enzyme inhibitory peptides from MRJP1.

Hypertension is considered as one of the most common diseases that affect human beings (both male and female) due to its high prevalence and also extending widely to both industrialize and developing countries. Angiotensin-converting enzyme (ACE) has a significant role in the regulation of blood pressure and ACE inhibition with inhibitory peptides is considered as a major target to prevent hypertension. In the current study, a blood pressure regulating honey protein (MRJP1) was examined to identify the ACE inhibitory peptides. The 3D structure of MRJP1 was predicted by utilizing the threading approach and further optimized by performing molecular dynamics simulation for 30 nanoseconds (ns) to improve the quality factor up to 92.43%. Root mean square deviation and root mean square fluctuations were calculated to evaluate the structural features and observed the fluctuations in the timescale of 30 ns. AHTpin server based on scoring vector machine of regression models, proteolysis and structural characterization approaches were implemented to identify the potential inhibitory peptides. The anti-hypertensive peptides were scrutinized based on the QSAR models of anti-hypertensive activity and the molecular docking analyses were performed to explore the binding affinities and potential interacting residues. The peptide "EALPHVPIFDR" showed the strong binding affinity and higher anti-hypertensive activity along with the global energy of -58.29 and docking score of 9590. The aromatic amino acids especially Tyr was observed as the key residue to design the dietary peptides and drugs like ACE inhibitors.

Ligand-Based Pharmacophore Modeling and Virtual Screening to Discover Novel CYP1A1 Inhibitors.

Backgound: Cytochrome P450, family 1, subfamily A, polypeptide 1 (CYP1A1) is an imperative enzyme due to its immersion in the biotransformation of a wide range of drugs and other xenobiotics. The involvement of enzymes in drug metabolism indicates an effective drug target for the development of novel therapeutics. The discovery of CYP1A1 specific inhibitors would be of particular relevance for the clinical pharmacology. METHODS: In the current work, in silico approaches were utilized to identify the novel potential compounds through a diverse set of reported inhibitors against CYP1A1. A dataset of reported compounds against CYP1 belongs to 10 different classes (alkaloids, coumarins, flavonoids, natural compounds, synthetic inhibitors, drugs, MBI's, PAHs, naphthoquinone and stilbenoids) was retrieved and utilized for the comparative molecular docking analyses followed by pharmacophore modeling. The total eleven novel compounds were scrutinized on the basis of the highest binding affinities and least binding energy values. RESULTS: ZINC08792486 compound attained the highest gold fitness score of 90.11 against CYP1A1 among all the scrutinized molecules. CONCLUSION: It has been elucidated that the residues Phe-224, Gly-316 and Ala-317 were conserved in all ligand-receptor interactions and critical for the development of effective therapies. The ADMET property analyses also predict better absorption and distribution of the selected hits that may be used in the future for in vitro validations and drug development.

Prevalence of Extended-Spectrum ß-Lactamases in Multi-drug Resistant Pseudomonas aeruginosa from Diabetic Foot Patients.

INTRODUCTION: Pseudomonas aeruginosa is one of the major pathogens associated with the acute tissue damage in patients having Diabetic Foot Ulcer (DFU). The treatment of such infections can be an uphill battle due to the serious resistance to all the mainstay antibiotics, owing to overzealous production of Extended-Spectrum Beta-Lactamases (ESBLs). Pakistan also has a high prevalence of diabetes and complications related to it, however genetic disposition of the pathogens remains underinvestigated. AIM: The main objective of the study was to determine the frequency of ESBLs in Multi-drug resistant P. aeruginosa from diabetic foot patients. METHODS: The duration of the present study was one year and 100 patients having DFU were enrolled. All the pus samples were subjected to the bacterial culture, gram staining, catalase test, oxidase test and antimicrobial susceptibility pattern to various antibiotics for the confirmation of P. aeruginosa. Of 23 positive isolates of P. aeruginosa, 10 were ESBLs positive as detected by double disk diffusion test. The positive ESBL strain shows an increase of ≥5mm in the zone of inhibition of the combination discs in comparison to the alone ceftazidime disc. RESULTS: The ESBLs positive strains were also tested for TEM-1, SHV-1, PER-1, and VEB-1, where: (07/10) strains carried SHV-1, (05/10) strains were positive for TEM-1, while none of the isolates were PCR-positive for PER-1 and VEB-1. CONCLUSION: The findings of the current study show a difference in the pattern of ESBL genes compared to that of other such endeavors. The present study also warrants the PCR-based detection of the type of ESBL as a potential factor to consider in deciding the therapeutic strategy at any point during the treatment.