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Introduction: The ongoing coronavirus disease 2019 (COVID-19), which emerged in December 2019, is a serious health concern throughout the world. Despite massive COVID-19 vaccination on a global scale, there is a rising need to develop more effective vaccines and drugs to curb the spread of coronavirus. Methodology: In this study, we screened the amino acid sequence of the RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 (the causative agent of COVID-19) for the identification of B and T cell epitopes using various immunoinformatic tools. These identified potent B and T cell epitopes with high antigenicity scores were linked together to design the multi-epitope vaccine construct. The physicochemical properties, overall quality, and stability of the designed vaccine construct were confirmed by suitable bioinformatic tools. Results: After proper in silico prediction and screening, we identified 3 B cell, 18 CTL, and 10 HTL epitopes from the RdRp protein sequence. The screened epitopes were non-toxic, non-allergenic, and highly antigenic in nature as revealed by appropriate servers. Molecular docking revealed stable interactions of the designed multi-epitope vaccine with human TLR3. Moreover, in silico immune simulations showed a substantial immunogenic response of the designed vaccine. Conclusions: These findings suggest that our designed multi-epitope vaccine possessing intrinsic T cell and B cell epitopes with high antigenicity scores could be considered for the ongoing development of peptide-based novel vaccines against COVID-19. However, further in vitro and in vivo studies need to be performed to confirm our in silico observations.
Background Rheumatoid arthritis (RA) is a chronic systemic inflammatory disorder which mainly affects small joints, occurs most commonly in middle-aged adults, and can be fatal in severe cases. The exact etiology of RA remains unknown. However, uncontrolled expression of pro-inflammatory cytokines and chemokines can contribute to the pathogenesis of RA. Aim In the current study, we assessed the potential of serum concentrations of interleukin (IL)-1β, IL-6, tumor necrosis factor (TNF)-α, IL-8, and C-C motif chemokine ligand (CCL)5 as early predictive markers for RA. Methods In addition to clinical examination, blood samples were collected from 100 Saudi patients recently diagnosed with early RA for basic and serological tests, including rheumatoid factor (RF), C-reactive protein (CRP), and erythrocyte sedimentation rate (ESR). Sera of 32 healthy individuals were used as controls. Specific enzyme-linked immunosorbent assay was used to quantify the serum IL-1β, IL-6, TNF-α, IL-8, and CCL5 levels in the samples. Results Our results indicated that RF, CRP, and ESR levels were higher in RA patients compared to controls. Furthermore, serum levels of IL-1β, IL-6, IL-8, and CCL5, but not TNF-α, significantly increased in RA patients compared to controls. Conclusion Overall, the findings suggested that IL-1β, IL-6, IL-8, and CCL5 can be used as biomarkers in the early diagnosis of RA.
Excitotoxicity is a type of neurodegenerative disorder. It caused by excessive glutamate receptor activation, which leads to neuronal malfunction and fatality. The N-methyl-D-aspartate (NMDA) receptors are found in glutamatergic neurons, and their excessive activation is primarily responsible for excitotoxicity. They are activated by both glutamate binding and postsynaptic depolarization, facilitating Ca2+ entry upon activation. Therefore, they are now widely acknowledged as being essential targets for excitotoxicity issues. Molecular docking and molecular dynamics (MD) simulation analyses have demonstrated that nobiletin efficiently targets the binding pocket of the NMDA receptor protein and exhibits stable dynamic behavior at the binding site. In this study, five potential neuroprotectants, nobiletin, silibinin, ononin, ginkgolide B, and epigallocatechin gallate (EGCG), were screened against the glutamate NMDA receptors in humans via computational methods. An in silico ADMET study was also performed, to predict the pharmacokinetics and toxicity profile for the expression of good drug-like behavior and a non-toxic nature. It was revealed that nobiletin fulfills the criteria for all of the drug-likeness rules (Veber, Lipinski, Ghose, Muegge, and Egan) and has neither PAINS nor structural alerts (Brenks). In conclusion, nobiletin demonstrated a possible promising neuroprotectant activities compared to other selected phytochemicals. Further, it can be evaluated in the laboratory for promising therapeutic approaches for in vitro and in vivo studies.
In view of the potential of traditional plant-based remedies (or phytomedicines) in the management of COVID-19, the present investigation was aimed at finding novel anti-SARS-CoV-2 molecules by in silico screening of bioactive phytochemicals (database) using computational methods and drug repurposing approach. A total of 160 compounds belonging to various phytochemical classes (flavonoids, limonoids, saponins, triterpenoids, steroids etc.) were selected (as initial hits) and screened against three specific therapeutic targets (Mpro/ 3CLpro, PLpro and RdRp) of SARS-CoV-2 by docking, molecular dynamics simulation and drug-likeness/ADMET studies. From our studies, six phytochemicals were identified as notable ant-SARS-CoV-2 agents (best hit molecules) with promising inhibitory effects effective against protease (Mpro and PLpro) and polymerase (RdRp) enzymes. These compounds are namely, ginsenoside Rg2, saikosaponin A, somniferine, betulinic acid, soyasapogenol C and azadirachtin A. On the basis of binding modes and dynamics studies of protein-ligand intercations, ginsenoside Rg2, saikosaponin A, somniferine were found to be the most potent (in silico) inhibitors potentially active against Mpro, PLpro and RdRp, respectively. The present investigation can be directed towards further experimental studies in order to confirm the anti-SARS-CoV-2 efficacy along with toxicities of identified phytomolecules.
The main aim of this study is to analyze effective thrombolytic drugs of natural origin for the treatment of stroke. Thrombolytic activity of natural sources has been reported and active molecules have been isolated and characterized. In this study, a total of ten compounds from nature were selected for docking studies. Caesalpinine c, caesalpinine a, vanillylamine, terpinen-4-Ol, dihydrocapsaicin and 3-carene showed fibrinolytic properties on analysis with PASS server. The present work is based on computer aided molecular modeling and the strength of the ligand was validated using binding energy. Caesalpinine c exhibited good docking score and this compound showed potent thrombolytic activity than other compounds. The drug likeliness varied based on the chemical and physical properties of the ligand. Lipinski’s rule of five was accepted by all of the selected compounds. Pfizer’s rule, and GSK rule were accepted in caesalpinine C. The drug likeliness properties of the all ten selected ligands were accepted in most of the cases and few rejections were observed mostly in Golden Triangle rule. However further in vitro or in vivo trials are required to validate thrombolytic potential of caesalpinine c and vanillylamine.