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Organized microbial gene expression under the concept of operons is a well-established concept. An operon-esque gene arrangement in the plant kingdom has been brought to the limelight with the help of recent developments in genetics, biochemistry and bioinformatics. We aim to explore the interactions between various gene products (enzymes) from the gene clusters of the 12 chromosomes in Oryza sativa Japonica and Oryza sativa Indica. Sequence information of the all the reviewed signature and tailoring genes were retrieved. The 3-dimentional structures of these proteins were predicted using Bioinformatics tools. The interactions among various predicted structures were ascertained by molecular docking techniques. The hypothesis that the various signature gene products and the corresponding tailoring gene products of the gene clusters of Oryza undergo protein-protein interaction was substantiated by the reliable molecular docking results reveals perfect interaction which leads to production of metabolites. The dendrogram generated for each signature gene products displays the evolutionary relationship with similar proteins from other species or the predicted/hypothetical proteins suggested by the algorithm. [ABSTRACT FROM AUTHOR]

Background: At present, viral diseases become major concern for the world. SARS-CoV2 and SFTS viruses are deadly in nature, and there is a need for developing best treatments for them. Modern in silico approaches were found to be very handy in determining putative drug molecules. In this study, we analyze interaction of beta-sesquiphellandrene (compound belongs to ginger) with spike protein (Sp) and membrane glycoprotein polyprotein (MPp). Results: Our molecular docking and simulation study reveals the perfect binding pocket of Sp and MPp holding beta-sesquiphellandrene (bS). Binding energies for MPp-bS and Sp-bS were found to be − 9.5 kcal/mol and − 10.3 kcal/mol respectively. RMSD and RMSF values for docked complexes were found to be in selectable range, i.e., 1 to 3 Å and 1 to 8 Å respectively. Modern computational tools were used here to make this investigation fast and effective. Further, ADME analysis reveals the therapeutic validations for beta-sesquiphellandrene to act as a useful pharmacoactive compound. Beta-sesquiphellandrene provides not only inhibitory effect on spike protein of SARS-CoV2 but also similar inhibitory effects on membrane glycoprotein polyprotein complex of SFTS virus, which hampers the pathological initiation of the diseases caused by both the viruses, i.e., COVID-19 and severe fever with thrombocytopenia syndrome. Conclusion: This method of computational analysis was found to be rapid and effective, and opens new doors in the domain of in silico drug discovery. Beta-sesquiphellandrene can be used as effective medicine to control these harmful pathogens after wet lab validations. [ABSTRACT FROM AUTHOR]

Around the world, emergence and re-emergence of Dengue Virus (DENV) are one of the serious public health concerns. The infection of DENV to human population is mainly caused by the bite of an Aedes mosquito. In an estimate, it is found that annually around 100–125 million new dengue incidences are reported from approximately 120 endemic countries. The lone licensed dengue vaccine was not effective to prevent the disease globally. Many dengue vaccines are under clinical trial but there are concerns about the trial reports on safety and efficacy of vaccine. In these circumstances, an epitope-based peptide vaccine is expected to be safe and efficacious against dengue. In this study, the computational prediction of T cell epitope-based peptide vaccine for dengue virus strain BR/97-111 Envelop protein is performed. Total 28 CTL epitopes were predicted using NetCTL 1.2 server. Out of these, five were found to possess antigenicity through VaxiJen 2.0. Further, toxicity prediction using ToxinPred and their conservancy prediction resulted in three epitopes, i.e. TSEIQLTDY, IGIGILLTW and IAVGMVTLY epitope peptide. All these were physically docked and studied for molecular dynamics simulation. In-depth analysis of these results suggests that the predicted three epitopes could be used as a potent vaccine candidate against global dengue disease challenges, although an experimental validation is required for final confirmation. [ABSTRACT FROM AUTHOR]

• Several flavonoid based SARS-CoV 3CLpro inhibitors were rationally designed by incorporating gamma lactam ring and various fluoro substituted heterocyclic ring systems. • The ligands were tested for drug-likeness, oral bioavailability, toxicity, synthetic accessibility, and ADMET properties. • Docking simulations confirmed strong binding affinity and inhibition potential of the ligands against the receptor SARS-CoV 3CL protease (3CLpro). • Ligand L4, L8 and L14 emerged as the lead compounds. The current outbreak of Coronavirus Disease 2019 (COVID-19) pandemic has reported thousands of deaths worldwide due to the rapid transmission rate and the lack of antiviral drugs and vaccinations. There is an urgent need to develop potential antiviral drug candidates for the prevention of COVID-19 infection. In the present study, a series of potential inhibitors targeting SARS-CoV 3CL protease were rationally designed by incorporating gamma lactam ring, and various fluoro substituted heterocyclic ring systems to the flavonoid scaffold. The prediction of drug-likeness, oral bioavailability, toxicity, synthetic accessibility, and ADMET properties was made by computational means. Quercetin was used as standard. The binding affinity of the ligands towards the 3CL protease target was examined using docking simulations. The designed ligands possess favourable pharmacokinetic and pharmacodynamic properties. Ligand L4, L8, and L14 appeared to be the lead compounds in the series and can be considered for further in-vivo and in-vitro validation. [Display omitted] [ABSTRACT FROM AUTHOR]