Publications – STEM Skills Lab https://new.stemskillslab.com We make you thinkable Sat, 31 Dec 2022 05:37:22 +0000 en-US hourly 1 https://wordpress.org/?v=6.9.1 213064967 Synthesis, quantum mechanical calculations, molecular docking, Hirshfeld surface analysis and ADMET estimation studies https://new.stemskillslab.com/2022/09/24/synthesis-quantum-mechanical-calculations-molecular-docking-hirshfeld-surface-analysis-and-admet-estimation-studies/ https://new.stemskillslab.com/2022/09/24/synthesis-quantum-mechanical-calculations-molecular-docking-hirshfeld-surface-analysis-and-admet-estimation-studies/#respond Sat, 24 Sep 2022 08:21:22 +0000 https://stemskillslab.com/?p=1853 Abstract


Synthesis, crystallographic characterization, spectroscopic (FT-IR, UV-Vis, NMR) and density functional studies of (E)-3-(anthracene-10-yl)-1-(napthalen-1-yl)prop-2-en-1-one (3ANP) have been reported. The molecular structure obtained from single crystal X-ray diffraction method of the investigated compound was compared with theoretical values by DFT method at B3LYP with 6-311G(d,p) basis set. The 3ANP crystallizes in triclinic space group P1 with a = 8.3426(5), b = 10.4643(6), c = 11.3925(6). Hirshfeld surface analysis was performed to confirm the existence of intra- intermolecular and other interactions using Crystal Explorer. In addition to the optimized geometrical structure, molecular electrostatic potential (MEP), natural bond orbital (NBO) analysis, non-linear optical (NLO) property, HOMO, LUMO, mulliken population analysis have been investigated. The electronic properties of the compound were examined using TD-DFT calculations. The calculated vibrational frequencies have been compared with the experimental FT-IR values. Gauge invariant atomic orbital (GIAO) method was used to calculate 1H and 13C NMR chemical shifts in the ground state and was compared with the experimental NMR spectra. Further, the analysis using rules for drug-likeness and ADMET prediction revealed the druggability of the compound. Molecular docking showed the binding energy of -9.4 Kcal/mol and other interactions of 3ANP molecule with protein PDB ID: 1FCQ.


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Structural Insights in Mammalian Sialyltransferases and Fucosyltransferases|Research Paper by StemSkill Lab https://new.stemskillslab.com/2022/09/24/structural-insights-in-mammalian-sialyltransferases-and-fucosyltransferasesresearch-paper-by-stemskill-lab/ https://new.stemskillslab.com/2022/09/24/structural-insights-in-mammalian-sialyltransferases-and-fucosyltransferasesresearch-paper-by-stemskill-lab/#respond Sat, 24 Sep 2022 08:09:19 +0000 https://stemskillslab.com/?p=1850 Abstract


Mammalian cell surfaces are modified with complex arrays of glycans that play major roles in health and disease. Abnormal glycosylation is a hallmark of cancer; terminal sialic acid and fucose in particular have high levels in tumor cells, with positive implications for malignancy. Increased sialylation and fucosylation are due to the upregulation of a set of sialyltransferases (STs) and fucosyltransferases (FUTs), which are potential drug targets in cancer. In the past, several advances in glycostructural biology have been made with the determination of crystal structures of several important STs and FUTs in mammals. Additionally, how the independent evolution of STs and FUTs occurred with a limited set of global folds and the diverse modular ability of catalytic domains toward substrates has been elucidated. This review highlights advances in the understanding of the structural architecture, substrate binding interactions, and catalysis of STs and FUTs in mammals. While this general understanding is emerging, use of this information to design inhibitors of STs and FUTs will be helpful in providing further insights into their role in the manifestation of cancer and developing targeted therapeutics in cancer.

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Immunoinformatics-Aided Design and In Vivo Validation of a Peptide-Based Multiepitope Vaccine Targeting Canine Circovirus https://new.stemskillslab.com/2022/09/24/immunoinformatics-aided-design-and-in-vivo-validation-of-a-peptide-based-multiepitope-vaccine-targeting-canine-circovirus/ https://new.stemskillslab.com/2022/09/24/immunoinformatics-aided-design-and-in-vivo-validation-of-a-peptide-based-multiepitope-vaccine-targeting-canine-circovirus/#respond Sat, 24 Sep 2022 07:55:22 +0000 https://stemskillslab.com/?p=1846 Abstract


Canine circovirus (CanineCV) is a deadly pathogen affecting both domestic and wild carnivores, including dogs. No vaccine against CanineCV is available commercially or under clinical trials. In the present study, we have designed a promising multiepitope vaccine (MEV) construct targeting multiple strains of CanineCV. A total of 545 MHCII binding CD4+T cell epitope peptides were predicted from the capsid and replicase protein from each strain of CanineCV. Five conserved epitope peptides among the three CanineCV strains were selected. The final vaccine was constructed using antigenic, nontoxic, and conserved multiple epitopes identified in silico. Further, molecular docking and molecular dynamics simulations predicted stable interactions between the predicted MEV and canine receptor TLR-5. One of the mapped epitope peptides was synthesized to validate antigenicity and immunogenicity. In vivo analysis of the selected epitope clearly indicates CD4+T-cell-dependent generation of antibodies, which further suggests that the designed MEV construct holds promise as a candidate for vaccine against CanineCV.

Read the Full Article on American Chemical Society

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Immunoinformatics Aided Design | Peptide Based Multi-Epitope Vaccine of Dengue Virus | Research Paper by Stemskills Lab https://new.stemskillslab.com/2022/09/14/immunoinformatics-aided-design-and-in-vivo-validation-of-a-cross-reactive-peptide-based-multi-epitope-vaccine-targeting-multiple-serotypes-of-dengue-virus/ https://new.stemskillslab.com/2022/09/14/immunoinformatics-aided-design-and-in-vivo-validation-of-a-cross-reactive-peptide-based-multi-epitope-vaccine-targeting-multiple-serotypes-of-dengue-virus/#respond Wed, 14 Sep 2022 15:15:03 +0000 https://stemskillslab.com/?p=1819 Abstract


Dengue virus (DENV) is an arboviral disease affecting more than 400 million people annually. Only a single vaccine formulation is available commercially and many others are still under clinical trials. Despite all the efforts in vaccine designing, the improvement in vaccine formulation against DENV is very much needed. In this study, we used a roboust immunoinformatics approach, targeting all the four serotypes of DENV to design a multi-epitope vaccine. A total of 13501 MHC II binding CD4+ epitope peptides were predicted from polyprotein sequences of four dengue virus serotypes. Among them, ten conserved epitope peptides that were interferon-inducing were selected and found to be conserved among all the four dengue serotypes. The vaccine was formulated using antigenic, non-toxic and conserved multi epitopes discovered in the in-silico study. Further, the molecular docking and molecular dynamics predicted stable interactions between predicted vaccine and immune receptor, TLR-5. Finally, one of the mapped epitope peptides was synthesized for the validation of antigenicity and antibody production ability where the in-vivo tests on rabbit model was conducted. Our in-vivo analysis clearly indicate that the imunogen designed in this study could stimulate the production of antibodies which further suggest that the vaccine designed possesses good immunogenicity.

Read the Full Article on Frontiers in Immunology

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