Creating NoSQL Biological Databases with Ontologies for Query Relaxation

AbstractThe complexity of building biological databases is well-known and ontologies play an extremely important role in biological databases. However, much of the emphasis on the role of ontologies in biological databases has been on the construction of databases. In this paper, we explore a somewhat overlooked aspect regarding ontologies in biological databases, namely, how ontologies can be used to assist better database retrieval. In particular, we show how ontologies can be used to revise user submitted queries for query relaxation. In addition, since our research is conducted at today's “big data” era, our investigation is centered on NoSQL databases which serve as a kind of “representatives” of big data. This paper contains two major parts: First we describe our methodology of building two NoSQL application databases (MongoDB and AllegroGraph) using GO ontology, and then discuss how to achieve query relaxation through GO ontology. We report our experiments and show sample queries and results. Our research on query relaxation on NoSQL databases is complementary to existing work in big data and in biological databases and deserves further exploration

Design, synthesis, anticancer evaluation and molecular docking studies of 1,2,3-triazole incorporated 1,3,4-oxadiazole-Triazine derivatives

A new library of 1,2,3-triazole-incorporated 1,3,4-oxadiazole-triazine derivatives (9a-j) was designed, synthesized, and tested in vitro for anticancer activity against PC3 and DU-145 (prostate cancer), A549 (lung cancer), and MCF-7 (breast cancer) cancer cell lines using the MTT assay with etoposide as the control drug. The compounds exhibited remarkable anticancer activity, with IC50 values ranging from 0.16 ± 0.083 μM to 11.8 ± 7.46 μM, whereas the positive control ranged from 1.97 0.45 μM to 3.08 0.135 μM. Compound 9 d with a 4-pyridyl moiety shown exceptional anticancer activity against PC3, A549, MCF-7, and DU-145 cell lines, with IC50 values of 0.17 ± 0.063 μM, 0.19 ± 0.075 μM, 0.51 ± 0.083 μM, and 0.16 ± 0.083 μM, respectively

Novel 5-Substituted Oxindoles Derivatives as Bruton\u27s Tyrosine Kinase Inhibitors: Design, Synthesis, Docking, Molecular Dynamic Simulation, and Biological Evaluation

Bruton\u27s tyrosine kinase (BTK) is a non-RTK cytoplasmic kinase predominantly expressed by haemopoietic lineages, particularly B-cells. A new Oxindole-based focused library was designed to identify potent compounds targeting the BTK protein as anticancer agents. This study used rational approaches like structure-based pharmacophore modelling, docking, and ADME properties to select compounds. The Molecular dynamics simulation analysis carried out at 20 ns supported the stability of compound 9g within the binding pocket. All the compounds were synthesized and subjected to biological screening on two BTK-expressing cancer cell lines, RAMOS and K562, and six non-BTK cancer cell lines, A549, HCT116 (parental and p53-/-), U2OS, JURKAT, and CCRF-CEM, and two non-malignant cell lines, BJ and MRC-5. This study resulted in the identification of four new compounds, 9b, 9f, 9g, and 9h, which displayed potent activity against BTK-high RAMOS cells. These four compounds, each possessing free binding energies of -10.8, -11.1, -11.3, and -10.8 Kcal/mol, demonstrated antiproliferative and cytotoxic effects in RAMOS cells with IC50 values falling within the lower sub-micromolar range

Novel 5‑Substituted Oxindole Derivatives as Bruton’s Tyrosine Kinase Inhibitors: Design, Synthesis, Docking, Molecular Dynamics Simulation, and Biological Evaluation

Bruton’s tyrosine kinase (BTK) is a non-RTK cytoplasmic kinase predominantly expressed by hemopoietic lineages, particularly B-cells. A new oxindole-based focused library was designed to identify potent compounds targeting the BTK protein as anticancer agents. This study used rational approaches like structure-based pharmacophore modeling, docking, and ADME properties to select compounds. Molecular dynamics simulations carried out at 20 ns supported the stability of compound 9g within the binding pocket. All the compounds were synthesized and subjected to biological screening on two BTK-expressing cancer cell lines, RAMOS and K562; six non-BTK cancer cell lines, A549, HCT116 (parental and p53–/–), U2OS, JURKAT, and CCRF-CEM; and two non-malignant fibroblast lines, BJ and MRC-5. This study resulted in the identification of four new compounds, 9b, 9f, 9g, and 9h, possessing free binding energies of −10.8, −11.1, −11.3, and −10.8 kcal/mol, respectively, and displaying selective cytotoxicity against BTK-high RAMOS cells. Further analysis demonstrated the antiproliferative activity of 9h in RAMOS cells through selective inhibition of pBTK (Tyr223) without affecting Lyn and Syk, upstream proteins in the BCR signaling pathway. In conclusion, we identified a promising oxindole derivative (9h) that shows specificity in modulating BTK signaling pathways