Molecular Docking of Interaction between E-Cadherin Protein and Conformational Structure of Cyclic Peptide ADTC3 (Ac-CADTPC-NH2) Simulated on 20 ns

Docking Studies and Molecular Dynamics Simulation of Ipomoea batatas L. Leaves Compounds as Lipoxygenase (LOX) Inhibitor

Background

Inflammatory mediators produced by cyclooxygenase (COX) and lipoxygenase (LOX) pathways are responsible for many human diseases, such as cancer, arthritis, and neurological disorders. Flavonoid-containing plants, such as Ipomoea batatas leaves, have shown potential anti-inflammatory activity.

Objectives

This study aimed to predict the actions of 10 compounds in I. batatas leaves, which are YGM-0a [cyanidin 3-0-sophoroside-5-0-glucosede], YGM-0f [cyanidin 3-O-(2-0-(6-0-(E)-p-coumaroyl-β-D-glucopyranosyl)-β-D-glucopyranoside)-5-0-β-D-glucopyranoside], YGM-1a [cyanidin 3-(6,6'-caffeylp-hydroxybenzoylsophoroside) -5-glucoside], YGM-1b [cyanidin 3-(6,6'-dicaffeylsophor-oside)-5-glucoside], YGM-2 [cyanidin 3-(6-caffeylsophoroside)-5-glucoside], YGM-3 [cyanidin 3-(6,6'-caffeyl-ferulylsophoroside)-5-glucoside], YGM-4b [peonidin 3-(6,6'-dicaffeylsophoroside)-5- glucoside], YGM-5a [peonidin 3-(6,6'-caffeylphydroxybenzo-ylsophoroside)-5-gluco-side], YGM-5b [cyanidin 3-6-caffeylsophoroside)-5-glucosede], and YGM-6 [peonidin 3-(6,6'-caffeylferulylsophoroside)-5-glucoside] as LOX inhibitors, and also predict the stability of ligand-LOX complex.

Materials and Methods

The compounds were screened through docking studies using PLANTS. Also, the molecular dynamics simulation was conducted using GROMACS at 310K.

Results

The results showed that the most significant binding affinity toward LOX was shown by YGM-0a and YGM-0a, and the LOX complex in molecular dynamics simulation showed stability for 20 ns.

Conclusion

Based on Docking Studies and Molecular Dynamics Simulation of I. Batatas Leaves compounds, YGM-0a was shown to be the most probable LOX inhibitor.

Design New Compound of Meisoindigo Derivative as Anti Breast Cancer Based on QSAR Approach

Design new compounds of Meisoindigo using the QSAR approach with semiempirical methods have been successfully made with better biological activity as anti-breast cancer results. The research method used to design the new compound of meisoindigo derivatives uses the semiempirical methods. The research procedure divide into tree step, molecular modeling, QSAR equation analysis, and design of new compounds. The PM3 method was chosen as a better method because it has model results that are more representative of physicochemical aspects. The selection of the best model is made by multilinear regression statistical analysis. New compounds derived from the design are expected to bind to the Cyclin-Dependent Kinase 4 (CDK4) enzyme that helps in the cell cycle to prevent cell division. Based on the design, the compound of (E)-2-(2-oxo-1-(2-(trifluoromethyl) benzyl)indolin-3-ylidene)-N-(quinoline-7-yl) acetamide choose as a new compound with more better biological activity (log 1/IC50 = 6.992) than before (log 1/IC50 = 5.823)

Interaction Studies Between Cyclic Peptide ADT-C3 (Ac-CADTPC-NH2) with E-Cadherin Protein using the Molecular Docking Method Simulated on 120ns

The treatment of diseases that attack the brain is very difficult, because the delivery of drug molecules to the brain is often hindered by the blood-brain barrier (BBB). So that the drug delivery is not right on the target cell. Thus, was developed a method in modulation of intercellular junctions using ADTC3 cadherin peptide, Where the cadherin peptide is derived from the cadherin sequence itself. The method used in this research is molecular dynamics (DM) and molecular docking. In this study have been evaluated some peptide conformation in modulating intercellular junction. The results show that cyclic peptide ADT-C3 (Ac-CADTPC-NH2) was conducted DM for 120 ns (120000 ps), which has considerable activity in modulating intercellular junctions with binding energies of -33.10 kJ.mol-1 and Ki of 1.58 μM at the 79187 ps conformation. The binding site on residues Asp1, Trp2, Ile4, Lys25, Ser26, Asn27, Met92 in the adhesion arm-acceptor pocket region.