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All Journal Indonesian Journal of Chemistry
Winarto Haryadi
Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Sekip Utara, Yogyakarta 55281, Indonesia
Chemical Engineering, Chemistry & Bioengineering Chemistry

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Stability, Hydrogen Bond Occupancy Analysis and Binding Free Energy Calculation from Flavonol Docked in DAPK1 Active Site Using Molecular Dynamic Simulation Approaches Adi Tiara Zikri; Harno Dwi Pranowo; Winarto Haryadi
Indonesian Journal of Chemistry Vol 21, No 2 (2021)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijc.56087

Abstract

Stability and hydrogen bond occupancy analysis of flavonol derivative docked in DAPK1 have been carried out using molecular dynamics simulation approach. Six flavonol derivatives were docked in DAPK1 as protein target, then continued with molecular dynamics simulation. NVT and NPT ensembles were used to equilibrate the system, followed by 20 ns sampling time for each system. Structural stability and hydrogen bond occupancy analyses were carried out at the NVT ensemble, while free binding energy analysis was done at NPT ensemble. From all compounds used in this work, compound B (5,7-dihydroxy-2-(4-hydroxyphenyl)-6-methoxy-4H-chromen-4-one) has a similar interaction with reference ligands (quercetin, kaempferol, and fisetin), and the most stable complex system has the maximum RMSD around 2 Å. Compound C complex has -48.06 kJ/mol binding free energy score, and it was slightly different from quercetin, kaempferol, and fisetin complexes. Even though complex C has similar binding free energy with the reference compound, complex B shows more stable interactions due to their hydrogen bond and occupancy.
Enhancing the Amino Acid and Reducing the Metal Ions Contents in the Hydrolysate Resulting from Hydrothermal Carbonization of Chicken Feather Waste by Chemical Phosphorylation Agus Kuncaka; Wahyu Tri Supardi; Winarto Haryadi; Adhitasari Suratman; Priatmoko Priatmoko
Indonesian Journal of Chemistry Vol 23, No 1 (2023)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijc.73725

Abstract

Chemical phosphorylation of hydrolysate resulting from hydrothermal carbonization of chicken feather waste was performed to enhance the amino acids and reduce the metal ions content. The aim of this research is to improve the functional properties of chicken feathers hydrolysate without impairing the nutritional availability thereof with the cheapest chemical method by phosphorylation. Phosphorylated hydrolysate can function as animal feed and fertilizer. The hydrolysate of chicken feathers was obtained by hydrothermal carbonization in an alkaline condition using a CaO and KOH catalyst, by the ratio of water:dry matter of chicken feathers is 5:1, at 9–10 atm pressure, and in a temperature of 190–200 °C during 3 h. Phosphorylation has been carried out by reacting the hydrolysate with H3PO4 85% in pH of 5, 6, 7 and using the original hydrolysate as control. The sample that has been prepared was characterized and semi-quantitative analyzed by HPLC and AAS. The phosphorylation results showed that the total maximum protein of soluble protein, their minimum metal ions, and anion in soluble protein was obtained at pH 7, while the higher the pH, the lower the liquid protein that was obtained.
Co-Authors Adhitasari Suratman Adi Tiara Zikri Agus Kuncaka Harno Dwi Pranowo Priatmoko Priatmoko Wahyu Tri Supardi