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All Journal ANNALES BOGORIENSES Teknologi Indonesia Annales Bogorienses
Gita Syahputra
IPB
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Computer Science & IT Immunology & microbiology Medicine & Pharmacology

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Molecular Docking and Molecular Dynamics Study of Alcoholic Compounds as Mycobactericidal Agents Using InhA, MabA and PanK as Receptors Syahputra, Gita; Arwansyah, Arwansyah; Kusharyoto, Wien
ANNALES BOGORIENSES Vol 22, No 2 (2018): Annales Bogorienses
Publisher : Research Center for Biotechnology - Indonesian Institute of Sciences (LIPI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/ann.bogor.2018.v22.n2.101-115

Abstract

     Tuberculosis (TB) infection is one of the primaryinfectious diseases in many developing countries; even there are minor cases in some developed countries. TB infection spread through the air and ismore probable when using improper disinfectant on medical and laboratory equipment which related to TB research. The appropriate disinfectants which are commonly usedin laboratory equipment can reduce the risk of transmission of TB disease. Alcoholic compoundsare one of the common disinfectants with a broad spectrum activity towardsmicrobes,viruses, and fungus. We employed molecular docking and molecular dynamics simulation to support virtual screening and ligand-receptor complex binding observation in searching for an appropriate mycobactericidal agent.Based on the analysis of molecular docking and molecular dynamics, pentadecanol has potency as a mycobactericidal agent with PanK as itsspecific receptor. The Gibbs free energy (∆G) for the interaction of pentadecanol with PanKhas been found to be -5.5 kcal/mol. Molecular dynamics analysis at 300K and 1 atm for 5 ns showed a little change in the confirmation of the binding site, whilepentadecanolwas still being bound by its binding siteon PanK.
VARIATION IN POINT MUTATIONS OF L -ARABINOSE ISOMERASE Thermotoga thermarum (TTAI) THROUGH THE ANALYSIS OF ENZYME STRUCTURE AND DOCKING SIMULATION Syahputra, Gita; Kusharyoto, Wien
Teknologi Indonesia Vol 40, No 1 (2017)
Publisher : LIPI Press

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Abstract

D-tagatose is one of the products of L-arabinose isomerase which can be applied to food, cosmetics, and health. D-tagatose produced by L-AI has a low quantity. L-AI enzyme from thermophilic bacteria as Thermotoga thermarum (TTAI) can produce higher quantity of D-tagatose than mesophilic bacteria. Point mutation can increase L-AI activity. The analysis of enzyme structure and docking simulation can determine the variation in point mutations. Based on analysis of enzyme structure and docking simulation, TTAI has 494 amino acids compiled by 17 of α-helix dan 18 of β-strand. The analysis of TTAI structure get several active side residues Gln16, Leu18, Tyr19, Phe81, Gln125, His126,Met183, Phe273, Glu300, Glu327, Tyr329, His344, Met345, Ile366, His442, His443. The docking simulation suggested that the residues for binding D-tagatose are Trp422 and Tyr331. Two point mutations, i.e. M183A and F273L, are recommended based on the analysis of TTAI structure, homology structure, residues, and docking simulation. This variation in mutation can be used for further research in vitro. 
Molecular Docking and Molecular Dynamics Study of Alcoholic Compounds as Mycobactericidal Agents Using InhA, MabA and PanK as Receptors Syahputra, Gita; Arwansyah, Arwansyah; Kusharyoto, Wien
Annales Bogorienses Vol. 22 No. 2 (2018): Annales Bogorienses
Publisher : BRIN

Show Abstract | Download Original | Original Source | Check in Google Scholar

Abstract

Tuberculosis (TB) infection is one of the primaryinfectious diseases in many developing countries; even there are minor cases in some developed countries. TB infection spread through the air and ismore probable when using improper disinfectant on medical and laboratory equipment which related to TB research. The appropriate disinfectants which are commonly usedin laboratory equipment can reduce the risk of transmission of TB disease. Alcoholic compoundsare one of the common disinfectants with a broad spectrum activity towardsmicrobes,viruses, and fungus. We employed molecular docking and molecular dynamics simulation to support virtual screening and ligand-receptor complex binding observation in searching for an appropriate mycobactericidal agent.Based on the analysis of molecular docking and molecular dynamics, pentadecanol has potency as a mycobactericidal agent with PanK as itsspecific receptor. The Gibbs free energy (∆G) for the interaction of pentadecanol with PanKhas been found to be -5.5 kcal/mol. Molecular dynamics analysis at 300K and 1 atm for 5 ns showed a little change in the confirmation of the binding site, whilepentadecanolwas still being bound by its binding siteon PanK.
Co-Authors Arwansyah Arwansyah Kusharyoto, Wien Kusharyoto, Wien Kusharyoto, Wien