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All Journal Eksakta : Berkala Ilmiah Bidang MIPA
Mirella Fonda Maahury
Department of Chemistry, Faculty of Mathematics and Natural Science (FMIPA), Universitas Pattimura, Ambon, Indonesia
Agriculture, Biological Sciences & Forestry Astronomy Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Civil Engineering, Building, Construction & Architecture Computer Science & IT Energy Engineering Environmental Science Materials Science & Nanotechnology Mathematics Mechanical Engineering

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Modeling the Relationship of Net Atomic Charge with the Activity of 5-Aminopyrazole Derivative Compounds as Antioxidants with AM1 Method Nagmah Putri Dinda Toni; Fajriah Azra; Mirella Fonda Maahury
EKSAKTA: Berkala Ilmiah Bidang MIPA Vol. 23 No. 04 (2022): Eksakta: Berkala Ilmiah Bidang MIPA (E-ISSN : 2549-7464)
Publisher : Faculty of Mathematics and Natural Sciences (FMIPA), Universitas Negeri Padang, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24036/eksakta/vol23-iss04/334

Abstract

This study was conducted to analyze the quantitative relationship between structure and net atomic charge modeling activity of 21 5-aminopyrazole derivatives as antioxidants. This study aims to determine the value of the net atomic charge and obtain the best HKSA equation. The method used in this study is the semi-empirical method of Austin Model 1 with geometry optimization. The selection of the best equation model is done by statistical analysis using the method of correlation analysis and multiple regression with Backward to the calculated descriptor data. From the results of the study, it was found that model 1 as the HKSA equation model was chosen with the equation Log IC50 = Log IC50 = 1.648+(0.914*qN1)-(3.662*qN2)-(1.99*qC3)+( 0.004*qC4)+(1.052* qC5 )+(1.226*qN6) where n = 6 ; R = 0.724 ; R2 = 0.524 ; SE = 0.1462 ; Sig = 0.068 ; PRESS = 0.2994. This study shows that atomic charge plays an important role in enhancing antioxidant activity.
Computational Calculation and Molecular Docking of Thymol and O-Benzoyl Thymol as Inhibitor TYK2 Enzyme Mirella Fonda Maahury; Muhammad Daswar A. Baharudin; Rahadian Zainul; Ahmad Khudzairi Khalid; Vikash Jakmola; Maksim Rebezov
EKSAKTA: Berkala Ilmiah Bidang MIPA Vol. 23 No. 03 (2023): Eksakta : Berkala Ilmiah Bidang MIPA (E-ISSN : 2549-7464)
Publisher : Faculty of Mathematics and Natural Sciences (FMIPA), Universitas Negeri Padang, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24036/eksakta/vol23-iss03/405

Abstract

Thymol is the active ingredient in plants from Thymus vulgaris (thymus). The calculations and molecular docking have been done computationally for the thymol and o-benzoyl thymol. This computational calculation aims to obtain a stable structure and electronic properties of thymol and o-benzoyl thymol. The computational analysis used DFT for geometry optimization in the gas phase using B3LYP functional and 3-211G(d) as the basis set. The optimized structure of thymol and o-benzoyl thymol is not planar. The functional benzoyl decreases the bond length, increases the bond angle, and turns the dihedral. The electronic properties, such as atomic charge and density of HOMO-LUMO, show the difference between the two molecules. The optimized structure of thymol and o-benzoyl thymol is used for molecular docking with the TYK2 enzyme (tyrosine kinase). In this research, thymol and o-benzoyl thymol can inhibit TYK2 enzyme with the bond affinity is about -5.909 kcal/mol and -7.456 kcal/mol, respectively, for thymol o-benzoyl thymol. The primary molecular interaction is hydrophobic.
Co-Authors Ahmad Khudzairi Khalid Fajriah Azra Maksim Rebezov Muhammad Daswar A. Baharudin Nagmah Putri Dinda Toni Rahadian Zainul Vikash Jakmola