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All Journal Jurnal Riset Kimia ALKIMIA : Jurnal Ilmu Kimia dan Terapan
Nugraha, Gerry
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Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Environmental Science Social Sciences

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Pembuatan Protokol Penapisan Virtual Berbasis Stuktur (pvbs) untuk Identifikasi Ligan Inhibitor Reseptor Platelet-Activating Factor (PAF-r) sebagai Target Terapeutik Asma menggunakan YASARA Nugraha, Gerry; Istyastono, Enade Perdana
Jurnal Riset Kimia Vol 11, No 1 (2020): March
Publisher : Universitas Andalas

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.25077/jrk.v11i1.346

Abstract

Platelet-activating factor receptors (PAF-r) is known as one of the receptors that affect asthma, while the Y-21480 ligand is reported as an effective, specific, and active PAF-r antagonist for asthma patients. Research in building structure-based virtual screening protocol (SBVS) for identification of PAF-r ligand inhibitors has been performed, the receptor crystal structure was obtained from the Protein Data Bank (PDB ID: 5zkp), while the ligand used as a leading compound is Y-24180, obtained from U.S. National Library of Medicine. Interactions between ligands and receptors are observed through molecular dynamics simulations using the YASARA program at intervals up to 20 nanoseconds, ligand-receptor binding stability occurs after a time interval of 2 nanoseconds, the lowest ligand-receptor binding energy occurs at a time interval of 1,401 picoseconds. Internal validation by re-docking 1,000 times the ligand to receptor resulted in a value of Root Mean Square Deviation (RMSD) of 0.6037 Å,  confirmed that SBVS protocol was accurately able to reproduce the Y-24180 ligand pose on the 5zkp crystal structure,  the protocol can be used as a new approach for investigation or design of compounds that have therapeutic potential as anti-asthma.
Pemodelan dan Analisis QSAR Turunan Aminosulfenil Metilkarbamat sebagai Insektisida menggunakan Metode Semiempirik Austin Model 1 Siswanta, Dwi; Nugraha, Gerry
ALKIMIA Vol 1 No 1 (2017): ALKIMIA
Publisher : SCIENCE AND TECHNOLOGY FACULTY OF UNIVERSITAS ISLAM NEGERI RADEN FATAH PALEMBANG

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (146.338 KB) | DOI: 10.19109/alkimia.v1i1.1330

Abstract

Telah diteliti pemodelan insektisida turunan aminosulfenil metilkarbamat berdasarkan model QSAR (Quantitative Structure Activity Relationship). Senyawa turunan aminosulfenil metilkarbamat dan data aktivitas inhibitor asetilkolinesterasenya diperoleh dari literatur. Perhitungan deskriptor elektronik, polaritas dan pemodelan struktur senyawa turunan aminosulfenil metilkarbamat dilakukan dengan metode semiempirik Austin Model 1 (AM1). Analisis QSAR dilakukan dengan analisis regresi multilinier untuk memperoleh persamaan QSAR terbaik untuk memprediksi aktivitas inhibitor asetilkolinesterase pada serangga dan mamalia, persamaan tersebut adalah: Serangga Log LD50 = 28,655 + 409,682 qC2 + 111,990 qO4 – 68,932 qC5 + 79,603 qC9 + 36,628 qO12 + 14,228 qO15 + 18,116 qC16 – 15,488 qS17 + 5,022 qN18 – 0,105 dipol – 0,044 Log P + 0,054 Polarisabilitas (n= 43, R= 0,928, SD= 0,176, Fhitung/Ftabel= 6,865, PRESS= 0,242) Mamalia Log LD50 = 6,984 + 28,671 qO15 - 6,986 qN18 - 0,091 dipol -0,180 Log P + 0,053 Polarisabilitas (n = 13, R = 0,977, SD = 0,042, Fhitung/Ftabel= 7,326, PRESS = 0,006) Berdasarkan model diatas, dirancang senyawa insektisida baru turunan aminosulfenil metilkarbamat dengan aktivitas inhibitor asetilkolinesterase yang tinggi terhadap serangga tapi rendah terhadap mamalia. Senyawa yang tersubstitusi ganda dengan kurkumin dan – (CH2)2COOC2H5 yaitu etil 3-((((((2,2- dimetil-2,3-dihidrobenzofuran-7-il)oksi)karbonil) (metil)amino)tio) ((4-((1E,6E)-7-(4–hidroksi-3-metoksifenil)- 3,5- dioksohepta- 1,6-dien-1il) -2-metoksifenoksi) metil)amino) propanoat memiliki aktivitas inhibitor asetilkolinesterase yang tinggi terhadap serangga (LD50=0,71 µg/g) dan aktivitas inhibitor asetilkolinesterase yang rendah terhadap mamalia (LD50=20.769,86 g/kg). Senyawa ini direkomendasikan untuk disintesis di laboratorium sebagai senyawa insektisida baru.
Co-Authors Dwi Siswanta Enade Perdana Istyastono